27 Sep 2020

12 week lattice training plan - review

September 27, 2020

A few weeks ago I finished up the 12-week lattice light training plan. What follows is an enthusiastic endorsement of the plan and the training app that lattice provides, along with some reflections on where I’m at with climbing. My motivation for signing up was pretty simple. I knew we were heading into lockdown. I have a good fingerboard setup at home, I thought that in order to make the most of the enforced home time I should get some structured guidance on how to use my home board. ... (more)

Tags: climbing, training, goals, lattice, fingerboard, beastmaker

25 Sep 2020

Prakash lab - frugal science and the future of research

September 25, 2020

I just wanted to share some work coming out of the Prakash lab in Stanford. Manu Prakash is a young engineer and research scientist who has taken a very different approach to how to think about the tools we use to do science. He has focussed on building very cheap tools that can be used by anyone in the world. One of the first tools that his lab created was the foldscope - a microscope built from paper, and a small piece of plastic - that can be produced very cheaply and given out to people across the world (https://indiabioscience. ... (more)

Tags: science, research, engineering, cool, innovation

12 Jul 2020

Profit Trees and making business cases

July 12, 2020

This is a very nice overview of how to create a clear business case for design work, but the general approach of walking a tree to find leverage points to build up the argument can be applied any time that you want to make a business case. ... (more)

Tags: design, roi, exampel

03 Jul 2020

CODECHECK - reviewing code in publications

July 3, 2020

CODECHECK is a fascinating service - https://codecheck.org.uk/ That creates a workflow for academics to provide feedback on research code. The project is being led by Stephen Eglen and and Daniel Nüst. They describe what they do succinctly as CODECHECK is a process for independent reproduction of computations and awarding of time-stamped certificates for successful reproductions of scholarly articles. Checking software in research is a significant challenge, and I really like CODECHECK because it is an initiative that has emerged from researchers themselves. ... (more)

Tags: coding, research, software

02 Jul 2020

Using Datasette to publish data

July 2, 2020

In my department we have started to make a bit of space to allow for self learning to happen. I took the time to look at https://datasette.readthedocs.io/en/stable/, an ecosystem of tools that support data publishing. These tools are from Simon Willison, and they are fantastic. I’d been meaning to look at the them for some time now. I used a jupyter notebook to work my way around getting some data together, and working with the tool. ... (more)

Tags: data, data-publishing, datasette, crossref, notebook, jupyter

13 Feb 2020

Goodbye SAGE, hello BMJ!

February 13, 2020

I’m excited to share the news that from mid-April I will be joining the BMJ as their new CTO. I’ll be leaving SAGE on great terms with the teams here, and for sure there will be a little sadness and I’ll definitely miss my colleagues, but equally I’m super excited about the new challenges ahead. Crucially, at SAGE we are hiring for my replacement, so if you are interested in applying for one of the most fun roles in the Scholarly Publishing industry at the moment then reach out, I’m happy to chat about what we have been up to! ... (more)

Tags: career, sage, bmj

11 Dec 2019

thoughts on GetFTR

December 11, 2019

what does it do? By using a single sign-on system (like SAML, or OAuth) a researcher can have their browser remember who they are. Today most access to subscription content is done via IP authentication. A university pays a publisher to access the content that the publisher hosts, and the university sends over a list of the IP ranges that cover the university buildings. Any researcher on campus just gets access. ... (more)

Tags: getftr, wtfgetftwt, access, saml, publishing, libraries

06 Dec 2019

Some brief thoughts on scholarly publishing and climate change.

December 6, 2019

Who’s job is it to address the crisis of climate change? This question came up at an STM Tech Leaders workshop that I attended earlier this week? The answer is that we all are, and in that context we had a very interesting conversation on the topic. This is the first time that I’ve seen this topic come up in a forum like this, so a bit thank you to Dave Smith from the IET for pushing the topic forward. ... (more)

Tags: climate, crisis, ai

06 Dec 2019

STM Research data workshop.

December 6, 2019

The start of December is always a busy time for news in the STM / Product space. There is the annual STM meeting in London, and AWS re-invent also kicks off this week. As a result, within just a few days, I find that I have more things to write about than I can ever possibly have time to get through before the end of the year, we must plough on, and plough on we will. ... (more)

Tags: data, research, das, data-citation, impact, stm

05 Dec 2019

STM Research data workshop.

December 5, 2019

The start of December is always a busy time for news in the STM / Product space. There is the annual STM meeting in London, and AWS re-invent also kicks off this week. As a result, within just a few days, I find that I have more things to write about than I can ever possibly have time to get through before the end of the year, we must plough on, and plough on we will. ... (more)

Tags: data, research, das, data-citation, impact, stm

19 Nov 2019

Google data set search.

November 19, 2019

I’ve just got back from a fantastic workshop looking at infrastructure for research data discovery. I’ll blog about the workshop in due course, but I was asked to comment about Google Dataset Search - Dataset Search. I had the change to meet with Natasha Noi from Google who is behind the service. Natasha Noy – Google AI. As with many google services, it has been created by a small team, but with the underlying web scale infrastructure of Google to build on top of. ... (more)

Tags: data, repositories, google, discovery

13 Nov 2019

rescognito - a route towards a weighted scholarly graph.

November 13, 2019

I sat down with Richard Wynne. Richard has a long career in the publishing space, having been one of the senior team at Aries for a long time. Over the last year Richard has founded Rescognito. Rescognito is a service to allow institutions or individuals to award credits (or rescogs ) to anyone for anything within the scholarly ecosystem. You can reward article contributions, reviews, presentations, knowledge, providing open data. The schema is extendible, so if you have a particular use-case in mind it could be accommodated. ... (more)

Tags: graph, pid, orcid, startups, credit

12 Nov 2019

Where is research going - a Kudos report

November 12, 2019

I’ve finally gotten around to looking at the report that Kudos developed earlier this year looking into where research outputs go to, and where they get consumed, after they have been published. You get grab a copy of the report here How to build a global, engaged audience for your research.. The report is based on a survey of 10k researchers, supported with interviews and desk research. It’s a short read (19 pages), so go ahead and grab the report and have a look. ... (more)

Tags: impact, research, kudos

11 Nov 2019

Rave tech conference 2019

November 11, 2019

A few weeks ago I was at the aannual Rave publishing technology conference. It’s always an interesting event to attend. My main recollection from last year was the interest in blockchain. This year, as I reflect on how I feel about the meeting, I think I have two main things that have stayed with me. The first was the appeal from Tasha to ask us as a community and an industry to do more to think about removing barriers for early career researchers. ... (more)

Tags: rave, publishing, techmology

06 Nov 2019

Unpaywall Journals - possibly the most interesting thing to happen this year in library subscription land.

November 6, 2019

Heather and Jason from https://ourresearch.org/ have just released a preview of their new tool - unpaywall journals. You can have a look at the preview of this tool now - Unpaywall Journals. They previewed this two weeks ago at FORCE2019 and have clearly gone through a ton of work to get the tool the state it is in todday, so big congraatulations to them on the product release. For those of you not in the know they have a long track record of building useful open infrastructure in the scholarly communications spaace. ... (more)

Tags: unpaywall, force2019, subscriptions, open-access, publishing#

04 Nov 2019

Responsible metrics - the state of the art - Elizabeth Gadd at Force2019

November 4, 2019

At Force2019 the other day the one session that I really wanted to see, but missed, was the one by Dr. Elizabeth Gadd on responsible metrics. She has posted her slides here Responsible metrics: what’s the state of the art?. This is a great deck, and I highly encourage reading through it. My takeaways from reading through them are the following: misapplication of metrics is dangerous, leads to stress, has led to some tragic incidents. ... (more)

Tags: force2019, metrics, assessment, outcomes

04 Nov 2019

Responsible metrics, the state of the art, Elizabeth Gadd at Force2019

November 4, 2019

At Force2019 the other day the one session that I really wanted to see, but missed, was the one by Dr. Elizabeth Gadd on responsible metrics. She has posted her slides here Responsible metrics: what’s the state of the art?. This is a great deck, and I highly encourage reading through it. My takeaways from reading through them are the following: misapplication of metrics is dangerous, leads to stress, has led to some tragic incidents. ... (more)

Tags: force2019, metrics, assessment, outcomes

04 Nov 2019

Things holding back your analytics.

November 4, 2019

One of my colleagues sent me over this short report “”3 Things Are Holding Back Your Analytics, and Technology Isn’t One of Them. They think the following elements should be considered: How the analysis teams are structured - they need to report in a way that is understandable (i.e. not be too separate from the business), but at the same time be independent enough to provide unbiassed views. ... (more)

Tags: data-science, organisations, analysis, strategy

10 Sep 2019

Book review - Tiamat’s wrath - book nine of the expanse series.

September 10, 2019

This book review is really only for people who have been reading all of the expanse book series. If you have not then there are some spoilers in here. I finished this over my summer holiday, and it was a ton of fun. I noted that In the first few books of the series when the action was contained within the solar system a lot of book time was taken up describing the time it took to travel around the solar system, and the intricacies if the orbital mechanics that went into that. ... (more)

Tags: book-review, scifi, books

10 Sep 2019

The three body problem.

September 10, 2019

I’ve just zipped through this book in what feels like about a week, but was probably a bit longer. I didn’t like it. The book sets up engagement with a computer game as a key plot driver, along with specific behaviours of an alien civilisation. Both of these are central to the driver of the book and in both cases I wasn’t able to believe what was happening. They lacked internal consistency and plausibility, in particular the plot device of unpacking a proton and accessing higher dimensional spaces. ... (more)

Tags: book-review, scifi, book

05 Sep 2019

Are scholarly publishers technology companies?

September 5, 2019

There is tension in this question that gets to the heart of where a publisher should be putting its resources, and perhaps more importantly what the reasons are behind those investment decisions. The side of the argument that says they are not technology companies might say that at the heart of what publishers do is content, and so they are content and service companies. Invest then in acquisition, in reach, in marketing, in branding, in distribution and in making the sales process as cost effective asa possible. ... (more)

Tags: technology, publihsing, stem

05 Sep 2019

Strategies to reduce cognitive load, and make systems more robust whilst doing so, and why that’s important for product development.

September 5, 2019

At my current company we are looking at strategies for improving the resilience of our core systems, and looking at the issue of disaster recovery from a broad perspective. This comes under the heading business continuity management. From a product development perspective these considerations are also important. For successful products / product organisations consider these two perspectives: Most new business value that we create from innovation projects comes from improvements or iterations to existing products over the creation of totally new products (from an evolutionary perspective this makes sense, products or services that are already making revenue have proved they they have an environmental fitness function that works, whereas new products are like genetic modifications, the vast majority of which lead towards extinct endpoints. ... (more)

Tags: bcm, engineering, toil, cognitive-load, product-development, microservices

01 Aug 2019

key questions about AI in the publishing knowledge industry

August 1, 2019

At the moment one thing that is front and centre in my thinking about AI and machine learning in publishing and the scholarly ecosystem is how to make the case for ROI for investment in the technology, and more specifically investing in making data actionable. Overall I think there is great promise for challenges like knowledge discovery and machine generated hypotheses, but there is massive potential for these technologies to also just make the quality of our work better, and to increase the value of our work by reducing and removing toil in the workplace. ... (more)

Tags: publishing, ai, rules, roi

01 Aug 2019

test blog post

August 1, 2019

This is a test post while trying to fix some domain issues with the blog. ... (more)

Tags: test

29 Nov 2018

AGILE or agile?

November 29, 2018

Three links today looking at the state of agile as a software development practice. Flavours of Agile In Flavours of Agile Pat Kua briefly describes and rates a number of agile processes. There are a ton here, and loads that I’d not heard of. One of the key messages that I get from reading this is that “AGILE” as a fixed practice has been growing, especially within in enterprise, and perhaps not to the benefit of actually delivering or simplifying the delivery of complex processes. ... (more)

Tags: software, agile

22 Nov 2018

Some ruminations on software architecture and diagramming

November 22, 2018

So Pat Kua recently tweeted: UML failed so here we have AML (Arbitrary Modeling Language) https://t.co/BnbgC8ZHTD — Pat Kua (@patkua) November 9, 2018 and this got me thinking about the worries I’ve had about not doing “diagramming” right, but the above tweet led me to read a ton of really interesting posts on software architecting. Bottom line is, as with so many things, pick the artefact that fits the purpose and the audience. ... (more)

Tags: diagramming, architecture, systems

26 Oct 2018

The state of retractions in the research literature.

October 26, 2018

The results below are oldish, but interesting around the rate of retractions in the scholarly literature, and there is currently a bit of a debate going on around retractions (e.g. What a massive database of retracted papers reveals about science publishing’s ‘death penalty’ | Science | AAAS Steen RG, Casadevall A, Fang FC (2013) Why Has the Number of Scientific Retractions Increased? PLoS ONE 8(7): e68397. doi:10.1371/journal.pone.0068397 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068397 https://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0068397.g001 The increase in retracted articles appears to reflect changes in the behaviour of both authors and institutions. ... (more)

Tags: peer-review, retractions

24 Oct 2018

RAVE publishing technology conference 2018

October 24, 2018

I took some notes on some of the sessions at the conference yesterday. Dave Smith - object oriented publishing. Dave makes a good case here about how we should think about the future of scholarly publishing — in terms of objects that can be reformed based on the needs and competencies of the readers. He points out that while we do have in place good ontologies and domain models, our entire view of publishing and our publishing infrastructures, remain laggy and are a barrier to moving in this direction. ... (more)

Tags: drafttoblog, publishing, rave, technology, innovations, blockchain

19 Oct 2018

Belmont Forum Round Table - data accessibility statements

October 19, 2018

Yesterday I attended a round table discussion hosted by the Belmont Forum about the release of their position on data accessibility statements and digital objects management plans. (It’s a bit of a mouthful, but the reason is that they are aiming to be clear and comprehensive around what they are asking to make it easier for researchers, publishers and other stakeholders to get to compliance around this policy.) You can read their position paper — Draft DAS Statement and Policy for October 2018 Plenary - Google Docs. ... (more)

Tags: data, research, funders, belmont, open-science

18 Oct 2018

One Two Four All - a technique for getting insights from groups

October 18, 2018

I’ve started working my way through The Surprising Power of Liberating Structures - a hand book of techniques for collaborative work. So far I’ve tried one technique from the book - one two four all. The idea is super simple and is an alternative to open brainstorming or post-it note sessions. Before describing the technique with a few comments, I’ll just point out one of the weaknesses of a group work activity like a retrospective. ... (more)

Tags: product-development, techniques, groupwork

17 Oct 2018

One Two Four All - a technique for getting insights from groups.

October 17, 2018

I’ve started working my way through The Surprising Power of Liberating Strucutres - a hand book of techniques for collaborative work. So far I’ve tried one technique from the book - one two four all. The idea is super simple and is an alternative to open brain storming or post-it note sessions. Before describing the technique with a few comments, I’ll just point out one of the weaknesses of a group work activity like a group retrospective. ... (more)

Tags: blog, draft, product-development, techniques, groupwork

04 Jul 2018

blockchain in STEM - part 3

July 4, 2018

Over the last few weeks I’ve been writing up some thoughts on the uses of blockchain in STEM. The first post I gave a general overview of my understand of blockchain. In the second post I looked at potential use cases of blockchain in STEM, and came up somewhat short. That said, a lot, really, a lot of very smart people are talking about this, and doing things in this space, so in this post I wanted to look at a few of those efforts and see how their thinking lines up or diverges from mine. ... (more)

Tags: blockchain#, hype-machine, stem, science, publihsing

04 Jul 2018

testing a new form of peer review - again

July 4, 2018

eLife is trying another experiment in peer review. When they launched back in 2012 they introduced a form of peer review known as consultative peer review. They are now looking at a new iteration on the peer review idea. Trials in how peer review is done are quite rare, so I think this is going to be interesting to keep track of. The new idea is that once an article has been accepted for full review by one of the editors, the journal is going to publish the article, along with all comments. ... (more)

Tags: elife, peer-review, interesting, scholarly-publishing

03 Jul 2018

notes on notes on “crossing the chasam”

July 3, 2018

The following is not about scholarly communication, but is a post about one tool from the world of product development, how to think about marketing your product or service so that you can cross the chasm. Academic researchers are simultaneously the most innovative and conservative of users. There is so much pain in the process of academic research that there is a constant re-invention and invention of tools and proceeds, but at the same time there is also a huge time pressure, so for any new tool, technique or service to get wide spread traction is really hard in the academic market place. ... (more)

Tags: product-development, chasm

29 Jun 2018

Distill is dedicated to making machine learning clear and dynamic

June 29, 2018

Distill is an experiment in bringing interactive documents and scholarly documents together. I’m often asked what the future of publishing might look like, and were we to embrace what the web offers it might look like distill. Two things though, make it look like a nice product. Right now paper flow into this journal is very low, and secondly they have advertised a large prize to attract work in this format. ... (more)

Tags: ai, learning, research, future-of-publishing, scpd

29 Jun 2018

Grants for Nonprofits | Grants for Researchers | Instrumentl

June 29, 2018

A startup to help you fast-track you grant application process. The hard thing here is building a robust and clean pipeline of info about grants. https://www.instrumentl.com/ ... (more)

Tags: scienceontheweb, business, academia, science

29 Jun 2018

JavaScript End to End Testing Framework | Cypress.io

June 29, 2018

https://www.cypress.io/ ... (more)

Tags: software, techdigest, javascript, testing, QA, cool

29 Jun 2018

Jobs to be Done A Case Study in the NHS | Digital transformation blog

June 29, 2018

This is a great post on using the jobs to be done framework. There are two specific enhancements that are discussed - how to weight those jobs, and how to use granularity of the jobs to aid the design process (less granularity gives more freedom in the design phase). The authors wanted to use surveys to get a sense of importance of the under served needs, but in the end had to resort to a simple variant of card sorting. ... (more)

Tags: scpd, design-thinking, jobs-to-be-done, NHS, product-development

29 Jun 2018

Narrative Science | Natural Language Generation Technology

June 29, 2018

I think what these people are doing is creating human readable summaries of large corpora of documents or signals based on AI. At some point this kind of approach is going to mature to the point of being able to replace many traditional editorial functions, but its going to happen in finance first. https://narrativescience.com/ ... (more)

Tags: ai

29 Jun 2018

Reaktor Breakpoint 2018 Ben Sauer, The rise of voice, and how to design for it - YouTube

June 29, 2018

This is a great overview of the sate of designing for voice. Ben is one the best designers / tech thinkers that I’ve ever worked with, and he gives a great overview of how to think about designing for voice in this talk. <a href=https://www.youtube.com/watch?v=wSFkRG_ZMKo>https://www.youtube.com/watch?v=wSFkRG_ZMKo ... (more)

Tags: product-development, voice, Alexa, siri

29 Jun 2018

Sentry | Error Tracking Software — JavaScript, Python, PHP, Ruby, more

June 29, 2018

https://sentry.io/welcome/ ... (more)

Tags: cool, techdigest, QA, software

29 Jun 2018

Voice Principles | Clearleft

June 29, 2018

This is a great checklist and overview of design principles for designing for voice assistants. It’s complied and created by CelarLeft. https://voiceprinciples.com/ ... (more)

Tags:

26 Jun 2018

blockchain in STEM - part 2

June 26, 2018

In my last post I gave an overview of what blockchain is, while also confusing House of Pain and Cypress Hill. (These posts are probably best read whilst listening to either of those songs). In this post I’m going to look at potential use cases for blockchain in STEM and scholarly publishing. Scholarly communications use cases. When thinking about any use cases in STEM I think the questions we need to answer are: ... (more)

Tags: blockchain, stem, publihsing, hype-machine

21 Jun 2018

Architect, The Killer Serverless Framework – Reify

June 21, 2018

A nice overview of an npm framework for creating server-less applications on AWS. It abstracts away a lot of the plumbing, which can have upsides and downsides. I’d love to see something equivalent in python. The actual framework is here: https://arc.codes https://blog.reifyworks.com/architect-the-killer-serverless-framework-41565372811b ... (more)

Tags: aws, serverless, node

21 Jun 2018

Limiting “Software Infant mortality” rate — decoding GO-JEK’s Deployment Checklist

June 21, 2018

A great example of using a “flight plan checklist” to reduce risk in software development. https://blog.gojekengineering.com/limiting-software-infant-mortality-rate-decoding-gojek-deployment-checklist-1c6cc3e28df ... (more)

Tags: devops, programming, software, pokayoka

21 Jun 2018

Model Zoo - Pretrained deep learning models for transfer learning, educational purposes, and more

June 21, 2018

This looks like an interesting corpus of machine learning models. One thing I’d not really thought about before is that we will now need to start thinking about how to publish the actual models that are used in scholarly research. Some of the models on this site provide ways to reference the work (e.g. https://modelzoo.co/model/image-to-image-translation-with-conditional-adversarial-networks). https://modelzoo.co/ ... (more)

Tags: ai, machine-learning, models, interesting, todi

21 Jun 2018

OA negotiation manifesto from university of California.

June 21, 2018

This is a really interesting initiative from the university of California. If the scholarly landscape looked like this then publishers would have to generate revenue entirely from services and derivative open products, rather than from content licensing. Most of the points is the manifesto are fairly unsurprising but two points stood out as interesting to me. Point 10 asks for all metadata to be made available including usage metadata. Are Counter reports sufficient for this, or is anything else needed? ... (more)

Tags: STM, business, publishing, library, interesting

21 Jun 2018

Ongoing experiment in ‘Extreme Open Science’ announced at Structural Genomics Consortium - HBGDki

June 21, 2018

It’s really encouraging to see the concept of open notebook Sciecne still being picked and adopted. It looks like the researchers are actively making their results available (https://opennotebook.thesgc.org). http://hbgdki.org/ongoing-experiment-extreme-open-science-announced-structural-genomics-consortium/ ... (more)

Tags: openscience, scienceontheweb, open-notebooks

21 Jun 2018

Preprints growth rate ten times higher than journal articles - Crossref

June 21, 2018

Great post looking into stats on preprints in crossref. Headline takeaways, preprint registration into crossref is 10x that of article growth, but it’s hard to read a lot into that as the absolute numbers are so different at the moment 2.4M per month (published articles) vs 10k per month (preprints). There is also some interesting data on preprint citations, preprint citations come in at best at a level of about 10% of the citations to the subsequently published article. ... (more)

Tags: publishing, preprints, crossref

21 Jun 2018

Research Software Engineering conference 2018 workshop abstract

June 21, 2018

About As SAGE is sponsoring the Research Software Engineers conference in September we get to submit a workshop. I’m thrilled to be able to attend this conference. Many years ago I used to write research software in astrophysics. Over the years I have learnt how complex the interplay is between specification, software writing and getting to the heart of user needs. Along with this is the critical question of how we find sustainable models for these kinds of activities. ... (more)

Tags: research-software-engineer, software, product-development, lean

21 Jun 2018

Scholia

June 21, 2018

Scholia is an amazing interface into scholarly information held inside id WikiData. It includes information about authors, articles and a very large chunk of the citation graph. You can see an article pate here: https://tools.wmflabs.org/scholia/work/Q24595162. The tool extracts topic information on articles, shows cites and citing articles (and how many citations each of these articles has) https://tools.wmflabs.org/scholia/ ... (more)

Tags: academia, graph, cool, citation, Wikidata, wikipedia, articles

21 Jun 2018

Unsupervised Extraction of Epidemic Syndromes from Participatory Influenza Surveillance Self-reported Symptoms | bioRxiv

June 21, 2018

This is a great example of “web science for good”. The researchers looked at online signals to predict the spread of flu. This is a preprint, I hope the code for this kind of work makes it out. How might we then best link this preprint to that code? https://www.biorxiv.org/content/early/2018/05/04/314591 ... (more)

Tags: webscience

19 Jun 2018

Blockchain in STEM - part 1

June 19, 2018

A lot of people are taking about “blockchain for science” and “blockchain for publishing”, but I’m skeptical. Some of the people taking about this are really smart, so I could be wrong. If we think of scholarly publishing as being like the connective tissue of science, and we accept that this idea is gaining purchase within our community that we have to realise that we are looking at a case of ... (more)

Tags: blockchain, publihsing, hype-machine

07 Jun 2018

Adequate statistical power in clinical trials is associated with the combination of a male first author and a female last author.

June 7, 2018

So if your last author is female the quality of the science is statistically better. I don’t know exactly what to make of this. We also have to understand a bit about the role of last authorship. In life sciences this is usually the corresponding author. I would not be surprised (given the study looks over a 40 year period) that what we are seeing is that women just produce more carful better science, but are being restricted from first authorship positions because of bias. ... (more)

Tags: science, gender, statistics, interesting

07 Jun 2018

Advanced computing with IPython

June 7, 2018

This post shows how to execute compiled commands in your IPython environments. That can allow you to, for example, pull in FORTRAN or C++ code to get speed on computationally heavy lines of code. https://lwn.net/SubscriberLink/756192/ebada7ecad32f3ad/ ... (more)

Tags: ipython, python, computing, scienceontheweb, cool

07 Jun 2018

After 5 years and $3M, here's everything we've learned from building Ghost

June 7, 2018

This is a great overview of how a not for profit open source technology company built a working business providing publishing tools. It speaks to how bad the landscape for publishing tools on the web is. Their product was originally created on kickstarter, and I remember when it launched, and being impressed with it back then. They have now pivoted away from trying to server small content individuals and are making money serving needs in the enterprise. ... (more)

Tags: business, open-source, publishing

07 Jun 2018

Digital Radar - STM landscape

June 7, 2018

Thoughtworks have created a tool to allow you to build your own “Digital Radar”. The one linked to here was put together a few years ago by people at the BMJ to look at the technology landscape in STM publishing (There are some really interesting things in there in some interesting locations). <a href=https://radar.thoughtworks.com/?sheetId=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1zQPRcn76XHKxex7ytdmTKC9nXMPPK0Tv0-hMlSY6xVU%2Fpubhtml>https://radar.thoughtworks.com/?sheetId=https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1zQPRcn76XHKxex7ytdmTKC9nXMPPK0Tv0-hMlSY6xVU%2Fpubhtml ... (more)

Tags: strategy, technology, visualisation, cool, STM

07 Jun 2018

Internet Archive, Code for Science and Society, and California Digital Library to Partner on a Data Sharing and Preservation Pilot Project

June 7, 2018

Some major players are getting together to trial decentralised data sharing using the Dat protocol - https://datproject.org. Dat for me is one of the dark horses of the infrastructure landscape. It has great power, some amazing developers, has already created some great value, and is still not known by many people yet. Also, this is not blockchain based, and yet manages to be decentralised. Those of you who know me will know why that pleases me. ... (more)

Tags: dat, CDL, data, not-blockchain, scienceontheweb, cool

07 Jun 2018

Open Knowledge Maps - social science map

June 7, 2018

Open knowledge maps show the relationship between different papers, based on a keyword search. They have been gong for some time now (originally built on top of Mendeley data). I ran into them again this week as we start to think about how to visualise the relationship between different aspects of research. The one linked to here is for social science and here is one for “computational social science”: https://openknowledgemaps.org/map/70627a849484345cdfd04c914de0a2e2. Their news pages shows that the project and team are still active, which is great. ... (more)

Tags: scienceontheweb, social-science, visualisation, maps, cool

07 Jun 2018

Strategy in a Lean Enterprise - lean value tree.

June 7, 2018

I’ve been working with lean value tree as a framework for some time now, but there are few online resources about this. The linked presentation does a great job of giving an overview of the tool. In particular I like how they call out the need to describe the promise of value to the customer, something that we could definitely do more of. Another presentation on the same topic is this one: https://www. ... (more)

Tags: agile, product-management, lean, LVT, strategy

07 Jun 2018

The Cost of Developers – by Ben Thompson

June 7, 2018

This is a fascinating post on what dynamics are in place between large companies and developers. The bottom line is that Microsoft has had to pay a large sum (>$7B) to acquire a developer friendly platform because they currently don’t really have one. In contrast Apple has a lot of leverage over developers on iOS, but not on other platforms. I’m not sure if there is a connection to researchers in the STM space, but some journals certainly have a lot of leverage over researchers. ... (more)

Tags: github, microsoft, developers, ecosystems, platforms, interesting

07 Jun 2018

VIPER - The Visual Project Explorer

June 7, 2018

This is a tool for visualising EC funded projects listed in OpenAire using the infrastructure of Open Knowledge maps. For digging into projects that you know, I think this has some value, but I’d like to see some global overview of where funding is flowing. https://openknowledgemaps.org/viper/ ... (more)

Tags: funding, visualisation, scienceontheweb, cool

06 Jun 2018

About Backyard Brains

June 6, 2018

https://backyardbrains.com/about/ ... (more)

Tags: scienceontheweb, citizenscience, neuroscience

06 Jun 2018

Cool slide deck about the advantages of using the shell for data science.

June 6, 2018

I love this short presentation on using the shell for data science. Many of the things hat are described in the presentation are just plain useful anyway, searching over csv files, finding things, renaming things. https://cdn.oreillystatic.com/en/assets/1/event/267/50%20reasons%20to%20learn%20the%20shell%20for%20doing%20data%20science%20Presentation.pdf ... (more)

Tags: datascience, presentation, strata, utilities, shell

06 Jun 2018

How to Visualize an XML Sitemap Using Python - Ayima

June 6, 2018

This looks like a great way to quickly get an overview of your site architecture, a vital step when thinking about wide spread changes. https://www.ayima.com/blog/how-to-visualize-an-xml-sitemap-using-python.html ... (more)

Tags: python, programming, blog, web-development

06 Jun 2018

Impact of Social Sciences – The academic papers researchers regard as significant are not those that are highly cited

June 6, 2018

http://blogs.lse.ac.uk/impactofsocialsciences/2018/05/14/the-academic-papers-researchers-regard-as-significant-are-not-those-that-are-highly-cited/ ... (more)

Tags: altmetrics, science

06 Jun 2018

Mindcontrol A web application for brain segmentation quality control - ScienceDirect

June 6, 2018

paper about an open source tool for studying neuroscience images developed by Anisha Keshavan, and others. https://www.sciencedirect.com/science/article/pii/S1053811917302707 ... (more)

Tags: scienceontheweb, cool, openscience, neuroscience

06 Jun 2018

The Guardian view on digitising culture make manuscripts more illuminating | Editorial | Opinion | The Guardian

June 6, 2018

a nice description of IIF from the guardian. https://www.theguardian.com/commentisfree/2018/may/28/the-guardian-view-on-digitising-culture-make-manuscripts-more-illuminating ... (more)

Tags: iiif, cool, data, images

18 May 2018

eLife Innovation Sprint - appstract.pub

May 18, 2018

Last week the eLife innovation sprint happened in Cambridge. It was done in collaboration with the Mozilla global sprint. I was able to participate for some of the event, and I’ll write up a bit more about the project I worked on later. There is a slide deck that summarises all of the projects from the two days: Slides of outputs from the sprint: eLifeSprint2018_introductions_people&projects - Google Slides. Briefly, this was hands down one of the most productive two-day sprints that I’ve ever been involved in. ... (more)

Tags: hackathon, elife, mozilla, open-science, cool, citizen-science

16 May 2018

A new new way to make biological data more easily citable

May 16, 2018

Working under Force11 the California digital library and the EBI have made progress on making identifiers to data held in biological data repositories more easily resolvable. The have done this by setting up infrastructure and standards to support creating globally unique prefixes for the data repositories involved. You can see some examples in this table: Table 2: Examples of persistent, citable URLs for a single accession (NCBI Taxon 9606), with default and specified providers. ... (more)

Tags: data, data-citation, force11

16 May 2018

Alexa is becoming less popular as a baby name since the Amazon service launched.

May 16, 2018

Mark this one down as totally not surprising. https://www.recode.net/2018/5/13/17345722/alexa-amazon-echo-baby-name-girls-apple-siri ... (more)

Tags: amazon, ai

16 May 2018

Computer replaces workers, workers ty to turn into data scientists.

May 16, 2018

http://www.latimes.com/business/technology/la-fi-tn-automation-training-20180504-story.html The headline is a bit click-baitey. I think the big takeaway from this article is that there is a significant shift in how companies are doing training with the advent of online learning. Unsurprising, but hopefully good news for efforts like sage campus. ... (more)

Tags: ai, economy, training

16 May 2018

Google employees resigning in protest at potential militarisation of AI

May 16, 2018

https://gizmodo.com/google-employees-resign-in-protest-against-pentagon-con-1825729300 File this one under “don’t be evil”. Of course what is also interesting is that there is actual pushback from the employees, within an industry that has sometimes been called a “morality free zone”. ... (more)

Tags: google, ethics

16 May 2018

Is caution justified when thinking about docker?

May 16, 2018

I’ve been fascinated by docker for the past few years, and there is clearly a “rush to dockerise” I’ve been Neville’s by how easy it is to get complex systems up and running locally, so perhaps it’s time to read with some caution some of the potential downsides. http://www.smashcompany.com/technology/docker-is-a-dangerous-gamble-which-we-will-regret Argues about those. He article highlights exactly why I like docker: Me: “I can write a bash script. Or “make”. Or any other kind of installer, of which there are dozens. ... (more)

Tags: software, docker, architecture

16 May 2018

US phone companies are selling your real time location data.

May 16, 2018

https://www.zdnet.com/article/us-cell-carriers-selling-access-to-real-time-location-data/ File this one under “you do it to yourself” Of course the key thing here is that directly selling this data to law enforcement is illegal, but indirectly selling it is not. The market is acting as an evolutionary force to find ways to extract money by moving around laws that are out in place to protect citizens. In this case the economy can move at a faster pace with business innovation that the law can to protect citizens. ... (more)

Tags: big-data, ethics

11 May 2018

Hunting for structure in nested JSON with python just got a whole lot easier

May 11, 2018

A very common python task that I find myself stumbling over repeatedly is trying to get the syntax right to address or retrieve a specific value to a key in a dented JSON document, in particular if that key is some way down the tree. I’ve just found the library https://github.com/mahmoud/glom which is written up really nicely here: https://sedimental.org/glom_restructured_data.html Before looking at this modele in detail I had thought that I could pass a reference to a key to glom without specifying its location fully in the structure of the input file, but after looking at this for a moment it became clear that this is not what it does, but rather is good at helping to remap nested data structures into new structures, and accessing the data you want via path like queries. ... (more)

Tags: asilearn, python, python, glom, json, programming, tips

09 May 2018

Some initial thoughts on the Google Duplex demo

May 9, 2018

The Verge also covered this well: www.theverge.com/2018/5/9/17334658/google-ai-phone-call-assistant-duplex-ethical-social-implications and they have a quote from Joanna Bryson, who talked at SAGE just before Christmas. Her quote is finished out with the following. There are no obvious answers to these questions, but as Bryson points out, Google is at least doing the world a service by bringing attention to this technology. It’s not the only company developing these services, and it certainly won’t be the only one to use them. ... (more)

Tags: ai, ethics

04 May 2018

choice magazine podcast Questions

May 4, 2018

This week I was interviewed for the ALA choice podcast, a podcast that the that is a weekly program featuring in-depth conversations about contemporary trends, best practices, and case studies important to academic librarians. Hosted by Bill Mickey, the Editorial Director at Choice The topic was about trends in big data and the role of the library, and it was really fun to participate in, and the panel I was on included Caroline Muglia from the University of Southern California Libraries as well as Andy Rutkowski and Eimmy Karina Solis from USC libraries. ... (more)

Tags: computational-socical-science, research, big-data, tools, software

27 Apr 2018

AI and discovery tools

April 27, 2018

I got asked to contribute an answer to an upcoming feature looking at trends in scholarly discovery. There are four questions and I’ve been asked to think about an answer to the last of these four. In a sentence or two, please tell us what you understand is meant by ‘discovery’? For a researcher, how has the discovery experience developed in recent years? How can researchers decide which tools are going to do the right job for them? ... (more)

Tags: ai, machine-learning, discovery

27 Apr 2018

Where once we dreamt of many gardens, now we have many walls

April 27, 2018

I’m reading through Anil Dash’s great blog post looking back at the way the web used to be in terms of how we thought of it, and how it was implemented. (As an aside, I’m deeply fascinated by Glitch, but have not had the time to date to spend on it that I would have wished). In addition to his comment about how websites are now assembled, component by component, there is another aspect to modern development that I’ve strongly noticed, and that is of specialisation. ... (more)

Tags: web, internet, dreams, hopes, fears, future, dat

19 Apr 2018

Microsoft Surface Hub - very first impressions

April 19, 2018

I just had my first hands on experience with the Microsoft surface hub. I tried out sketching a lean canvas on the surface to see how it would work. Things I liked writing was responsive pressure sensitivity worked well two people can write at the same time there is sketch to shape recognition, and it’s OK its just about big enough to work on, but bigger would be better Things I liked in principle, but was not able to check whether they work in practice being able to capture the output of the session digitally being able to remotely work on the surface with another team at the same time Things I didn’t like selecting and moving items really just was too hard to figure out under / erase was fiddly sometimes the built in grid would get in the way when I had object recognition on, it would sometimes turn my “D”s into triangles not as flexible as working with post it notes, in terms of being able to move and cluster ideas Conclusion Overall this is getting there, but for me its not quite there yet. ... (more)

Tags: microsoft, tools, collaboration

19 Apr 2018

python - running commands from within a directory

April 19, 2018

A neat python snippet for jumping into a directory, running a script, and jumping out again, found on Stackoverflow, provided by Brian Hunt. from subprocess import Popen, PIPE import os import sys class cd: """Context manager for changing the current working directory see https://stackoverflow.com/questions/431684/how-do-i-cd-in-python """ def __init__(self, newPath): self.newPath = os.path.expanduser(newPath) def __enter__(self): self.savedPath = os.getcwd() os.chdir(self.newPath) def __exit__(self, etype, value, traceback): os.chdir(self.savedPath) with cd("~/blog/partiallyattended"): title = new_post.title process = subprocess. ... (more)

Tags: asilearn, python

19 Apr 2018

Where should you host your Kubernetes solution?

April 19, 2018

I previously Kicked the tyres on kubernetes, with an example of how to deploy it onto Google’s infrastructure, but if you want to scale out and start dong some real work with this piece of infrastructure where should you go to have a hosted Kubernetes solution? I honestly don’t have an answer to that. The Kubernetes site provides a large list of providers. A friend of mine has been considering between https://stackpoint. ... (more)

Tags: asilearn, kubernetes, infrastructure

18 Apr 2018

scholarly comms product meetup - V2 - announcement

April 18, 2018

Back in November of last year we ran the first scholarly comms meetup with a focus on product management. There are lots of great meetups out there for people who work in scholarly comms, but we felt that there might be an unscratched need to have a meeting where the focus was not explicitly on community building, or on new technologies, or on public outreach, or on new trends and technologies, but solely on the product management work that is required to develop these kinds of tools. ... (more)

Tags: scholarly-comms, product-development, publishing, meetup, sage, altmetrics

09 Nov 2017

The robots are coming, the promise and perils of AI - questions

November 9, 2017

I’m at the Charleston conference, my first time, and we had a panel discussion this morning talking about AI. On the panel were: Heather Staines Director of Partnerships, Hypothes.is Peter Brantley Director of Online Strategy, UC Davis Elizabeth Caley Chief of Staff, Meta, Chan Zuckerberg Initiative Ruth Pickering Co-founder and Chief Strategy Officer, Yewno and myself. It was a pleasure to be on a panel with these amazing people. There was a lot of interest from the audience, and we didn’t get anywhere close to talking through all of the questions that we had discussed as a panel ahead of the session, so I’m going to blog the questions that we had prepared. ... (more)

Tags: AI, publishing, libraries, charleston, dystopia, machine learning, future

14 Sep 2017

Kubernetes - As I Learn

September 14, 2017

I’m currently working on supporting a JupyterHub installation for a series of online courses that we are launching at SAGE. Along the way I’ve had to get my head around deploying the software using kubernetes. This is a stack that I’ve been aware of for quite a while, but I’ve not worked with it before. In order to help with debugging my installation I’m writing up a guide on some of the kubernetes commands that I found useful when deploying a service onto google cloud. ... (more)

Tags: kubernetes, infrastructure, docker, containers, cloud

14 Sep 2017

Software Publishing To Maximise Data Value, slides from ALPSP

September 14, 2017

Here are some annotated slides from my ALPSP talk today. ... (more)

Tags: publishing, docker, containers, software, ALPSP, ALPSP17, data

13 Sep 2017

Moving from Jekyll to Hugo - urls

September 13, 2017

I’ve been changing the static blog generator that I use and am slowly moving from Jekyll to Hugo. My main reason is the better support for tags and categories that Hugo supports, but I’m not finding the templating as intuitive in Hugo as in Jekyll, so it’s not a slam-dunk. There are a couple of small differences between the two systems that are making me reconfigure my blogging workflow a bit. ... (more)

Tags: hugo, jekyll, blogging, scripting, python

20 Jul 2017

I'm hiring a product manager

July 20, 2017

So, I’m hiring a product manager. We are working on developing new green field products. We have a small, really fun team, and we are using a lot of lean tools to try to get to product-market fit with relativly low risk. To apply submit a CV using our [hiring portal](https://uk.sagepub.com/en-gb/eur/sage-vacancies]. Here are some more details about the role: What we are doing SAGE is innovating around how we might support social science researchers engaging with big data and new technology. ... (more)

Tags: hiring, product management, computational social science, SAGE

13 Jul 2017

ic2s2 - Thursday, closing keynotes

July 13, 2017

ic2s2 - Thursday, closing keynotes Economic AI - Matt Taddy Economic AI breaks complex systemic questions into simple sets of prediction tasks, that can be attacked with off the shelf ML techniques. Today economists are being asked to answer basic economic questions but at a ridiculous scale (within companies like Microsoft or Amazon). There are just not enough economists out there to do all the work being asked of them. ... (more)

Tags: ic2s2, conference

13 Jul 2017

ic2s2 Thursday morning keynotes

July 13, 2017

ic2s2 Thursday morning keynotes Daniel Romero - Examining the Effects of Exogenous Shocks on Social Networks and Collaborative Crowds We are looking at the dynamics of social networks. The dynamics of networks are becoming increasingly well understood, but the question here is what happens to a network when there is a big external shock to the system? One example that they looked at came from a hedge fund, the data included full IM communication amongst about 182 people, about 22M items. ... (more)

Tags: ic2s2, conference, computational social science

12 Jul 2017

ic2s2 Wednesday morning keynotes

July 12, 2017

IC2s2 Wednesday Morning Keynotes Cecliia Mascolo - human behaviour studies through the lens of mobile sensing and complex networks She has been involved for many years in making and deploying sensors. The talk today will look at work they have been doing on foursquare data. In London they have data of about 0.5M check-ins over nine months over about 40k users. They also have social network data for these people, so they can connect their social network with the geo-spatial behaviour of these people. ... (more)

Tags: ic2s2, computational social science, conference

12 Jul 2017

IC2s2 Wikipedia track, Wednesday

July 12, 2017

Ic2s2 wikipedia track Studying Content Survival, Authorship & Controversy – By Tracing Every Word Change on Wikipedia - Fabian Flöck, Kenan Erdogan and Maribel Acosta Arriving late to this talk. [TokTrack](TokTrack: A Complete Token Provenance and Change Tracking Dataset for the English Wikipedia | Zenodo) - data is available on Zenodo, 13.5B tokens. There is a [wikiwho](GitHub - wikiwho/WikiWho: An algorithm to compute token-level provenance and changes for Wiki revisioned content. ... (more)

Tags: ic12s2, computational social science, conference

11 Jul 2017

IC2s2 - Tuesday Morning

July 11, 2017

IC2s2 - Tuesday Morning Open Remarks, President of GESIS main note is his call for the potential creation of a new disciple, computational social science opening session, chaired by Duncan Watts Ciro Cattuto - ISI foundation, director of the data science lab is behind sociopattersn.org have many deployments over the last 10 years they make the data open at sociopatterns.org/datasets really cool work on interaction patterns in schools and hospitals can see the gender separation as age going on, also really interesting network study on depression, gender and social network position I like the dimensional reduction techniques on looking at time resolved graphs. ... (more)

Tags: ic2s2, computational social science, conference

11 Jul 2017

IC2s2 Tuesday Afternoon Keynotes

July 11, 2017

IC2s2 Tuesday afternoon Dashun Wang - Predictive Signals Behind Success Dashun starts by talking about weather predictions, natural phenomena can be observed, modelled and predicted. Can success be measured modelled and predicted? Obviously Dashun thinks so, and we are gong to be looking at the result of a number of studies in this talk. Science of Science Aim is to build on top of the work of others, but add to it the massive data that we now have access to, along with the tools that we have developed. ... (more)

Tags: ic2s2, computational socical science, conference

10 Jul 2017

IC2s2 2017, conference preview

July 10, 2017

I’m about to head to Köln for the International Conference on Computational Social Science (IC2S2) and I’m pretty excited for a whole bunch of reasons. I’ve been fascinated by network science, and the potential application of techniques from that science to the rest of research, for quite a while, but generally this has been an interest that I have entertained from a distance. I had the pleasure of attending an early instance of the NetSci conference series back in 2008, and even contributed to a working paper looking at the implications of the intersection between social data and network algorithms (Mining for Social Serendipity), however the academic track has not been my track at all, and with one thing or another this was a community that my career moved me away from for some time. ... (more)

Tags: ic2s2, conference, Köln, computational social science, SAGE

16 Mar 2017

Futurepub10

March 16, 2017

This week I attended futurepub10, I love these events, I’ve been to a bunch, and the format of short talks, and lots of time to catchup with people is just great. # A new Cartography of Collaboration - Daniel Hook, CEO Digital Science (work with Ian Calvert). Digital science have produced a report on collaboration, and this talk was covering one of chapters from that. I was interested to see what the key takeaways are that you can describe in a five minute talk. ... (more)

Tags: futurepub, futurepub10, publishing, innovation, networks, music, discovery, yenow

15 Mar 2017

Three posts about product development

March 15, 2017

I’m catching up on some reading at the moment. Trying to make headway on some other work while jet lagged is proving a challenge. Anyway, here are a couple of nice posts about product development that popped up in my feed (hat tip to Mind the Product Weekly Newsletter. ## What do people do in the spaces in between? When thinking about what people do with your product, also think about what they don’t do, and how to help them get to where they are going. ... (more)

Tags: product development, lean, agile, lean value tree

10 Jan 2017

PLOS are looking for a new CEO

January 10, 2017

So I hear that PLOS are looking for a new CEO. They are making the process fairly open, so if you are interested you can read more here. I got to thinking about some of the challenges and opportunities facing PLOS over the weekend. Over the years I’ve gotten to know a lot of PLOS folk, and I think it’s an amazing organisation. It has proved the viability of open access, and their business model is being copied by a lot of other publishers. ... (more)

Tags: plos, publishing, management, leadership, open-access

10 Jan 2017

Reverse DOI lookups with Crossref

January 10, 2017

Today I had a need to think about how to do a reverse lookup of a formatted citation to find a DOI. @CrossrefOrg helped out and pointed me to the reverse api endpoint. It workes like this: http://api.crossref.org/reverse Created a json payload file “citation.json” formatted as follows: [ " Curtis, J. R., Wenrich, M. D., Carline, J. D., Shannon, S. E., Ambrozy, D. M., & Ramsey, P. G. (2001). Understanding physicians’ skills at providing end-of-life care: Perspectives of patients, families, and health care workers. ... (more)

Tags: publishing, citations, doi, programming, crossref

15 Dec 2016

Hello SAGE!

December 15, 2016

Hello SAGE! I joined SAGE at the start of September. Hello SAGE!! Here I outline some of my initial impressions. First up, I’ve been really delighted to meet so many great people at SAGE. I’ve received great support from everyone in the company. I generally find publishing folk to be very friendly. This is a friendly industry, working on the fabric of knowledge, knowing that your work can help to make a difference, trying to make the work of academics a bit easier. ... (more)

Tags: computational-social-science, work, life, SAGE, eLife

15 Dec 2016

What do we mean when we talk about Big Data?

December 15, 2016

What do we mean when we talk about Big Data? The following blog post about this article provides the following definition of big data: “High volume data that frequently combines highly structured administrative data actively collected by public sector organisations with continuously and automatically collected structured and unstructured real-time data that are often passively created by public and private entities through their internet.” The article is behind a paywall, but the blog is pretty clearly laid out. ... (more)

Tags: big data, research, social science, computational social science

13 Dec 2016

What we mean when we talk about preprints

December 13, 2016

Cameron Neylon, Damian Pattinson, Geoffrey Bilder, and Jennifer Lin have just posted a cracker of a preprint onto biorxiv. On the origin of nonequivalent states: how we can talk about preprints Increasingly, preprints are at the center of conversations across the research ecosystem. But disagreements remain about the role they play. Do they “count” for research assessment? Is it ok to post preprints in more than one place? In this paper, we argue that these discussions often conflate two separate issues, the history of the manuscript and the status granted it by different communities. ... (more)

Tags: preprints, open-access, publishing

09 Dec 2016

Social Humanities DataHack event

December 9, 2016

How do people represent themselves on social media, and how are they represented by others? Which qualities and virtues are emphasized (or ignored)? How polarised are these (re)presentations? There is a workshop looking at this very question happening in Oxford in early January. The morning will be a series of workshops on tools for tackling a question like the above (I’m thinking of attending the Wikipedia and Topic Modelling workshop), and the afternoon will be a hackathon looking at some data sets. ... (more)

Tags: computational social science, hackathon

09 Dec 2016

Textometrica, a tool review

December 9, 2016

A quick spin with Textometrica Yesterday I had a good conversation with Simon Lindgren, the creator of textometrica. I decided to try out the tool before chatting to him. Textometrica encapsulates a process for understanding the relationship and distribution of the occurrence of concepts in a body of plain text. It provides a multi-step online tool for the analysis. The advantage of using this tool is that you don’t need to be able to do any coding to get to a point where you have some quite interesting analysis of your corpus. ... (more)

Tags: text analysis, big data, computational social science

08 Dec 2016

Covalent Data, first impressions

December 8, 2016

Covalent Data is a tool to search over research topics. It seems to have the following features: Is a DB of grants, papers, people and institutions. claims to use machine learning to tie these entities together. search results don’t seem to have a way to be exported, so for example though the grant awards results do list the amount of each grant, to get a total amount against a search term, you would need to do the work of extracting each data point manually. ... (more)

Tags: research, funding, database

08 Dec 2016

Something broke in a Jekyll upgrade (a.k.a, sometimes I hate software)

December 8, 2016

This is a short story about software, some of the things I hate about it, my lack of knowledge of ruby, and a desire to own my own words. For various reasons I’m working on a brand new machine, I decided that I want to start posting to my own blog again (as well as cross posting to Medium, because fuck it, why not). That involved dusting down my Jekyll site and seeing if I could get it to work again. ... (more)

Tags: Jekyll, software, blogging, friction, ruby

21 Jun 2016

I’m voting IN, and you should too

June 21, 2016

Well, here we are, two days out from the referendum. I’m voting IN, but that’s not the main point of this post. The fact that we are having this referendum at all, the fact that it is going to be so close, the fact that it has unleashed a wave of ill informed anger across the divide, all of these things have made me worry and despair a little about the state of politics in Britain. ... (more)

Tags: European Union, UK, brexit, horror, EU

15 Jun 2016

Goodbye eLife!

June 15, 2016

# Goodbye eLife! So after nearly four and a half years I am moving on from eLife. I’ve had an amazing time, worked with some amazing people, and we have gotten a few really nice things done. First off, we are hiring a replacement for my role, this is an amazing opportunity to effect real change in scholarly publishing. eLife has just announced follow on funding of £25M to sustain us through to 2022. ... (more)

Tags: elife, work, publishing, amazing-times

17 May 2015

A(peeling) Peer Review, a proposal.

May 17, 2015

eLife’s peer review process is really good. One of the key attributes of this is that reviewers are not blind to one another, and they have to consult with one another. This largely removes the third reviewer problem. We also publish the decision letters and the author responses to the decision letter. Reviewers have the option of revealing themselves to authors. As with most review systms our reviewers know who the authors are. ... (more)

Tags: peer review, open science, transparency, publishing

11 May 2015

data science vs statistics talk at the RSS

May 11, 2015

Tonight I attend a debate held at the Royal Statistics Society. It was en entertaining, and wide ranging discussion with a great panel, and fairly intelligent questions from the floor. Two fun facts: One of the founding members of the society was Charles Babbage The society is located within spitting distance of the grave of William Thomas Bayes So, here are the notes, rough and ready, and I missed a lot in my note taking, but I hope I get a flavour of the discussion across. ... (more)

Tags: data science, statistics, royal statistics society

16 Apr 2015

aws london summit notes

April 16, 2015

Amazon Web Summit London 2015 ## Keynote There were about three thousand people at the summit. I chatted to a few people throughout the day. Their experience with AWS ranged from moderate use through to just being at the evaluation stage. The keynote highlighted AWS’s approach of wanting to put the customer in control, and to remove all unnecessary work from the customer in terms of managing IT. AWS has grown enormously, they are estimated to have five times the compute power on hand than all other cloud providers combined. ... (more)

Tags: aws, amazon, machine learning, elife, elife-bot, storage, conference, london

13 Mar 2015

RIP Terry Pratchett

March 13, 2015

I must have been fourteen, fifteen years old, I was passing through a train station in Northern Ireland and I picked up a copy of Mort, from that point on I was hooked. How could it not speak to me, a gangly awkward teenager, trying to find my way in the world. I devoured the books as they came out, within a few more years I had a healthy stack. ... (more)

Tags: diskworld, DEATH, heros, sadness

05 Mar 2015

Some thoughts about product management

March 5, 2015

I moved into digital product management in 2007. I had no formal training, and for much of the last eight years I’ve been learning on the job. There are a huge number of resources out there, great lectures, books, conferences, blog posts. In this short post I just want to reflect a bit on what I’ve learned on this topic through direct personal experience. I continue to learn, and my thinking continues to evolve, so this post is more of a look back, than a look to the future. ... (more)

Tags: product development, software, product management, lessons, mendeley, nature, connotea, elife

19 Feb 2015

Wittgenstein and Physics, Cross College Oxford one day seminar

February 19, 2015

(image via peternijenhuis) Last year I attended a one day seminar on Wittgenstein and Physics. It was held at Cross College Oxford and was the first in a planned series of talks on the history and philosophy of science. It’s been a long time since I’ve done physics seriously, and longer still since I took classes on the history and philosophy of science, so I attended very much in the mode of the interested outsider. ... (more)

Tags: physics, philosophy, Wittgenstein, Einstein, oxford, Boltzmann,

11 Feb 2015

Climbing outlook for 2015

February 11, 2015

Last year I hit on the best way to set climbing goals (this was after many years of failing to hit my goals). The best way to do it was to set very short term goals, not ones for the end of the year, but rather quarter by quarter, and modify and update those goals as I went. In addition, I found that focussing not on outcomes, but on process, also helped a lot. ... (more)

Tags: climbing, Spain, training, injury

04 Feb 2015

The 70/90 Rule

February 4, 2015

I was having a conversation last week with a good friend who works in the financial services sector. We were discussing technical debt, and the tendency of certain teams to want to do everything themselves. He described some colleagues in a team that is tasked with managing a large data pipeline for calculation of risks in a particular market. This is central to the bottom line of the company. Oh, they also used to run their own mailing list server! ... (more)

Tags: productivity, lifehack, jekyll, technical debt, github, blogging

28 Jan 2015

FuturePub Jan 2015 - Lens Next

January 28, 2015

On 2015-01-27 I gave one of the short talks at the FuturePub event. My slidedeck is here. I wanted to give a quick update on where the Lens viewer for research articles is heading. Lens is a great platform for experimentation, and we have been iterating on some ideas towards the end of 2014 that have now made it into the 2.0 release. The main update is that Lens can now be configured to accept information from a 3rd party source and display that information in the right hand resources pane. ... (more)

Tags: , , lens, elife lens, publishing, STM, lens, elife

19 Jan 2015

Some thoughts on FORCE2015, science trust and ethics.

January 19, 2015

Last week I was at the FORCE2015 conference. I enjoyed it greatly. This was the 2015 instance of the FORCE11/Beyond the pdf conference. I’d been aware of these meetings since the first one was announced back in 2011, but this was my first chance to attend one. (If I recall, I’d even been invited to the DagStuhl workshop, but had been unable to attend. I’d been to one DagStuhl workshop on science and social networks many years ago, and that had been one of the best short meetings that I’d ever attended, so I’d been sad not to be able to go to the Beyond the PDF meeting). ... (more)

Tags: FORCE2015, Beyond the pdf, conference, Oxford, trust, science, ethics

26 Sep 2014

synthesis of breakout session from day 1 - institutions and metrics

September 26, 2014

Thanks to – Kevin Dolby, Martijn Roelandse, Mike Taylor and Andrea Michalek for taking the notes from each of the breakout sessions, I have synthesised them here. Altmetrics could be used as a way to indicate the pathway of impact Institutions should define their game plan, what do we want to achieve, what metrics can help get us there they could give guidance to researchers on what platforms to adopt (the landscape is cluttered, but at the same time Institutions probably don’t know), that said funders are behind the principle that universities drive what metrics they want to collect, and the set of standards, instead of prescribing metrics (don’t get led by what gets measured, define the change you want to affect first). ... (more)

Tags: 1am, alms, altmetrics

24 Sep 2014

FuturePub3 - September 2014 event

September 24, 2014

Welcome back for the next installment of FuturePub. There are tons of people at the meeting tonight, pizza and beers care of WriteLaTeX!! # Sumika Sakanishi - Product Manager - ODI They aim to encourage organisations to unlock data. They also work with individuals to help them unlock the value of open data. Open data is free to use, reuse and redistribute it, e.g. CC-BY. The open data instutute have created the open data certificate, an online tool to help open data owners publish their data. ... (more)

Tags: futurepub, publication, open access, papers, open data, ODI

24 Sep 2014

thoughts on the ERC data workshop

September 24, 2014

On Thursday and Friday of last week I attended a European Research Council workshop on managing research data. It was well attended with about 130 participants brining views from across the academic disciplines. I’ve blogged my raw notes from day one and day two. In this post I reflect on the points I noticed that were raised over the two days. People have been talking about the increasing importance of research information for many years now, and a hope was raised in the opening comments that we might be able to provide solutions to the problems posed by the issues of research data, by the end of the workshop. ... (more)

Tags: data, open-access, EU, ERC, data management, publishing

21 Sep 2014

ERC data management workshop, day 1

September 21, 2014

initial thoughts about the workshop. Opening remarks. Setting the scene. Sabrina Leonelli - the epistemology of data-intesive science. [Dr Hans Pfeiffenberger - Open Science – opportunities, challenges … @datasciencefeed.](#dr-hans-pfeiffenberger-open-science-opportunities-challenges-datasciencefeedhttpstwittercomdatasciencefeed) Bernd Pulverer - finding and accessing the data behind figures. Dr Roar Skålin - Norwegian researchers want to share, but are afraid of jeopardising their career. Summary of points from the scene setting. Afternoon breakout session - Life Sciences. ... (more)

Tags: data, open-access, EU, ERC, data management, publishing

21 Sep 2014

ERC data management workshop, day 2

September 21, 2014

Life sciences breakout - key points. Physical sciences breakout - key points. Humanities breakout - key points. Open discussion on morning presentations. Breakout session on incentives. [Paul Ayris - Implementing the Future: the LERU roadmap for research data.](#paul-ayris-implementing-the-future-the-leruhttpleruorg-roadmap-for-research-data) Sünje Dallmeier‐Tiessen - Incentives for Open Science Attribution, Recognition, Collaboration. Veerle Van den Eynden and Libby Bishop - Incentives for sharing research data, evidence from an EU study. Open discussion after breakout session. ... (more)

Tags: data, open-access, EU, ERC, data management, publishing

11 Aug 2014

Some pittfalls in using iPython to generate talk slides

August 11, 2014

Yesterday I gave a talk using iPython notebook to generate the talk slides. You can get the notebook on github, and you can see a live version of the slides. It succeeded in generating an artefact that was somewhat literate, in that the code and documentation are nicely woven together, so anyone who has the time can get to exactly the same point that I got to, with this repo, however there were also a couple of problems that I ran into that make me feel that this is not yet ready for mainstream use, specifically: ... (more)

Tags: iPython, iPython notebook, python, slides, reveal.js, talks, wikimania2014

09 Aug 2014

shortcuts that I use for the git command line

August 9, 2014

I use git a lot, it’s pretty complicated, and it has a lot of command line optoins that I can never remember. I’ve copied a couple of shortcuts from the web, and here are two that I use a lot. These are presented in the form of fish shell scripts. function gl git log –graph –abbrev-commit –decorate –date=relative –format=format:'%C(bold blue)%h%C(reset) - %C(bold green)(%ar)%C(reset) %C(white)%s%C(reset) %C(dim white)- %an%C(reset)%C(bold yellow)%d%C(reset)’ –all end ... (more)

Tags: git, command line

29 Jul 2014

looking for ideas for our wikimania talk on open scholarship tools

July 29, 2014

Inspired somewhat by the aweome http://sciencetoolbox.org, along with Martin Fenner, we proposed a session for the upcoming Wikimania conference. We will be talking about Open Scholarship Tools on Sunday the 10th of August at 9:30 am. In our outline for our talk we have decided to possibly think about: CrossRef API (and possibly also the DataCite and ORCID APIs) Pandoc Rstudio Zotero iPython Notebook Plotly Datawrapper What do you think we should try to cover in our 30 minute slot? ... (more)

Tags: wikimania, open access, London, toolbox

30 May 2014

Designing better UX deliverables - Anna Dahlström

May 30, 2014

This talk happened a few weeks ago now, but the topic is timeless, so there is no harm in getting my notes up a bit late. Anna Dahlstrom(@annadahlstrom) came up to Cambridge to give a talk on how to design better UX deliverables, but more broadly the talk had many lessons about how to present results to different stakeholders, not just for UX. A litte bit about Anna Anna had gone from only working with HMRC to working agency side - multiple clients, multiple project, different industries. ... (more)

Tags: UX, IA, camusability

30 May 2014

FuturePub - future of publishing event, hosted by NESTA and WriteLaTeX

May 30, 2014

This is the second #futurepub event that I’ve been to. I also attended the last one The event was hosted by Nesta. Nesta have just launched the “new longitude” prize - which looks pretty interesting. There were six rapid fire talks, and I found the presentation format to be excellent. As with the previous event, this one was organised by the WriteLaTeX guys, and I’d just like to extend a big thanks to them for again putting on a great little event. ... (more)

Tags: publishing, futurepub, altmetrics,

16 Apr 2014

Trial by public, open peer review and the power of attention.

April 16, 2014

There are two very interesting recent examples of review by community on highly exciting results. They both share one very important characteristic, but stand in stark contrast to one another in almost every other regard. The first is the [paper on making STAP cells via use of an acid bath] lemon juice. If confirmed, the result is transformative. The result was published after peer review to tremendous fanfare in Nature. Very quickly the community tried to replicate the result with no confirming replication happening. ... (more)

Tags: open peer review, open science, bicep2, retraction, science

14 Apr 2014

April digital strategy forum

April 14, 2014

On the 1st of April I had the pleasure of being invited to a digital strategy forum event hosted by the Wellcome Trust. People involved in digital and online projects from across a number of not for profit organisations gathered to hear some short talks about using, and contributing to, open source, agile project development and responsive design. Open Source development. Open Sourcing Wellcome Library Player – Tom Crane, Digirati agency The player can be embedded in other sites. ... (more)

Tags: public sector, product development, agile, open source

08 Apr 2014

Php user group March 2013 - BeHat.

April 8, 2014

Background. On Monday the 31st of March I attended the Cambridge PHP Meetup, the topic was BeHat testing. Johnathan Gough gave the talk. This is something we are getting started with in eLife. We have a few small tests in place, we have a few regressions on the site that we want to tackle, and we are looking to use it as a way of pinning down requirements from the company for new features that we want to roll out. ... (more)

Tags: php, testing, gherkin, behat

30 Mar 2014

Climbing goals update 1, 2014

March 30, 2014

I wrote a large post at the start of this year reviewing my climbing goals over previous years, and laying out my goals for 2014. A key modification for me in 2014 is changing to a strategy where I set goals quarterly, rather than yearly. Let’s review Q1. Goals for q1 2014 try at least 12 routes of 6c or harder I managed to try exactly 12 routes of 6c in the last 12 weeks, and my last try yielded success. ... (more)

Tags: climbing, bouldering, training, goals

23 Mar 2014

Discussing Open Access - a comment

March 23, 2014

Discussing Open Access http://discussingoa.wordpress.com/ I read through this piece by Rick Anderson. It’s a very good piece. It does an excellent job of articulating some of the challenges of subscription publishing and of various forms of open access publishing. I have a couple of relativly minor issues with it. The impression I got from reading it was that OA advocates are more shouty and incapable of a serious debate on the issue than advocates of a subscription model, and possibly those who pursue subscription models are more open minded. ... (more)

Tags: open-access, rhetoric

31 Jan 2014

How to create threads between publications and clinical trial registraion numbers

January 31, 2014

Yesterday I attended an interesting meeting to discuss how to improve the connection between clinical trial registration ids and publications. My raw notes from the meeting follow. This is being discussed as publication threads, but the idea discussed here stands apart from the kind of publication threads that the endcode project worked on. attendees ATTENDEES - organisations: eLife f1000 PLOS BMC Springer lancet BMJ crossref attendees - people Geoffrey Bilder, CrossRef, Director of Strategic Initiatives Rachael Lammey, CrossRef, Product Manager CrossMark Daniel Shanahan, BioMed Central, Associate Publisher Tim Stevenson, BioMed Central, Product Manager Deborah Kahn, BioMed Central, EVP Publishing Caroline Black, BioMed Central, Senior Publisher Katherine Barton, BMJ, Operations Manager Josie Breen, BMJ, Head of Editorial Production Isaac Jones, BMJ, Production Manager Ian Mulvany, eLife, Head of Technology Iain Hrynaszkiewicz, F1000, Outreach Director Karen Rowlett, F1000Research, Managing Editor Helene Faure, ISRCTN Database Manager Hannah Jones, The Lancet, Managing Editor Dan Lewsley, The Lancet, Head of Production Joseph Brown, PLoS, Senior Editorial Manager Volker Boeing, Springer, Director, Process and Content Management Mirjam Kessler, Springer, Bibliographic Metadata Manager ... (more)

Tags: publishing, crossref, threaded publications, eLife

18 Jan 2014

Review of climbing goals, goals for 2014

January 18, 2014

For the last couple of years I have done an end of year review of my climbing over the previous year, and set myself some goals for the coming year. Rather than doing exactly the same thing this time, I thought it would be good to look back at several of these reviews over the past couple of years, look at the data on my climbing, and see if I could discover any insights. ... (more)

Tags: climbing, bouldering, goals, shoreditch boulder

18 Jan 2014

WriteLateX/Overleaf launch event at the British Library

January 18, 2014

Last Thursday I attended the launch event for OverLeaf. The event was composed of a set of very short talks, followed by a good chance to chat to people. It was a pretty nice evening. Dr Bibiana Campos Seijo - MRSC - magazines publisher and editor of chemistry world. Science is changing, publising is changing, a lot of this is being driven by technology. There is information overlaod. Publishers need to try to provide solutions to these issues. ... (more)

Tags: LaTeX, science, publishing, tools, authoring, WriteLaTeX

08 Jan 2014

advice on publishing research online

January 8, 2014

I have posted this post as a comment on the thread over at software carpentry in answer to the question What do we teach about writing/publishing papers in a webby world? I ended up writing a bit more than I expected, so here are the main peices of advice: tl;dr: - use a reference management tool - try to find the fastest venue to publish in - try to publish in an OA journal ... (more)

Tags: publishing, science, software carpentry

04 Dec 2013

STM innovations seminar, London, 2013

December 4, 2013

Today I’m at the STM innovations seminar. The twitter tag for today is #ukinno. The program is online. I’m going to take a light approach to blogging today, I’ll probably hang out mostly on Twitter. ## 9.35 The Research Data Revolution, Sayeed Choudhury, Associate Dean for Research Data Management, Johns Hopkins University Data has become a major topic of interest from all sectors of society with headlines such as “Data is the new oil” to assertions from McKinsey that data is the fourth factor of production. ... (more)

Tags: data, STM, publishing, lens

03 Dec 2013

STM brainstorming session - 2013

December 3, 2013

Just attended the STM brainstroming session. I’ll update these notes in due course, and fix spelling issues, but I wanted to get the post live first. Notes I’ll just mention the things that I found interesting. ## Round1 Science Gists get a mention, yay!! Google scholar library gets a mention. Visualising data as maps is mentioned, mentions that there are no standards Howard mentions much richer tagging in the article, and upfront semantic tagging. ... (more)

Tags: STM, publishing, open access, trends, industry, interesting

02 Dec 2013

Hidden In Plain Sight

December 2, 2013

I was bouldering yesterday. At my local block - a lump of granite embedded in the middle of shore ditch park. I’ve been climbing on this block pretty much since the week it was put in place. Yesterday I saw that a hold I’d never noticed had been chalked up. It’s a great hold, at about shoulder height. It fits that pads of two and a half fingers, and in spite of being quite small, it feels pretty positive. ... (more)

Tags: bouldering, Climbing, Shoreditch

19 Nov 2013

Setting up Vagrant, Librarian-Chef and Vagrant aws plugins on OSX Mavericks.

November 19, 2013

I have a new macbook pro. I want to install vagrant, chef and librarian, with the vagrant-aws plugins. I’m working on OSX Mavericks, and I want to get as clean an install as possible. For the most part I am also using the fish shell. This is what I’ve just run through over the last 20 minutes. Install command line tools from the terminal $ xcode-select --install Next we are going to install homebrew, with homebrew we will install rvm and with rvm we will install ruby. ... (more)

Tags: OSX, Mavericks, mac, development, chef, ruby, vagrant, aws, sys-ops, tutorial, librarian, rvm

10 Nov 2013

Spoton13

November 10, 2013

I managed to squeeze in a few hours on Friday attending the spoton conference in London. I’ve been at each one since 2008, and have had the good fortune to present something at most of them. This time I had been asked to sit in on a panel to talk about elife’s policy around media relations, but as I was flying in that morning from an editorial board meeting held in Washington it was not clear to me that I would make it in time, so the fantastic @sciencescoops (Jennifer Mitchell) represented for eLife in my place. ... (more)

Tags: Spoton, solo13, science online, open access, Lou

06 Nov 2013

Vertigo

November 6, 2013

This post was mostly written earlier this summer, in the days after I had finished reading a book. I’ve just finished reading W. G. Seabald’s Vertigo. This is the second of his books that I’ve read over the last decade, and it is as haunting as the first. The first of his I read was The rings of Saturn. Towards the closing pages of the book I was filled with a great expectation that I might possibly experience some deep revelation. ... (more)

Tags: Seabald, Fontainbleau, memory

17 Oct 2013

PLOS ALM 13 day 2

October 17, 2013

Connecting ALM and Literature As I took part in the first session I don’t have many notes from it. I’ve posted the slides from my talk, and I’ll write up some more on those in due course. For me the standout talk of the session, if not the entire meeting, was from Jevin West who talked about using networked ranked data to provide recommendations. The algorithms his group are working on are being tested on [SSRN][ssrn], and will be rolled out to PLOS. ... (more)

Tags: alm, altmetrics, plos, publishing, conference, recommendations

16 Oct 2013

NISO ALM standardization workshop

October 16, 2013

This was a one day workshop discuss the creation of standards around Article Level Metrics. NISO has a grant from the Sloan foundation to look into this, and this event was the first of three planned information gathering events. My own opinion on this topic has changed over the past year, evolving from being strongly opposed, to broadly supporting the idea of building some kind of standard or best practice for the field. ... (more)

Tags: alm, altmetrics, niso, standards

16 Oct 2013

PLOS ALM 13, day1

October 16, 2013

## Cameron Neylon - Introduction & Welcome Interesting - this is the first PLOS ALM meeting that is a “normal” scheduled presentation. Time is going to be tight. Pete Binfield ALM: Looking back, moving forward A large chunk of OA does not select for impact - this is why ALMs are key for this space. PLOS didn’t invent ALMs - Frontiers were doing it a little ahead of PLOS’s launch. Web of science didn’t tell PLOS until 2010 that PLOS one was being tracked for an impact factor. ... (more)

Tags: alm, altmetrics, plos, publishing, conference

30 Sep 2013

Cambridge usability group - UX and agile

September 30, 2013

Sophie Freiermuth(@wickedgeekie)) from Baguette UX gave tonight’s talk on how lessons learnt from operating as a UXer within an agile environment. I thought it was a great talk. When at Mendeley we always faced the problem of trying to square the challenge to fitting an inherently creative process into the systems that emerged while we attempted to adopt agile processes, in my time there we learnt a lot, we had some success and some areas where we obviously needed to learn more, so I was delighted to hear a very thoughtful presentation from the perspective of someone who it seems has worked with quite a few teams implementing agile in a variety of flavours. ... (more)

Tags: UX, CUG, agile, lean, design, development

30 Sep 2013

Cambridge usability group - UX and agile

September 30, 2013

Sophie Freiermuth(@wickedgeekie)) from Baguette UX gave tonight’s talk on how lessons learnt from operating as a UXer within an agile environment. I thought it was a great talk. When at Mendeley we always faced the problem of trying to square the challenge to fitting an inherently creative process into the systems that emerged while we attempted to adopt agile processes, in my time there we learnt a lot, we had some success and some areas where we obviously needed to learn more, so I was delighted to hear a very thoughtful presentation from the perspective of someone who it seems has worked with quite a few teams implementing agile in a variety of flavours. ... (more)

Tags: UX, CUG, agile, lean, design, development

29 Jul 2013

Some advice on learning web development.

July 29, 2013

Here is some advice I gave a few months ago to a friend on becoming a web dev. I think it still holds up. The most important thing I have lots of advice, it I think the most important advice that I have boils down to do work. Build up a portfolio, and get comfortable and fluid with the tools that you will use to do web development. We look for skilled passionate people, and the best way to show that, is to show projects that you have been working on. ... (more)

Tags: web, github, advice, hiring

02 Jul 2013

EC consultation on Open Data - a report.

July 2, 2013

This is a report on todays consultation on open data that was help by the EC. The notes are long, so I have put my conclusions and general comments at the start. General comments There was not much disagreement throughout the day. There were repeated calls for the need to incentivise researchers to engage in data sharing, but not too many concrete proposals on how to do this. It does seem from my perspective that libraries could do an amazing job here, but that will depend on to which extent these libraries have deep technical expertise. ... (more)

Tags: open access, open data, horizon 2020, EU, science, publishing, eLife

02 Jul 2013

EC consultation on Open Data - my presentation.

July 2, 2013

The following is the written representation that I made to the EC hearing on Open Data on behalf of Co-Action publishers, Copernicus Publications, eLife, F1000 Research, FigShare, Frontiers, Open Books Publishers, PeerJ, the Public Library of Science, Ubiquity Press and Bloomsbury Qatar Foundation Journals (QScience). I had a five minute slot to present, and the key recommendations at the end of this written response formed the basis of that presentation. I added one slide at the end with a personal view on some of the challenges of getting researchers to share data. ... (more)

Tags: open access, open data, horizon 2020, EU, science, publishing, eLife

16 May 2013

Some Thoughts on web scale annotation.

May 16, 2013

Mark Ware recently asked me some questions about the state of web scale annotation, based on my impressions from the recent iannotate conference (at which I gave a short talk on the idea of research threads) What is the eLife view of annotation systems? We like the fact that there is now a W3C standard for Open Annotations (OA). We are encouraged that so many projects out there are looking to make their annotations interoperable with this standard. ... (more)

Tags: annotation, open annotation, iannotate, elife

27 Apr 2013

Some thoughts on the Taylor and Francis Survey.

April 27, 2013

I took a look at the T&F survey with interest. I’m also very aware of the concerns and confusions that exist around licensing. I’m also aware of the “one size doesn’t fit all” argument. I’ll address the T&F survey first, and then I’ll briefly discuss CC-BY pros and cons, purely from the point of view of my own understanding of these issues - I might be very wrong on this. ... (more)

Tags: OA, cc-by, publishing, dog in manger

23 Apr 2013

Communicating better, moving from virtualenv to vagrant/Chef

April 23, 2013

I’ve been using virtualenv for a while, but in the past few months, since taking up the role of head of technology for eLife, I’ve been giving much more thought about how to build scalable development environments. Ever since I was managing connotea, one of the biggest pains has been configuration management. I seem to have spent almost more time on configuring environments than on actually doing any development work (disclaimer, I don’t actually do much coding, I usually do more product management, but it’s really useful to know the development pain points). ... (more)

Tags: python, chef, vagrant, sysops, ipython, development, communication

24 Mar 2013

Climbing review of 2012, goals 2013.

March 24, 2013

212 climbing review. OK, time to review the year. I wrote out some goals at the start of last year. Goals for 2012 were remain injury free (not done) significantly reduce the amount of alcohol that I consume (done) fall off at least 10 routes of 6c or harder/month (not done) redpoint 7a, but don’t stop trying harder things (not done) get three campus board sessions or power hand sessions into my training per month (done) My training diary from 2011 looked like: ... (more)

Tags: climbing, bouldering, training

24 Mar 2013

Font, Spring 2011, quick report

March 24, 2013

Well, it’s been almost a week since I got back from Fontainbleau. It was, as usual, a magical trip. Were took advantage of the row of bank holidays to get in a nice long spell in the forest without having to take too much time off work. I’d been training like a fair old bastard in order to get fit for Marie Rose, but in the end a couple of injuries stopped me going near the route, which was a pity. ... (more)

Tags: bouldering, climbing, font, training, fontainbleau, injuries

24 Mar 2013

Font, Spring 2013, preview

March 24, 2013

I’m about to head to Fontainbleau for another short climbing trip. I’ve been going there since 2003, this will be my 10th anniversary of going to font. The first time I went there I brought a lot of expectations with me. I was climbing pretty well and I fully expected that I should be able to run up problems of about font 6a. I think I fell off of that first 3a 6 times before I got it. ... (more)

Tags: bouldering, climbing, font, training, fontainbleau

30 Jan 2013

ENCODE - an example of open publication and data integration.

January 30, 2013

On Monday the 14th of January we met at the PLOS offices in Cambridge to hear a talk from Euan Birney on lessons learned from publishing data rich publications though the encode project. This was the first time that Euan was far less worried about the print, and far more worried about how well the online version was going to work. Dimensions of the project 5 TeraBases 1715 times the size of the Human Genome 3k experiments 410 authors on the main paper 6 high profile papers ~35 companion papers The output should not be thought of as papers, but as the raw data. ... (more)

Tags: publishing, data, open-access, ENCODE, threads

23 Jan 2013

Product Tank 6, big data

January 23, 2013

I’m at PridcutTank 6. Todays topic is big data. Hether Savory - Open Data User Group She is the chair of the open data user group. She is using a recipe analogy for the use of data in the creation of products - data is an ingredient, but you have to get the ingredients right. (There are a number of people in the audience who work with public sector data, and more people who work with open data, but most people know about this, but they don’t use it). ... (more)

Tags: product tank, data, open data

12 Nov 2012

SpotOn day 2.

November 12, 2012

Yesterday was awesome, let’s see how today goes. I was watching from afar, as my wife attended, and now I’m here for the afternoon sessions. sessions: Ben Goldacre publishing data, what’s in it for researchers? now on to the sessions! [Incentivising Open Access][ioa]. (top) Nice panel, you can see the list of the panel on the site homepage, I’ll again, mostly focus on the trend of the discussion. ... (more)

Tags: , STM, conference, solo, spoton, London, publishing

11 Nov 2012

SpotOn day 1.

November 11, 2012

I’ll keep a partial, live-idsh blog going during the day. I’ve been going to these things, I think, since about 2008. I really like these meetings. I’m going to probably keep these notes pretty lightweight. sessions: Ben Goldacre Kamila Session on whether science journalism will be replaced Altmetric track now on to the sessions! Ben Goldacre - opening keynote, on data. . (top) Ben is talking about the issues that arise when you place a lot of data in one place. ... (more)

Tags: , STM, conference, solo, spoton, London, publishing

11 Nov 2012

The new food.

November 11, 2012

I got to spend a really fun forty minutes or so this morning with Pat Brown, down at the home of Lyrical Foods, the new project that he is involved in. They are aiming to replace the dairy and cattle industry by producing food from plant derived products that is indistinguisable from the original products. They have already created artisinal cheeses that are indistingushable from milk-based cheeses, and I understand that they are currently working on fake blood, that has the same response profile to cooking, as real blood does. ... (more)

Tags: every day matters, biochemistry, food, science, cheese, the future is coming

10 Nov 2012

Last minute changes to our solo12journals line up.

November 10, 2012

* {margin:0; padding:0} body {font:11px/1.5 Verdana, Arial, Helvetica, sans-serif; background:#FFF} #text {margin:50px auto; width:500px} .hotspot {color:#900; padding-bottom:1px; border-bottom:1px dotted #900; cursor:pointer} #tt {position:absolute; display:block; background:url(images/tt_left.gif) top left no-repeat} #tttop {display:block; height:5px; margin-left:5px; background:url(images/tt_top.gif) top right no-repeat; overflow:hidden} #ttcont {display:block; padding:2px 12px 3px 7px; margin-left:5px; background:#666; color:#FFF} #ttbot {display:block; height:5px; margin-left:5px; background:url(images/tt_bottom.gif) top right no-repeat; overflow:hidden} I'm really excited about the session that we will be running at SpotOn London in just two days time! ... (more)

Tags: , , STM, conference, solo, London, publishing

28 Oct 2012

The journal is dead, long live the journal - abstract.

October 28, 2012

With Anna Sharman and Bob O’Hara, I’ll be hosting a session on the future of academic journals at SpotOnLondon (formerly ScienceOnline London). You can check out the session details here. They have posted the short version of the abstract on the site, I’m posting the longer version here, and you can also see our google planning document. We will update with details on the panel very soon. Abstract Today’s online articles and journals remain mostly an online mirror of print products. ... (more)

Tags: STM, open access, megajournals, solo12

11 Oct 2012

Data literature integration workshop.

October 11, 2012

Literature Data integration workshop 2012-10-10 There are many people attending today. I’m not sure whether the attendee list will be released. I’ve taken notes, but rather rapidly. I may have ended up mis appropriating comments, missed comments, or inserted comments that didn’t happen, so take the below with the appropriate health warnings. I still need to check on the links, and pull together a link list at the bottom, but I wanted to get the write up out while it was still in front of me. ... (more)

Tags: data, literature, publishing, STM, EBI, workshops

03 Oct 2012

Mind the product 2012, notes.

October 3, 2012

Last Friday I attended the amazing Mind the product conference in London. It was really inspirational. There were about 500 attendees, and having so many people with a concern for the same aspect of the product development process in one room led to a real buzz. The speakers were excellent, sadly I had to leave a little after lunch. The videos will be posted, keep an eye on the mind the product main site. ... (more)

Tags: web, product developmet,

02 Oct 2012

Going for gold, open access debate.

October 2, 2012

Update, audio of the meeting is now available on figshare Last Thursday I attended the SciCommForum debate “Open access: going for gold?” held at Imperial College. Below are my notes from the event. The notes are fairly raw, and not comprehensive. The debate is going to be looking at open access in the context of the RCUK policy, it is being hosted by Richard Van Noorden (RVN), Mark Thorley (MT) from RCUK, and Stephen Curry (SC). ... (more)

Tags: open access, gold, STM, green

22 Aug 2012

The slow web, more thoughtful experiences.

August 22, 2012

I’ve been concerned for a few years about the flow of data that we are producing, and how to handle the angst of not being able to keep up with everything, ever. I think it started when I became a very heavy user of google reader back in 2006 or so. There is little doubt that the web is moving more in this direction, Anil Dash recently called for people to stop creating web pages, and to start creating only streams. ... (more)

Tags: web, slowness, STM, filter-failure, elife, music

17 Jul 2012

academic ghost towns, Google scholar and Mendeley

July 17, 2012

I’m on a mission to clear out my instapapper backlocg, so I’m going to be blogging olds rather than news. There was a nice piece in the Atlantic last month talking about how Google could provide a better social experience by activating it’s latent networks, rather than mimicking facebook. But think about Scholar as a latent social network. Each paper contains its own social network that Google already crawls. Every bibliography is filled with other social networks. ... (more)

Tags: Google scholar, Google, mendeley, research

17 Jul 2012

sharing documents with google apps for your domain

July 17, 2012

I’ve just rolled out google apps for your domain for eLife. At about the same time google rolled out gdrive. We were having difficulty figuring out how to share documents across the domain without having to invite people individually to the document. The document sharing options provide the ability to make documents findable by other members of the domain, but when we tried to search for these documents, we were not finding them. ... (more)

Tags: google, gdrive, gdocs

12 Jul 2012

The cost of production

July 12, 2012

Last week an interesting discussion on the cost of copy editing popped up over on Stephen Curry’s blog. In addition the comment thread at the recent Science editorial seems to make this post somewhat timely. I used to manage the copy editing of a good portion of physical science related content from Springer from 2002 – 2005. I’m also currently in the process of setting up a new online-only journal. ... (more)

Tags: STM, publishing, openaccess, open-access

11 Jul 2012

XMP wrangling on OS X

July 11, 2012

XMP XMP is the extensible metadata platform from Adobe. It can be used to embed structured metadata into a file. I think it’s most common usage is for storing image metadata in image files, but it also has a use in embedding metadata in PDF files. Adobe provide an SDK that you can use to start coding applications for working with XMP. They provide a guide for developers, and I’ve posted a copy so you can have a quick look if you are interested, without downloading the full SDK. ... (more)

Tags: xmp, pdf, adobe, metadata

08 Jul 2012

What use metaphor?

July 8, 2012

I watched a little of the q&a at CERN this week. One question stood out. A journalist, who didn’t want to be named, asked the panel a question along the following lines: “what were the panel’s favourite and least favourite metaphor for the Higgs boson, and what were their thoughts on the god-particle expression.” He pointed out that given such a complex story many who will b e explaining it to the general public will need to reach for metaphor, and when it comes to the god particle term, as much as some may not like it, it has to be recognised that it has entered public consciousness. ... (more)

Tags: science-communication, higgs, bosons, metaphor

02 Jul 2012

Elio

July 2, 2012

As i write these words my son is a little under a day old. Everything changes, that’s what they tell you, all the friends who have started down this journey before us, our relatives, elders. There are emotions unlocked inside me, an almost physical new presence, sometimes quiescent, sometimes flooding over me, triggered by the banal miracles - the sound of a breath, a gurgle, just the telling of the story of the birth. ... (more)

Tags: family

26 Jun 2012

Did you just tell me to go fuck myself?

June 26, 2012

So this morning I had a scan with a consultant and he has diagnosed me with Dupuytren’s Contracture. I’ve been a climber since the summer of 1990, nearly 22 years now. It’s been amazing, I’ve gotten into some pretty special situations, and I’ve gotten pretty fit. There is some evidence that there is a higher incedence of Dupuytren’s Contracture amongst climbers. There is a great write up about a climbers experience of this condition on ukclimbing. ... (more)

Tags: open-access, climbing, twitter, Dupuytren's Contracture

18 Jun 2012

Some Thoughts on Peer Review and Altmetrics

June 18, 2012

The upcoming altmetrics meeting, and a submitted abstract by Kelli Barr prompted me to note down some of my own thoughts on peer review and altmetrics. I would love to make it over to the meeting, but with just a few days now before my first child is born, it ain’t gonna happen. I’ve not read Kelly’s paper, but after reading the abstract my take home message from it would be something along the lines of “don’t replace peer review with altmetrics because you will just replace one bias with another, and at least with peer review the bias is contained within the academic community” ... (more)

Tags: peer review, altmetrics, publishing, open-access

17 Jun 2012

Augmented Peer Review

June 17, 2012

Last year I was asked to contribute to a special issue on the evolution of peer review. I got quite excited about doing this, but then realised that I really didn’t have the time to write a paper. I’m not a practicing academic, I build products, and while at Mendeley I really had far too much on my plate to find the time to write up a paper. However the topic does interest me, and I am a strong believer that web scale technologies can help with the scientific communication process though a large number of avenues. ... (more)

Tags: peer review, altmetrics, publishing, open-access

17 Jun 2012

Super quick start guide to fluidinfo

June 17, 2012

This is a quick and dirty guide to getting started with fish, the command line tool for fulidinfo. I did it by setting up a virtualenv, as I find it a lot easier to manage python dependancies that way. Setup a virtualenv: % mkvirtual env fi Open the virtual env session: % workon fi Install httplib2: % pip install httplib2 Install readline: % pip install readline Get fish, you can either get it from github and install from source, last time I checked that was: ... (more)

Tags: fluidinfo, python, readwriteweb

08 May 2012

The Tractaus, a mini-review

May 8, 2012

This is the only book that Wittgenstein published in his lifetime. At the onset of the first world war Wittgenstein enlisted in the Austrian army. He was captured and served out the end of the war in a POW camp. It was here that the manuscript for the Tractatus was completed (footnote, I can’t recall where I read this, either in an encyclopaedia entry on Wittgenstein, or in Wittgenstein’s Poker, either way perhaps someone can otherwise confirm this statement? ... (more)

Tags: philosophy, wittgenstein, book-review

05 May 2012

Leaving Mendeley

May 5, 2012

I’m starting to draft this post on the train on the commute to my new job at eLife. After almost two years I’ve taken the decision to move on from Mendeley. They were without doubt the two best and most challenging years of my career to date. Working in a start up is an amazing, frustrating, enlightening, energising and rewarding experience. No single post can do justice to that time, and each time in the past weeks that I have drafted this post in my head it has had a slightly different timbre, so take this for what it is, a reflection in a moment. ... (more)

Tags: career, life, Mendeley, open-access, eLife

18 Jan 2012

Mendeley, an investment branch of the citation bank.

January 18, 2012

The awesome Rod Page has a great post on utilising Mendeley as a bank for citation data. He recommends that projects such as the Biodiversity Heritage Library should build on top of the kind of infrastructure that we have already created at Mendeley. I’m a big fan of this as an idea, and indeed one of my goals for Mendeley is for us to create a system that makes it easier for others to build great tools for researchers. ... (more)

Tags: citations, mendeley

17 Jan 2012

SOPA and PIPA stink, but the RWA is more dangerous to science.

January 17, 2012

There are three bills up for consideration in the US Government which if passed will have a significant negative impact on academic research. These are the Stop Online Piracy Act (SOPA), the Protect IP Act (PIPA), and the Research Works Act (RWA). SOPA and PIPA will have a negative impact by putting censorship controls into the hands of the entertainment industry, and permitting legal process to affect the underlying architecture of the web. ... (more)

Tags: copyright, science, open access, OA, publishing, internet, shit sandwich

08 Jan 2012

Climbing Goals 2012, review 2011

January 8, 2012

Well, it’s been a while since I wrote up my climbing goals for 2010, and I totally missed doing this for last year, so as we ease our way into 2012 it’s high time that I do the same again. The key goals for 2010 were: redpoint fr 7a boulder V5 trad E1 some trips to do some trad climbing Well, since then I achieved the following: onsight 6c+ indoors redpoint 6c outside boulder V4 a few HVS’s So, not quite breaking through to where I wanted to be, but there is a feeling of definite progress. ... (more)

Tags: climbing, goals, resolutions

21 Nov 2011

example title

November 21, 2011

Back in 2010 I was pointed at zanran, a search engine that looks for data in graphs. I’ve been playing around with some sample searches, and decided to try drowning deaths swimming pool. Incidentally all of the results that came back were figures for young children. I guess this is because that is the group where there is the most concern, and so there is more published data about this group. ... (more)

Tags: data, search, zanran

20 Nov 2011

Update on MathJax

November 20, 2011

MathJax has come a long way since I last looked at it. There is now a CDN hosting the js files, which makes calling it really really easy. It’s being adopted by GiHub for their wiki engine. Using it with markdown can cause a few bumps, but there seems to be a bunch of ways around this: [mathjax in markdown][mim] using some mathjax configuration and custom css [amazing implimentation][ai] in a notetaking app [php, mathjax and wordpress][phpm] Writing a block of %%\LaTeX%% like this ... (more)

Tags: mathjax, latex, github-pages, javascript

13 Oct 2011

Converting between dates and unix time in Python

October 13, 2011

Going from a date to a unix time: >>> from datetime import date >>> from time import mktime >>> start = date(2011, 9, 26) >>> mktime(start.timetuple()) 1316991600.0 Going from a unix time to a date: >>> from time import strftime >>> from datetime import datetime >>> datetime.fromtimestamp(int("1284101485")).strftime('%Y-%m-%d%H:%M:%S') '2010-09-10 07:51:25' ... (more)

Tags: python, time, unix

07 Oct 2011

Nature, Whiskey and me

October 7, 2011

In my earlier post on Megajournals I hinted that I felt that there could be a future in which this business model provided sufficient funds to allow a publishing house like NPG to make it’s flagship journal Nature an open access journal. This topic came up late one evening at coasp and I ended up making a bet with Matias Piipari. I bet that within 10 years Nature would become a fully open access journal. ... (more)

Tags: open access, whiskey, publishing, coasp

06 Oct 2011

Hindawi have an awesome reviewing system.

October 6, 2011

Hindawi publishers is a really interesting outfit. They are an open access only publisher based in Egypt. They combing a fantastic use of technology with the ability to afford a large amount of human curation over the data that they use to streamline their publication and reviewing systems. One of their publishing vehicles is called the International Scholarly Research Network and at the recent coasp conference Paul Peters gave an overview of how their peer review system works, I think it’s genius. ... (more)

Tags: open access, publishing, coasp

03 Oct 2011

Megajournals

October 3, 2011

The idea of megajournals had not really formalised in my head before, but at the COASP meeting the talk was all about “Megajournals”. [PLoSOne][plosone] is the archetype for this kind of journal, and it had not really struck me before as a huge revolution in the publishing industry, but after listening to a couple of days worth of talks on the topic I’m convincible. Megajournals are so called because they are structured to be able to publish many more articles than has been the normal practice with traditional journals. ... (more)

Tags: megajournals, publishing, open-access, coasp, peer-review, science, nature

03 Oct 2011

The rude health of Open Access Publishing.

October 3, 2011

TL;DR OA publishing is maturing with a scalable business model that all the big publishers are jumping all over. Money will be made (but less than before), and more content will be more open. The poor lamentable nay-sayers who carp on unheard in the darkness will be forgotten, and their Cassandra-like predictions will fade to be recalled as little more than the mutterings of fools (OK, that last bit is probably opinion). ... (more)

Tags: conference, open-access, publishing, coasp

02 Sep 2011

Science Online London Keynote, Michael Nielson on Open Sciecne

September 2, 2011

Michael Nielson Keynote on Open Science He rightly points out that he is probably going to be talking to the converted, so his talk is aimed at looking for resources that can help us to find answers about how to make open science works. He starts talking about an example of failure in open science. his example is an open notebook science from Tobias J Osbourne. He built up a readership of about 100 readers on a highly technical field, but he was not getting much participation, and very little feedback. ... (more)

Tags: solo11, conference, keynote, open-science, science

02 Sep 2011

SOLO11, day1, morning sessions.

September 2, 2011

Session on engaging with peer review This is a very nice panel discussion. For my money there are a number of key points that arose during the discussion: discussions with the public needs to happen where the public is being half assed about engaging the public discourse around papers, and then hiding behind peer review when you run into criticism is really bad, as for example what happened with the arsenic story nasa and science the public needs to be educated that peer review is not binary peer review comments should be made public (not everyone agrees) where we have representations of papers we should look to link to conversations about those papers (trackbacks and so forth) There is a very interesting comment in the Q&A from [Martin Fenner][mf] about peer review in clinical medicine. ... (more)

Tags: solo11, science-online, science, API, nature, peer-review

01 Sep 2011

Talkfest, science and community

September 1, 2011

Introduction So this is a short TalkFest event looking at the public, communities and online science. I’m sure there will be plenty of online discussion around this topic, below are some very rough notes that I took during the event. It was very enjoyable. The people on the panel are D. Amy Sanders from the Welcome Trust, Rob Simpson, (a.k.a OrbitingFrog), Linda Davies and Stephen Cury. The panel was convened by Alice Bell ... (more)

Tags: TalkFest, solo11, science, online, science-online

30 Aug 2011

ArXiV at 20, a brief review.

August 30, 2011

I just read the brief article by Paul Ginsparg about 20 years of the ArXiV. I think the article is a must read for anyone who is thinking about scientific communication. It’s short, and very readable. The things that stand out for me from this article are the following: There are real costs associated with running services on the web. Ginsparg originally imagined that the service that he created could run automatically and that he would be able to get back to his research projects very quickly. ... (more)

Tags: review, paper, arxiv, physics, open science

08 Aug 2011

Serendipity, a chance encounter (obviously)

August 8, 2011

Tonight there was a lovely sameas event on the topic of serendipity. I’d stared a blog post about this back in May as a response to to a post that Frank Norman wrote about enablining serendipidous discovery in the digital library. Well, that post kind of lingered, malingered in my drafts directory, so I thought I’d best get on get something out there, spurred on by the event tonight. I studied in Edinburgh for a few years, it’s a beautiful city, and in the heart of the old town Victoria Street sweeps in a steep curve down to the cowgate. ... (more)

Tags: discovery, serendipity, sameas, happyness

31 Mar 2011

Robert Bunsen's Birthday

March 31, 2011

Google’s homepage cartoon today tells me that it’s Robert Bunsen’s birthday. He is famous for the invention of the burner named after him, but his contribution to our understanding of the universe around us runs much much deeper than that. He co-created the science of spectroscopy with Gustav Kirchhoff. This is something I learned about when I was living for a while in Heidelberg, one of the university building’s along the Hauptstrasse is named after Bunsen. ... (more)

Tags: chemistry, science, astronomg, quantum mechanics, philosophy, epistimology

30 Mar 2011

Sits meeting notes, November 2010.

March 30, 2011

2010-11-04 sits Right, the meeting is starting, it’s an open meeting, so we don’t have a specific agenda, but as the day goes on topics for discussion will emerge, and these will be time-boxed for discussion. As the participation list is available on the eventbrite site, I’m not going to capture that here. Some topics from the last meeting signatures on digital objects correct identifiers on digital objects author identifiers lightweight languages toolsets sword, sword2 Some potential topics for this meeting authentication and access control rdf and linked data within institutions and repositories data curation reasonable workflow components, best practices lightweight tool sharing web archiving sustainable storage tool sharing data curation, big data, and what the concept of curation means for repositories ... (more)

Tags: sits, jisc, DLF2010

29 Mar 2011

mini-review of "Measuring the User Experience on a Large Scale"

March 29, 2011

Measuring the User Experience on a Large Scale: User-Centered Metrics for Web Applications by Kerry Rodden, Hilary Hutchinson, and Xin Fu Rodden, Hutchinson and Fu describe a framework for measuring the user experience of web apps through mining server logs. Since they are based at Google one assumes that the framework that they are describing has been battle tested. They focus on metrics that measure user centric aspects of the online experience, in contrast to business centric (such as PULSE metrics: Page-views, Uptime, Latency, Seven day actives, Earnings). ... (more)

Tags: paper, user experience, data, google

27 Feb 2011

Our gospels define us

February 27, 2011

I’m reading a fascinating book about the Wittgenstein family. It’s called House Wittgenstein, a family a war. The book main focuses on Paul Wittgenstein, the left armed concert pianist, nonetheless there are many things detailed in this book that have dramatically informed my opinion on both Ludwig Wittgenstein and his philosophy. Two things I want to mention here, firstly much of Ludwig’s approach to life was influenced by Tolstoy’s work The Gospel in Brief (The parallels between the two works are drawn out very nicely here), secondly Wittgenstein’s close family constantly refer to him as being a saint in their personal correspondences. ... (more)

Tags: philosophy, religion, wittgenstein, tolstoy, scientology

06 Feb 2011

Rat in the Snow

February 6, 2011

I’s a beautiful morning in New York, the sun is shining, and the snow blankets central park. Yeserday the rain and mist made it feel like a bit of a shit-house, but today it’s a fantastic day. I brought my climbing boots on this trip just in case I might find a few hours to squeeze in an attempt on the polish traverse on rat rock, and this morning I had my chance to get up and see what state the rock was in. ... (more)

Tags: climbing, bouldering, focus, rat rock, NYC

04 Jan 2011

Turning the Physics ArXiV into an Open Peer Review System.

January 4, 2011

Axel Boldt posted an interesting short paper discussing how to turn the physics ArXiV into an open peer review system. It’s a short read, about three pages, but if you are familiar with the problems around peer review then you can just jump to part three of the paper which is a little under a page. The solution proposed is to create a new role of editor on the ArXiV, and allow anyone to propose their paper for review. ... (more)

Tags: publishing, arxiv, peer review

20 Dec 2010

Cancelled :( Drinks with Chris Wiggins.

December 20, 2010

CANCELLED Due to flight cancellations out of NY, Chris won’t be making it over to this side of the pond, so sadly we will be calling the event off. London is a great city to live in if you are interested in technology. It has to be one of the best cities in the world for people working on the interface between science, tech and te web. Tonight I’ll be going to the awesome Same As Christmass Quiz, and tomorrow night Chris Wiggins will be passing through from New York, and there will be a chance to meet up with him for a pint and a chat. ... (more)

Tags: data, geek, drinks, london, graph theory

13 Dec 2010

Wrangling image metadata

December 13, 2010

I’m trying to move away from iPhoto because I have lost too many pictures over the years from having multiple versions of an image lying around, from metadata being plopped all over the place. It is time to move to a more sustainable simple way of naming foldering and tagging my image archive. In the course of looking at this I have been playing around with Lightroom, and I want to ensure that I can add tags at a system level on my mac, and have them show up in Lightroom, and at the same time have Lightroom tags discoverable through spotlight searches. ... (more)

Tags: exif, picasa, lightroom, leap, mac, images, raw

14 Nov 2010

Video workflow with a mac using iMovie and capturing with a Lumix GF1

November 14, 2010

I’m figuring out the best way to shoot video with my Lumix GF1 on a mac using iMovie. The GF1 offers two main options for video capture, HD JPEG, and AVCHD. There is a great post describing the pros and cons of these two formats here [], and based on that I decided to experiment with AVCHD. After playing around a little I found a few oddities. JPEG capture writes the files onto the device as . ... (more)

Tags: photography, video, iMovie, mac, GF1, mp4, MOV, Handbrake, AVCHD

02 Nov 2010

Arriving in Paulo Alto for the DLF fall forum

November 2, 2010

(I’m posting some of these posts a few days after writing, but you’ll get that, won’t you) It’s five in the morning, and I’m well and truly jet lagged, but after the past week this is not the strangest I’ve been feeling so, it’s not too bad (the immunisation shots for my trip to Mexico left me in an entertainingly woozy state Friday evening). I’m over to cover the digital library federation meeting, and the satellite SITS meeting on thursday. ... (more)

Tags: dlf2010

02 Nov 2010

DLF opening keynote, beyond buckets and boxes

November 2, 2010

(notes taken yesterday) The keynote is starting, the DLF has grown by 15 new member organisations, and this is one of the best attended events that they have run, the room is packed, i didn’t realise that there were so many people in the hotel, its looking like its going to be an interesting meeting. The original vision for this group is to create a national digital library, they have been talking about this since 1994 (goodness, so much that needs to be cut through to get to where we know we need to get to). ... (more)

Tags: dlf2010, keynote, education, publishinig

02 Nov 2010

San Francisco, and science hack day discussions

November 2, 2010

(This was from Sunday) In an attempt to get over the jet lag, myself and Dave headed over to San Francisco yesterday, we had a good walk around, got lost twice, and then met pup with the lovely Ariel Waldman. I had to drop off some mendeley schwag for the upcoming San Francisco science hack day that Ariel is organising (we are giving a little sponsorship, yay!). It’s going to take place in two weeks, and it looks lie it’s going to be an awesome event. ... (more)

Tags: science hack day, dlf2010

18 Oct 2010

save mailfolder messages to a file using applescript

October 18, 2010

I’ll just start by explaining that I hate applescript. I wanted to create a script that would take a specific folder withing the script and save each message from that folder to a text file on my machine for post-processing. This is what I came up with. set fileRoot to "Macintosh HD:Users:path:" set messageList to {} tell application "Mail" set messageList to messageList & (messages of mailbox "mailbox name" of account "account" of application "Mail") set counter to 1 repeat with theMessage in messageList set fileNum to counter as string set theFilePath to fileRoot & "mailcontent" & fileNum & ". ... (more)

Tags: apple, mail, applescript

24 Sep 2010

Citation Style Language

September 24, 2010

Martin Fenner asked me to comment on Mendeley’s relationship with the Citation Style Language, so I thought I would pop up my thoughts on the blog too. Martin’s post below is the original message that I sent over to him. Hi Martin, thanks for getting in touch and asking about Mendeley’s relationship with CSL. There are basically three aspects of citation styling that I’d like to discuss, the first is about Mendeley’s involvement, the second is about the use of citation styling in the community, and amongst publishers, and the third is about how we identify things in academia, and how we format those identifiers. ... (more)

Tags: CSL, citations, Mendeley

14 Sep 2010

The Future of Knowledge Organisation on the Web, a one day conference.

September 14, 2010

I’m attending this event today, and I’m going to keep some notes as the day progresses. There are a couple of oddities about the event: No Coffee. That’s a bit of a pity No power outlets in the conference room. Not many conferences have that, but one would think that it is a no brainer, especially for any meeting about the web, and in particular linked data. To add to that, there also seems to be no public wifi. ... (more)

Tags: linked-data, SKOS, RDF, RDFa, pool-party, conference, London, Semantic Web, data.gov, postcode paper

13 Sep 2010

Slides from APS Talk, August, 2010

September 13, 2010

Back at the beginning of August I gave a talk at the American Phytopathological Society. It was a great opportunity to talk to some really interesting scientists. My talk slides are below. Unveiling the web, making the implicit explicit.View more documents from Ian Mulvany. ... (more)

Tags: talk, APS, science, crowd sourcing, YQL

07 Sep 2010

Connecting Scientific Resources, Slides

September 7, 2010

On Friday I hosted a session at Science Online London. Michael Habibi, Richard Wallis and Chris Taylor all gave great presentations. Michael’s presentation and Richards’s presentation are both online, and when the organisers post the other talks I’ll link to Chris’s presentation too. Michael, taking us through his talk Richard has a rapt audience Chris, getting passionate ... (more)

Tags: solo10, science online, slides

06 Sep 2010

science scraping with YQL

September 6, 2010

Last Saturday at Science Online London I gave a quick tutorial on YQL, and how it might be used to mash up scientific data sets. Below I list some of the sample queries that I was playing with. Before you get started with the console have a look through the documentation. I got a lot of milage out of the part about filters and joins. The blog post by Paul Hogan on using YQL for library maships was also very helpful. ... (more)

Tags: yql, science, scripting, hacking, cool, solo10

27 Aug 2010

Connecting Scientific Resources

August 27, 2010

I’m going to be hosting a session at science online London next weekend, I’m excited. I’ve been interested in the issues of connecting scientific data for a long time. In the last six months I’ve become particularly excited about the potential of web based tool like Yahoo Query Language. I was hoping to talk a little about that, but I’ve been lucky to get some amazing people to come and share their experiences about linking data, so I’m going to cede the floor to them. ... (more)

Tags: linked-data, science online, solo10

23 Aug 2010

Passing arguments in liquid templates.

August 23, 2010

I’ve recently moved my blog over to hosting on github using the Jekyll templating system. I was intrigued by the ability of Jekyll to create a listing for related posts, but in the end the quality was poor. There are two methods avilable, the more robust uses latent semantic indexing, but this is not supported by github. I can understand this, as the processing required is a bit too much of an overhead for a lightweight hosting service. ... (more)

Tags: ruby, liquid, templating

15 Aug 2010

Testing Code Hilighting

August 15, 2010

testing ruby def foo puts 'foo' end testing python for nice in this: print "how interesting" testing latex \[\sum_{n=1}^\infty\frac{1}{n} \text{ is divergent, but } \lim_{n \to\infty} \sum_{i=1}^n \frac{1}{i} -\lnn \text{exists.} \] ... (more)

Tags: test, hilighting

14 Jul 2010

Notes from JISC activity streams workshop

July 14, 2010

Dave Jennings giving the opening talk, http://www.slideshare.net/davidjennings abundance of content without structure is not to be feared, example comes from music. uses a Medneley slide to talk about the lastfm – Medneley bridge. talks about the amazon collaborative filter mentions how this can lead to a dystopia, Googlezon, the big brother of recommender system. talks about the future of pervasive recommender systems, and brain matching to content matching. john cage - my favourite music the music I haven’t heard yet. ... (more)

Tags: conference, JISC, report]

05 Jul 2010

Read mail in intervals on OS X

July 5, 2010

In order to check mail less frequently than the options available, following a hint from macosxhints: set up an applescript to tell mail to check for mail. put that script under a launchd deamon with an interval use lingon to setup the deamon so far it seems to be working, yay! http://www.macosxhints.com/article.php?story=20010427022452992 use ... (more)

Tags: email, productivity, mac

03 Jul 2010

my first post

July 3, 2010

I’m trying to understand jekyll here It seems to be quite nice, let’s see how we get on! ... (more)

Tags: test, git, jekyll

12 May 2010

hackney are fuckers.

May 12, 2010

http://www.whatdotheyknow.com/request/31711/response/79454/attach/html/3/1%202181984%2020100407%204th%20Tier%20List.xls.html fast food in hackney http://www.whatdotheyknow.com/request/27794/response/68154/attach/html/3/1%201952373%20Information%20Sheet.xls.html ... (more)

Tags: hackney, fuckers

04 May 2010

Edinburgh, first draft

May 4, 2010

I don't post my poetry often, indeed I don't write often, but I thought this one came out OK. Written over the past weekend for a good friend on the occasion of her birthday. Edinburgh, first draft, 01/05/2010 for andrea. Was it in Summer, when I lost myself among the graveyards? The moss covered steps of Greyfriars green and gleaming. Or was it someone's winter night along cobbled streets, where buildings wear a sharp puritan cut to their overcoats? ... (more)

Tags: poem

29 Apr 2010

A mini rant about LaTeX

April 29, 2010

Here is a comment I've just posted to a comment thread about LaTeX over here: http://blogs.nature.com/farhat/2010/04/16/collaborative-editing-with-latex. One of the commenters asked "Why not just use a word processor" Just using a word processor simply does not cut it when it comes to expressing complex mathematical ideas. LaTeX, and it's precursor TeX, have evolved to be the only tools that can currently express the richness of the ideas within advanced mathematics. ... (more)

Tags: latex

13 Apr 2010

creating a tumblog

April 13, 2010

After a few conversations with @zzgavin, I've come to the conclusion that there is a place for a tumblog in the toolkit of those who like to post content onto the web. There are often pieces of content that I want to call out, but don't have either the time or the interest to write a longer blog post about. For a while I thought that would be a ... (more)

Tags: tumblog

22 Mar 2010

The three ages of Elvis in potatoes!

March 22, 2010

potato_3stagesElvis 004 Originally uploaded by gioia_On Saturday we went to a party thrown by some friends of ours. It was kind of a delayed St. Patrick's day party, and everyone had to bring along a potato dressed up as a celebrity, or some such. We created our potato after the Father Ted episode "Competition Time", in which Ted, Dougal and Jack dress up as the three ages of Elvis. ... (more)

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17 Mar 2010

Kierkegaard, forgetting and existence

March 17, 2010

Reading though the excellent introduction to Kierkegaard's philosophy in the Guardian (http://www.guardian.co.uk/commentisfree/belief/2010/mar/15/kierkegaard-philosophy-existentialism), it is pointed out that one of the key underlying principles of his philosophy is that we have forgotten what it means to exist, and that the cause of this forgetting is the ever growing amount of knowledge in the world (a state of affairs that is now ever more apparent even than in his time).I am dubious about this claim. ... (more)

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19 Feb 2010

Python PEP for a graph API

February 19, 2010

I just stumbled across this http://wiki.python.org/moin/PythonGraphApi. I think it's great. The discussion has actually been going on since Aug 2004, so I don't know what the status of this PEP is. I would love to see something come out of it eventually.tags: graph, PEP, python ... (more)

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10 Feb 2010

Probabilistic language models, auto-correction tools and scientific discovery.

February 10, 2010

Probabilistic language models, auto-correction tools and scientific discovery. "Durgesh Kumar Dwivedi":http://network.nature.com/people/U56CB3E51/profile over on Nature Network just asked "Does anyone have any software or web address which corrects English grammar, preposition, edit and shortened the paragraphs?". This question brought to mind and idea that I had a few years ago. The idea is simple enough, use a large corpus of pre-vetted grammatically correct text as a training tool to compare sentences against. ... (more)

Tags: copy editing, probability, science, language models

08 Feb 2010

4 ways to set the heigth of your open social gadget

February 8, 2010

You have a couple of options for setting the height of your gadget. I'll run through four methods that seem to work. First two words of caution, if you are using the eclipse plugin to develop on, you won't see the second method described here working. I don't know why, but the code works in iGoogle, so it must be something to do with the eclipse OSDE env. The second word of warning is that the syntax hilighter I'm using on this post chokes on CDATA tags, so the CDATA tags in the code examples are wrong. ... (more)

Tags: opensocial-jquery, gadget, opensocial

04 Feb 2010

Banks and Credit Card companies are fuckers

February 4, 2010

Via Bruce Schneir's blog there is a link to a paper about a new security system that credit card companies are rolling out; a single sign on system. The paper is here: http://www.cl.cam.ac.uk/~rja14/Papers/fc10vbvsecurecode.pdf. The bottom line is that the system is pretty insecure, but it is incentivised by making the customer sign up to additional terms and conditions that puts more liability on them than on the banks or ... (more)

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04 Feb 2010

Cost benefit of publishing academic books,

February 4, 2010

Nature has just published an editorial (http://www.nature.com/nature/journal/v463/n7281/full/463588a.html) promoting the idea of writing text books (http://dx.doi.org/10.1038/463588a). Having worked for a number of years as a commissioning editor for a major academic publisher, responsible for more that 20% of academic book output, I have to say that the cost-benifit analysis for publishing books ends up saying that it just does not justify the effort for academics to write monographs. You probably won't see more ... (more)

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04 Feb 2010

Identity systems, science and the internet

February 4, 2010

I just posted the following on a forum (http://network.nature.com/groups/orcid/forum/topics/6547) on Nature Network, I thought it was interesting enough to repost:Bruce Schneier yesterday posted a very "interesting article":http://www.schneier.com/blog/archives/2010/02/anonymity_and_t_3.html that gets to the heart of identity systems on the web. The bottom line of the article is that anonymity will always be a given as the price for introducing verification or coining systems will always be too high, and even if present they won't be effective. ... (more)

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04 Feb 2010

What's the right amount to charge for phone content?

February 4, 2010

Having a discussion earlier today with one of my colleagues, we were discussing pricing models for iPhone applications. I buy a lot of apps on my iPhone, but the content that we were discussing pricing for is academic article content. This traditionally sells online for tens of dollars per unit. If one wants to sell such content on an iPhone, but at the same time retain the apparent value of the content how do you ... (more)

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02 Feb 2010

what makes a chocolate "cheeky"

February 2, 2010

I'm eating a chocolate bar which contains, I'm told, a 'cheeky caramel layer'. It's shit like this that makes me despair of our modern civilisation. According to the dictionary 'cheeky' means 'impudent; insolent', and it has the synonyms 'saucy, audacious, bold'. I guess that I am to feel that I have made a bold choice in opting for the opulence provided by that extra caramel, but I can't raise the ... (more)

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29 Jan 2010

opensocial development on eclipse, starting the web server

January 29, 2010

Unable to retrieve spec for http://localhost:8080/test/gadget.xml. HTTP error 404 ... (more)

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28 Jan 2010

quick thoughts on the iPad

January 28, 2010

I just commented over on the digatilist:I'm in two minds, but on balance I'm optimistic. What they are delivering is not a product, but a new platform, and one who's limitation has the potential to drive innovation in the open web. What I really don't like about what has been delivered is how closed the system is, and how much this is not a tool that a developer could use. ... (more)

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20 Jan 2010

Usage of graph layouts on Biostor

January 20, 2010

(co-author graph example) inspired by ... (more)

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04 Jan 2010

Climbing Goals 2010, review 2009.

January 4, 2010

Looking back at my goals for 2009, I've not done very well, however my current level of fitness is pretty good, so I think 2010 is going to be a good year. The main factors in holding back my climbing in 2009 were taking a few months off to get married and not being able to rent a car. Getting married was absolutely worth it, and the level of organisation and stability I have in my life now due to being married will only help in the long run. ... (more)

Tags: training, climbing, bouldering, goals

01 Dec 2009

dreaming of snow

December 1, 2009

DSC00458 Originally uploaded by Ian MulvanyI just got some great feedback on this picture from someone on flickr, it was taken back in February when I was on a skiing holiday in Switzerland. The house was built by my wife's grandfather, and we came to it, it buried in a drift, the air as sharp as the icicles. It was a magical week, and I'm keen to return. At this time of the year thoughts turn to such things. ... (more)

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01 Dec 2009

Keeping Dopplr and iCal in two way sync.

December 1, 2009

I don't know if the following is going to work, but I'm going to try it. Dopplr allows you to subscribe to your trips in iCal from a link from the trips page. You can also publish a calendar locally to the Dopplr servers that Dopplr will pull trips from. I've set up two calendars in my iCal, one for pushing into Dopplr, and another for pulling all Dopplr trips from. ... (more)

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20 Nov 2009

Strange anxiety dream

November 20, 2009

Last night I had a strange anxiety dream. I'm not usually prone to blogging this kind of thing, but it was pretty odd. I dreamt that I had been given command line access to a particle accelerator that was embedded in that antarctic ice sheet. I'd run some kind of a job and forgotten about it. Two weeks later I got a bill for £216, 000. I'm not sure if that was the bill for the data that was generated, or for ... (more)

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31 Oct 2009

Notes from the Google Wave London roadshow

October 31, 2009

Gtug blog post On Monday I was at the London Google wave roadshow presented by Lars and Stephanie. The previous Friday I had helped to run a hack day for science applications in wave, so with that experience fresh in my mind I was particularly interested to see what they would say about a few particular topics. We had a few problems in the hack day which could be summarised as follows: ... (more)

Tags: google, google-wave

19 Oct 2009

Django models vs. Pickling objects for object persistence.

October 19, 2009

I do a bit of code hacking and I often find myself putting objects into pickle files, and reading and writing them in order to fake object persistence. It's easy, but messy and it begins to leave lot's of pickle files sitting around in your path. I've decided to finally make the switch towards using a more grown up persistent object solution. I've decided to try out Django + SQLite. ... (more)

Tags: python, Django, SQLite

03 Oct 2009

An interesting invitation

October 3, 2009

Last week an interesting invitation popped up in my email box, I got a message from Richard Sterling asking if I would be interested in previewing the program that the government are rolling out as part of their open data project. They have set up a google group for developers, and I guess I'm on the waiting list, or something. I'm going to be interested to see what data sources surrounding science, ... (more)

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25 Aug 2009

Comparing Windmill to Safariwatir

August 25, 2009

the post seems to be missing :/ ... (more)

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17 Aug 2009

Cron, python and Google Wave

August 17, 2009

Documentation on getting a google wave robot written in python working with the Cron functionality is still a little sparse. Getting a cron job into the capabilities.xml file. Add the following directive to the main function of your python program: myRobot.RegisterCronJob('/path',60) When you look at you capabilities.xml file you should now see a new node in the file: ... (more)

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13 Aug 2009

Why I think the Drake equation is a crock of shit.

August 13, 2009

I had a brief discussion with a good friend and colleague this evening about the Drake equation. He has recently come to think that the equation can provide a good handle on understanding how many communicating civilizations exist in the universe, and how that reflects on the fragility of life on earth. A long time ago I had dismissed the Drake equation, feeling that it had very little to tell us about these matters. ... (more)

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29 Jul 2009

Swine flu t-shirts

July 29, 2009

I'm sitting at home in London with a head cold. For the dew minutes it took me to check my temperature (37 thank you very much) I was wondering whether it might be the old swine flu, but no, just a normal head cold.Made me think, someone should make a t-shirt with a biometric sensor that checks on true wearers' temperature. No fever and it would say "don't worry it's only a cold". ... (more)

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11 Jun 2009

Fluid Dynamics in the Browser

June 11, 2009

The Navier-Stokes equations: \frac{\partial \mathbf{v}}{\partial t} + ( \mathbf{v}\cdot\nabla ) \mathbf{v} = -\nabla p + \nu\Delta \mathbf{v} +\mathbf{f}(\boldsymbol{x},t) \frac{\partial \mathbf{v}}{\partial t} + ( \mathbf{v}\cdot\nabla ) \mathbf{v} = -\nabla p + \nu\Delta \mathbf{v} +\mathbf{f}(\boldsymbol{x},t) Describe the flow of an incompressible fluid. The equations are non-linear and are notoriously difficult to solve. I've always found them to be very beautiful and the fact that Sr George Stokes was an Irishman probably had some effect on my taking to the subject when I was an undergrad. ... (more)

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20 May 2009

unknown post

May 20, 2009

In February 2009 a mac security update broke my perl installation. You can read more about that on this Slashdot article (http://hivelogic.com/articles/view/top-10-programming-fonts) , ulimatly forcing me to reinstall my entire system. One of the main reasons for this is that I had a hevily customized perl setup as part of installing Connotea and I based this on top of the system perl. This was a bad idea, but was the quickest way to get Connotea up and running on my local machine at the time. ... (more)

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16 Apr 2009

Another great example of how being lazy can reap great rewards

April 16, 2009

Last year I got really obsessed with the idea of making my google email contacts list, my phone list and my desktop address book all sync together. I couldn't find a simple to use free application that would do all of this for me. For a while I was using Spanning Sync to keep calendars in sync. I had a Nokia N95, my desktop machine is a mac and my online life is mediated by Google. ... (more)

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14 Apr 2009

Neat blog on Sankey diagrams.

April 14, 2009

I just noticed a very nice blog dedicated to Sankey diagrams. As Phineas mentions in one post: Sankey diagrams are directed graphs. ... (more)

Tags: graphs, directed weighted graphs, sankey diagrams

14 Apr 2009

notes on "Classes of complex networks deﬁned by role-to-role connectivity proﬁles"

April 14, 2009

Looking for algorithms to do community detection (there are a bunch from the famous Girvan-Newman algorithm doi:10.1073/pnas.122653799 which seems to have gained popularity through being very simple, effiencet and usually pretty powerfull, through to a method doi:10.1103/PhysRevE.71.046117 by Ziv, Middendorf and Wiggins. I have to admit I don't understand that paper yet, but hope to come back to it.) I was pointed to a paper by Guimera, Sales-Pardo and Amaral. ... (more)

Tags: graphs, network science, modules, algorithm

14 Apr 2009

Why measure scientists and their work?

April 14, 2009

I'm interested in using graph theory to develop tools to improve science (whether I manage to do this is a moot point, I believe that someone will, and that such tools will be useful). One of the questions raised by any effort to introduce new systems that may be used to compare and contrast the work of scientists is whether such systems can have any net benefit when weighed against the potential pressure that they may place on working scientists. ... (more)

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13 Apr 2009

Directed Graph blog setup.

April 13, 2009

I've decided to use syntaxhiligher2 to do syntax hi-lighting and a call to Yourequations.com for rendering latex on the blog. Bot Cyborg has a good description of how to get this to work on blogger. The main advantage of this approach is that the pseudo code is written in the blog posts in plain encased in a pre statement, and the equations are also just vanilla latex in a pre statement. ... (more)

Tags: latex, centrality, blog, equation

13 Apr 2009

Grave of the reverend Thomas Bayes

April 13, 2009

I visited bunhill fields at the weekend. It's a non conformist graveyard just off of moorgate in London. Over the course of it's active life over 120,000 people were buried there, in a space a little under four acres. Notable residents include Daniel Defoe and William Blake, but the occupant I was most intrigued to see was Thomas Bayes, the founder of Bayseian statistics. The large tomb contains thebesmains of many members of the Bayes family. ... (more)

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13 Apr 2009

Moving over to the googleverse

April 13, 2009

Well, today I finally made a switch that I had been thinking about for a long time, I moved the hosting of my personal domain to google app engine with email being managed by google apps for my domain. http://www.mulvany.net is now a google app engine site. At the moment there is not much content there, but the google app engine tool allows me to run a perfect cop of my site off line, and to edit locally and then push live. ... (more)

Tags: blog, mulvany.net, google, google app engine

13 Apr 2009

Why I'm setting up this blog

April 13, 2009

Right, well, I'm pretty interested in graph theory. I work in publishing for the journal Nature on new web products, and I need a focussed way of getting my thoughts together on a range of topics that touch on science. I wanted a space that was more focussed than my personal blog. I have a few specific aims for this blog. Get some of my thoughts on publishing, science and the philosophy of science out of my head and into an archived public space ... (more)

Tags: goals, disclaimer

12 Apr 2009

Adding a tag cloud to blogger

April 12, 2009

I've been thinking about neat ways to make blogs approach research articles; about how to make some of the core features of a journal be more apparent in a blog, which has led me to think about blogger widgets. That led me to the Phydeaux3 blog where there is a kick ass implementation of a widget to display a tag cloud for blogger. Hopefully you can see that it works pretty well. ... (more)

Tags: tags, blogger, tag cloud, widget

12 Apr 2009

Getting listed on nature blogs

April 12, 2009

I'm gittin meself listed on nature blogs. I better whup this blog back into shape first though. ... (more)

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12 Apr 2009

testing latex and syntax hilighting on blogger

April 12, 2009

Some python code some links http://www.ramymostafa.com/?p=99 http://alexgorbatchev.com/wiki/SyntaxHighlighter http://www.botcyb.org/2008/10/rendering-latex-in-blogger.html http://blog.yourequations.com/ Syntaxhiligher2 (unreliable) def AuthenticateSession(username,password): blogger_service = service.GDataService(username,password) blogger_service.source = 'mulvanynet-BloggerTagger-1.0' blogger_service.service = 'blogger' blogger_service.server = 'www.blogger.com' blogger_service.ProgrammaticLogin() return blogger_service def PrintUserBlogInfo(blogger_service): query = service.Query() query.feed = '/feeds/default/blogs' feed = blogger_service.Get(query.ToUri()) blog_id = feed.entry[0].GetSelfLink().href.split("/")[-1] print feed.title.text print blog_id for entry in feed.entry: print "\t" + entry.title.text, print entry.GetSelfLink().href.split("/")[-1] def GetBlogFeed(blogger_service): query = service.Query() query.feed = "/feeds/default/blogs" feed = blogger_service.Get(query.ToUri()) return feed ... (more)

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10 Mar 2009

I woke up today and git-svn was broken.

March 10, 2009

Odd, it was working last time I used it. Today I got the following error git svn IO object version 1.22 does not match bootstrap parameter 1.23 at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XSLoader.pm line 94. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/IO/Handle.pm line 263. BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/IO/Handle.pm line 263. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/IO/Seekable.pm line 101. BEGIN failed--compilation aborted at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/IO/Seekable.pm line 101. Compilation failed in require at /System/Library/Perl/5.8.8/darwin-thread-multi-2level/IO/File.pm line 133. ... (more)

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09 Mar 2009

Rail in the UK is really pretty shitty

March 9, 2009

Last month I bought some rail tickets online, and got to London Bridge only to be told that I had to go to Liverpool Street in order to print out the tickets. Five minutes before my train was due to depart. I had to buy a new set of tickets for that days journey, and get up extra early the next day to make it to Liverpool street to print out my tickets. ... (more)

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02 Mar 2009

Five places to eat in New York, mmmmm

March 2, 2009

Five places to eat in New York, I used to live in New York a good few years ago, and now when friends ofmine are about to go there they sometimes ask me about what to do there. Ikeep trying to think of great places to go in the city, so here is a shortlist of five of my favorite places to eat in New York. Not fancy, notexhaustive, just five places that I remember fondly now that I look back onmy time there. ... (more)

Tags: New York, flickr, restaurant

02 Mar 2009

other tips for new york

March 2, 2009

Also Mona's bar on 13th and b (a bit of a dive, but all the better for it) The east village/alphabet street areas have great bars, there used to be one called the drugstore. Best Bagel: H&H on 75thish and broadway Ah, sure, it's not a bad wee city. Oh, the museums, they are pretty good too. The Metropolitan (it's free) The Frick Collection - Guggenheim (depending what's on) ... (more)

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18 Feb 2009

Not a smart way to do this.

February 18, 2009

I wanted to find out what all of the ... (more)

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18 Feb 2009

Training Diary Catchup

February 18, 2009

OK, so, I've fallen off the wagon in terms of climbing training, or in fact training of any kind. Last weekend was interesting. I did the introductory PADI course, but the week leading up to the weekend was swamped with work, and all of the nights of this week have filled up too. I think in order to get my running done I am going to have to transition to a morning run a few times a week. ... (more)

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18 Feb 2009

unknown post

February 18, 2009

I want to find out what all of the ISSN's are for the publications that are printed by Nature Publishing Group. They list all of their publications on the following page http://www.nature.com/siteindex/index.html. awk '{print "curl http://www.nature.com"$1"index.html | grep ISSN"}' nature-journal-links.txt ... (more)

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13 Feb 2009

Wrangling data from a mysql db

February 13, 2009

I am working on a project where I have to pass some data from tables in a MySQL DB over to some people who don't use a relational database. The question is, how I can best extract the data in a way that is useable to them? I've decided to prepare the data for them as XML, as this prevents problems with My approach uses a hacked together collection of scripts, because, well, as Mark Pilgrim says, because fuck you. ... (more)

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10 Feb 2009

Training diary, week 5

February 10, 2009

Saturday 1st SnowboardingFriday 7th Bouldering at the castleOK, I'm a bit late posting this training update. Last week was the snowy week in London, and I was lazy, boo me, however after not climbing for two weeks and given the very poor training week I was uncertain how things would go, which is to say I thought I would not be very good, however my expectations were unfounded and I had a ... (more)

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09 Feb 2009

Converting a mysql schmea into an entity relationship diagram

February 9, 2009

You will need to install XML support as a ScriptingAddition for script editor. You can get this from http://www.latenightsw.com/freeware/XMLTools2/. Quit and restart script editor after you have installed the extension. I found that when I was trying to compile the code script editor gave me a syntax error before I installed the extension. The syntax error dissapeard after I installed the extension, but the extensions themselves didn't work until I restarted script editor. ... (more)

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07 Feb 2009

Even Santa goes to see the rugby

February 7, 2009

... (more)

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02 Feb 2009

weekly training log, week 4

February 2, 2009

A week snowboarding in Switzerland, 6 days total with a rest day on the Wed. Pretty fantastic!I didn't get any running done, and looking at the current weather in London, it is looking like I won't get any running done this week either.My training summary for January 2009 then is as follows:Number of exercise sessions = 18 Number of days with exercise = 17 (54%) Total distance = 49 km ... (more)

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02 Feb 2009

Weekly training report, week 3

February 2, 2009

Saturday 17thMile end, decided to try power endurance training, picked a 6a to work on. 7 leads, and at the end I was still finding it really easy, which means it was too easy. 6a+ next time. I had a 4 1/2 min rest between leads. Also did some nice bouldering.Sunday 18th ran 12.2 km 80.5 min did this one http://www.gmap-pedometer.com/?r=2498524Monday 19th did some chin ups as a warm up and then 3 sets of semi-dead hangs, lasted ... (more)

Tags: climbing

21 Jan 2009

Code Higlighting in Blogger

January 21, 2009

pbl-ian:python-c root# clear pbl-ian:python-c root# swig -o erf_wrap.c -python erf.i pbl-ian:python-c root# gcc -o erf_wrap.os -c -fPIC -I/usr/include/python2.5 erf_wrap.c pbl-ian:python-c root# ls erf.i erf.py erf_wrap.c erf_wrap.os pbl-ian:python-c root# gcc -c erf_wrap.c -I/usr/include/python2.5 -I/usr/lib/python2.5 pbl-ian:python-c root# ls erf.i erf.py erf_wrap.c erf_wrap.o erf_wrap.os pbl-ian:python-c root# python Python 2.5.1 (r251:54863, Apr 15 2008, 22:57:26) [GCC 4.0.1 (Apple Inc. build 5465)] on darwin Type "help", "copyright", "credits" or "license" for more information. from erf import erf ... (more)

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21 Jan 2009

unknown post

January 21, 2009

///gi,'\n')); elements[i].replaceChild(newNode, childNode); } else if(elements[i].nodeName.toUpperCase() == "PRE") { brs = elements[i].getElementsByTagName("br"); for(var j = 0, brLength = brs.length; j ... (more)

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21 Jan 2009

wrapping c code for python using swig on Mac OS X

January 21, 2009

from john d cook http://www.johndcook.com/blog/2009/01/20/using-swig-to-expose-c-code-to-python/ from http://www.penzilla.net/tutorials/python/swig/ and combining the two I came up with a way to get this to work on Mac OS X bash$ cat erf.i %module erf #include double erf(double); bash$ swig -o erf_wrap.c -python erf.i bash$ gcc -o erf_wrap.os -c -fPIC -I/usr/include/python2.4 erf_wrap.c bash$ gcc -o _erf.so -shared erf_wrap.os bash$ python from erf import erf erf(1) 0.84270079294971489 ... (more)

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17 Jan 2009

Weekly training report, week 2

January 17, 2009

Friday 9th 2 hours at the castle, top roping with 5kg extra for Sunday 11th 57 min 8.75 km http://www.gmap-pedometer.com/?r=2483095Went bouldering at the Castle, it was good, nothing too heavy, just tried to do laps on a few nice problems to get tired. Monday 12th Westway, lead climbing. Decided to try some stamina sets, kind of. At least I timed how long it took to do the routes. 6a+ 3 min bang on. ... (more)

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14 Jan 2009

Is RSS dead, and why is it dying?

January 14, 2009

From Science of the invisible I picked up the link to the Read Write Web article on death of enterprise RSS. What is going on here? I'm working in the enterprise and I use RSS a hell of a lot. After trying a number of different strategies I now use Google reader, because it has the fastest way for me to get rid of content in the feeds. Why does the enterprise not get it? ... (more)

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12 Jan 2009

Nasty week ahead

January 12, 2009

... (more)

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09 Jan 2009

World War II, Science and Springer Authors

January 9, 2009

Springer have just launched a web app that lets you search for locations of authors, AuthorMapper. They have done this by building an XML database with the citation metadata for all of their papers. You search for terms or authors and it will generate a google map with the locations for your search terms, or people. The site also has some other infoporn, including a histogram for authors published by year for your search term. ... (more)

Tags: author mapper, war, springer, science

08 Jan 2009

Wekly training report, week 1.

January 8, 2009

Sunday 4th of January 8 km run, in 53 min, average heart rate about 149 bpm. http://www.gmap-pedometer.com/?r=2468786Monday 5th of January. Did a mini endurance set on my fingerboard. I've decided to do a 4 week set of power endurance training, with a view to improving my sport grade, just 4 weeks and then I'll switch to finger strength for four weeks. This bascially hurts and sucks, but hey, that's what you gotta do. ... (more)

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23 Dec 2008

Review of Climbing Goals for 2008.

December 23, 2008

Back in January I set myself some goals for my climbing in 2008. The results at the end of the year were mixed, which means that I succeeded with some of my goals and patently failed with others. The was: * Onsight Grit E2 * Redpoint f6c+ * 10 weekende+ trips in UK * 5 red problems in a day in font * 80 kg weight * build climbing wall ... (more)

Tags: goals, climbing, training

21 Dec 2008

a great presentation about books and community

December 21, 2008

My colleague Gavin Bell just uploaded a great presentation about creating communities of readers out of readers of books. You can see his presentation <a href="http://www.slideshare.net/gavin/gavin-bell-from-readers-of-books-to-a-community-of-readers-oreilly-toc08/">here on slideshare</a>. He gave this talk at the Tools Of Change conference in New York earlier this month. Read and post comments | Send to a friend ... (more)

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21 Dec 2008

A minor milestone in leisurely reading

December 21, 2008

Last night I finally finished Neil Stephenson's Quicksilver. Oh, don't get me wrong, I've read it, and the full trilogy, before, but for much of the past year I have been re-reading it aloud to my girlfriend. She has an eye strain which means that if she reads too much at night she gets headaches, and so I've been doing the recreational reading for the two of us over the past year. ... (more)

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21 Dec 2008

blogging darwin

December 21, 2008

One of my friends is writing a series of blogs about Darwin. It looks like a very nice series of blog posts, and I look forward to the rest. You can read it here. Of course as a physicist I disagree with one comment in this first post: "From an intellectual point of view, the Origin is the most significant work of the millennium, and the most important work of non-fiction ever. ... (more)

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21 Dec 2008

bus podcast idea

December 21, 2008

I had a great idea yesterday while I was engaged on a personal odyssey on London buses. I was on the top deck of, I think it was the 176, heading down past Old Street into the square mile, round St Paul's (with a quick glimpse of millennium bridge, and then on into the strand. The bus went past so many statues, churches and historical buildings, but I knew only a few of them. ... (more)

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21 Dec 2008

chasing cars

December 21, 2008

This morning as I was leaving Shoreditch park a guy in a black masarti with the top down passed my on my bike. I continued along the canal as usual and as I came past sainsbury's in islington saw the same guy in the same car, as I passed him! Bike 1, Masarati + London Traffic 0. Read and post comments | Send to a friend ... (more)

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21 Dec 2008

climbing milestone

December 21, 2008

Last night I got my first UK 6a boulder problem at the Castle climbing wall, it's been a while since I was making progress with my climbing, so that was great.My climbing diary is here: http://jottit.com/h94hx/ Read and post comments | Send to a friend ... (more)

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21 Dec 2008

Cloverfield

December 21, 2008

Cloverfield Originally uploaded by Ian Mulvany My Work Colleague make a cloverfield diarama in our sandbox today. We will be going into full scale production soon. Read and post comments | Send to a friend ... (more)

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21 Dec 2008

collaborative intelligence and the pidgeonhole problem

December 21, 2008

O'Reilly are hosting a Collaborative Intelligence foo camp this coming weekend. There is some discussion bubbling out already on crowdvine at a group that has been created for this meeting. One of the participants, Greg Linden, says the following: "Hi, Cass. Absolutely, this is called the pigeonhole problem and can be an issue if personalization is done poorly. Done right, personalization enhances discover by helping you find things you ... (more)

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21 Dec 2008

Creationism as Science,

December 21, 2008

I'm at the netsci08 conference and there is a really delightful talk about the network of papers published in the creationisim/evolution debate. The group looked at key people in the ID debate and people who acted as strong defenders of evolution. One can then make a graph of the links between the groups and intra-groups based on citation and co-citation. Now one area of social science that is pretty interesting in this debate ... (more)

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21 Dec 2008

digital archeology, finding traces in the bits

December 21, 2008

This article in Guardian today is describing a method of restoring colour to some original BBC tv shows whose master tapes were wiped in a purge of the BBC archives. The shows were originally made in colour, then the master tapes were destroyed to make more room in the BBC archive, however black and white copies were made for distribution to countries which didn't have colour TV capability. The black and white versions were on a smaller format (16 mm) ... (more)

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21 Dec 2008

drowning in the streamosphere

December 21, 2008

I've been thinking about the streamosphere (as coined by Euan Adie), and how I am starting to get dragged down in it again. I'm getting daily notifications from pounce, twitter, friendfeed, linked in (I've been ignoring facebook for ages, facebook, you bite my ass). What I really need is a way to manage my notifications and communications in the way that I now manage my rss feeds, through a bespoke piece of ... (more)

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21 Dec 2008

Efficient Name Disambiguation for Large-Scale Databases

December 21, 2008

I've been interested for a while now in entity disambiguation, particularly where the e ntities are the names of authors in academic journals. Jian Huang, Seyda Ertekin and C Lee Giles have a paper from 2006 in which they describe the method that they used to diambiguate the CiteSeer data set of over 700,000 article s. The paper is "Efficient Name Disambiguation for Large-Scale Databases". They were able to use this algorithim to disambiguate this data set ... (more)

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21 Dec 2008

further confustion

December 21, 2008

So, after a little more investigation it is clear that earlier links are broken and new links have the snap preview. Well, I guess I am just going to have to write links as plain text until they get this thing sorted out. tags: vox sucks Read and post comments | Send to a friend ... (more)

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21 Dec 2008

getting married and buying an iPhone are probably incompatible.

December 21, 2008

Having just gotten engaged and begun to look at the relative costs involved in organising a wedding I woke up this morning with the unavoidable realisation that the need to save for the wedding is going to make purchasing an iPhone, while I have a perfectly normal n95 that works rather well (especially since the broken key unstuck and started working again) untenable. My cunning plan had been ... (more)

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21 Dec 2008

How I learned to stop worrying and love RSS

December 21, 2008

I am, one might say, a bit of an RSS junkie. It has been the main source of news and information for me for about the last year or so, but I began to feel as if I was drowning in it. I subscribe to something over 80 feeds, some of which, like techcrunch, spit out over 40 or 50 items a day. A few days away from my feed reader and there could be well over 1000 entries ... (more)

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21 Dec 2008

how to learn python

December 21, 2008

In response to a query that popped up on Friend Feed: I taught myself years ago with O'Reilly's Learning Python. The web book 'Dive into Python' is essential, and the blog posts on respectively 'How to Code like a Pythonista' and 'How to think like a Pythonista' will get you a long way towards familiarizing yourself with common idoms in the language. Read and post comments | Send to a friend ... (more)

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21 Dec 2008

I didn't expect lock in so quickly

December 21, 2008

I've just signed up for an account with twidox, which is a start up that is collecting shared documents of interest to scientists, I believe. They are in the private beta stage, but had a link on their homepage for requesting an account. I got the following message when I hit the verification link: Registration is taking place! Many thanks for you interest in twidox. Your account has been activated. ... (more)

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21 Dec 2008

ikea is like a biological machine

December 21, 2008

We are just unpacking some more furniture and we have discovered that the spacers inside the boxes were made up of cut up pieces of IKEA furniture, probably items that had been returned. It reminded my of the cells ability to recycle old components. Read and post comments | Send to a friend ... (more)

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21 Dec 2008

incentives

December 21, 2008

So after reading about some economists who decided to use economic theory to loose weight I have decided to follow suit. They both decided to loose a certain amount of weight by a certain time and places $5000 in a bond. Whoever didn't make the weight lost their portion of the money to the other person. The idea was to affect behavior through an incentive that was significant. Well, I'm not a well paid economist, but I have decided to ... (more)

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21 Dec 2008

iPhone prediction market

December 21, 2008

Well, a prediction about a new market that will spring up (perhaps it already has) around the iPhone. So it costs $99 dollars to get an app that you have built onto the phone through the App Store. If I design a vanity app I'm not going to want to pay that much, but I might pay 5, 10 or even 15 dollars to see the child of my creativity bouncing around on the little ... (more)

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21 Dec 2008

Max OS X does not have gethrtime and as a result cannot load Time::HR

December 21, 2008

I just discovered this after poking around for an inordinate amount of time. The trick is to use Time::HiRes instead. Now someone should write a bridge function that overloads the Time::HR functions with Time::HiRes functions which would make a code change as easy as loading the overload module. Read and post comments | Send to a friend ... (more)

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21 Dec 2008

mozy backup service

December 21, 2008

I've been trying the free account this week. I've backed up 1.6 GB of data. It took, with given interruptions of a normal work day, about 4 days to backup this amount of Data. I am beginning to think that the world of offline remote backups is still a little bit away! Read and post comments | Send to a friend ... (more)

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21 Dec 2008

netsci08 blogging

December 21, 2008

I'm in Norwich all this week attending Netsci08 http://www.ifr.ac.uk/netsci08/, the internatinal workshop and conference on network science. It's a week long event, and broadly speaking it looks like there are three types themes that are being discussed here: biological networks, pure networks science and community detection in networks, principlaly emergent networks of the kind we see in the internet. I'm twittering about the meeting using the tag #netsci08, but it seems ... (more)

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21 Dec 2008

netsci08 opening keynote

December 21, 2008

Nicholas Christakis, Harvard, "eat drink and be merry, the spread of health phenomena in social networks". This talk is looking at the spread of desies throgh social interactions, rather than other types of interactins. The main study was looking at obesity using the Framingham Heart Study Social Network. This seems like a very famouse social network health related study, so I'm not going to go into detail about that, but the bottom line is that they were able to ... (more)

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21 Dec 2008

network branching, netsci08

December 21, 2008

I'm really torn by the number of great talks on today. There are three parallel sessions, and for each time slot I want to be in at least two places at once. I'm going to try to pick out talks that have some relation to online social networks, community detection and scientific networks, but some of the talks on the theory of clustering are conflicting directly with some use cases of looking at some online ... (more)

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21 Dec 2008

Networks in Space, Mark Newman, netsci08

December 21, 2008

Mark Newman, Networks in Space, This is about networks in geographic space. Mark is looking at properties of networks that are tied to geography. Transport networks are a good example, and we are looking at the difference between road and air networks. The road and air networks are very different, even though you use both of them for getting from A to B. There is different bahviour, could I say 'driving' the use of these ... (more)

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21 Dec 2008

networks; head to head

December 21, 2008

The second talk in the evening CREEN parallel session is from J. Holyst about phase transitions in coupled complex networks where the network properties are different in the two groups. In one group there are a smaller number of members, but they are tightly coupled. The second group is larger, but less tightly coupled. The model uses an Ising model. The less coupled group has higher fluctuation in ... (more)

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21 Dec 2008

nice idea for improving the six nations rugby tournament

December 21, 2008

Shaun Edwards <a href="http://blogs.guardian.co.uk/sport/2008/02/22/bonus_is_the_carrot_that_leads.html">writes</a> in The Guardian today that introducing the bonus points system to the Six Nations rugby tournament could help make it more entertaining (not that it needs much help in that regard, as it is a fantastic tournament as it is). I wholeheartedly agree. At the moment you get 2 points if you win a game, and 1 point if you draw. Under the bonus system you get an extra point if you score 4 tries and you get a bonus point if you are a losing team and you hold you opposition to a gap of 7 points or less. ... (more)

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21 Dec 2008

perl and again,

December 21, 2008

Ever since Ian Clarke mentioned the potential delights of python to me whilst passing me in a corridor back in 1999 I've been tinkering around with that language. Christ, that's almost 10 years. I like python, it gave a great sense of freedom after spending a heavy five years working with various flavours of FORTRAN, from FORTRAN 90, through to High Performance Fortran. Well, now here I am ... (more)

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21 Dec 2008

Predictably Irrational

December 21, 2008

I was in, of all places, Godalming, at the weekend and ended up browsing in a book store for a few moments. I saw what looked like a very interesting book, href="http://www.amazon.co.uk/Predictably-Irrational-Hidden-Forces-Decisions/dp/0007256523/ref=sr_1_1?ie=UTF8&s=books&qid=1211186399&sr=8-1">Predictably Irrational. The book looks at the processes behind bad or irrational decisions. The author is an economist and it seems the aim of the book is to help us to see the emotional effects that influence ... (more)

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21 Dec 2008

progress

December 21, 2008

If you are interested in the progress of my bet you can follow here: hmm, my embedded image is not showing up here, shame, well, the link is here: http://www.bellygraph.com/graph/view/300 Read and post comments | Send to a friend ... (more)

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21 Dec 2008

question of the day, evil vice presidents

December 21, 2008

So the question of the day is if Hillary Clinton becomes Vice-President, would she be more or less evil than Dick Cheney? Now Dick Cheney is evil Inc. but the guy has never really pretended to be anything that he isn't, whereas Hillary would obviously lie and make policy in any way possible to win votes, which means that though she might not be as intrinsically as evil as Dick Cheney, she ... (more)

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21 Dec 2008

sadly I've just discovered that vox sucks

December 21, 2008

I have been liking using vox to blog, mainly because I can email a blog post from any email client. This significantly reduces the effort involved in posting a blog post. I've just discovered that vox has enabled snap previews. I don't like them. OK, so, some people may like them, and that's OK, but I can't turn them off on my blog. That's not good. In addition, when I email a link the link is now broken in vox, so if I type ... (more)

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21 Dec 2008

scribed is cool, but

December 21, 2008

Scribd has rolled out a very nice interface to pdf documents. It is neat and slick, but I think what it is missing is support for getting at data or meta-data in the document. It would be a great boon to be able to click on a table in a document and have that tabular data open either in excel or in some online document tool. Likewise for entities in the document that might have associated metadata. ... (more)

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21 Dec 2008

social networks

December 21, 2008

There is a tension between the providers of social software, and the way we behave. When I move from one city to another my social network changes as that's very location dependent, but when I do have that network set up for the most part, I don't expect restrictions on where I can go in that city with my friends. For sure, some friends of mine might not be caught dead in the palace bar, they only drink in the ... (more)

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21 Dec 2008

Soft peer review

December 21, 2008

The following paper "Soft peer review: Social software and distributed scientific evaluation" was passed along to me by alf today. I think another copy has been haunting my file system for a few days, but this seemed like a good reason to sit down again with it. It's by Dario Taraborelli and the abstract is as follows: Abstract: The debate on the prospects of peer-review in the Internet age and the ... (more)

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21 Dec 2008

star wars

December 21, 2008

"The modified tactical standard missile 3 (SM-3) hit the satellite at an altitude of 150 miles (247km) while it was travelling at approximately 17,000 miles per hour." I find this somewhat scary. Read and post comments | Send to a friend ... (more)

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21 Dec 2008

subprime mortgage crises explained using stick figures

December 21, 2008

http://docs.google.com/Present?docid=dtfm9hj_30ccsw79f4 http://docs.google.com/Present?docid=dtfm9hj_30ccsw79f4 This is funny, and a little bit scary too. Read and post comments | Send to a friend ... (more)

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21 Dec 2008

test a link

December 21, 2008

test a link guardian Read and post comments | Send to a friend ... (more)

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21 Dec 2008

Testing out a new blog platform

December 21, 2008

So, I've been having some problems with the Vox service for some time, and now I have a twine invitation, so I am going to test out Twine as a platform for blogging. The way I blog is that I tend to write up my blog posts in a mail client and then mail these to the blog engine, but so far Vox as a service has been soso. ... (more)

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21 Dec 2008

The gap between Open Access and Editorial Quality

December 21, 2008

I'm reading a great article by Joe Esposito on Open Access. You can read the article here:http://quod.lib.umich.edu/cgi/t/text/text-idx?c=jep;cc=jep;rgn=main;view=text;idno=3336451.0011.203. The article's main claim is that attention is the barrier to disemination rather than access. Another claim of this article is that paid for publishing platforms are good for readers in that they act as an attention filter. One of the main claims of the article is that Open Content in a sea of ... (more)

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21 Dec 2008

Ubigraph

December 21, 2008

Ubigraph (http://ubietylab.net/ubigraph/) Ubigraph (sorry for the fucked up formatting, I think my blog host vox is still being shitty at recognising simple html formatting in input, mixed with line breaks, it's just a frickin url link for god's sake) is a nicely implemented engine for making 3-D graphs and plots. I installed it and got the default python interface up and running in about 5 minutes. My initial reaction was "this is cool". ... (more)

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21 Dec 2008

Upcoming.org Founder Creates Fireball (Fire Eagle + DodgeBall + Twitter)

December 21, 2008

Ahh, convergence, ahh, the ability to pinpoint your friends on your mobile phone. I've been waiting for this to happen. Sent to you by Ian Mulvany via Google Reader: Upcoming.org Founder Creates Fireball (Fire Eagle + DodgeBall + Twitter) via TechCrunch by Erick Schonfeld on 4/22/08 Remember DodgeBall, the early social mobile network that languished after Google bought it? So does Leonard Lin, a founding member of Upcoming.org who recently left Yahoo, where he organized Hack Days. ... (more)

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21 Dec 2008

We have been nominated for a webby

December 21, 2008

Nature, the company I work for, has been nominated for a Webby, woot!. OK, so we are up against Nasa's earth observatory, and some other great sites in the science field, but it's really nice to get a nod and see that some other people out there like the kind of work that we are doing. If you want to go and vote you can at this link herehttp://pv. ... (more)

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21 Dec 2008

what apps do I want on the iPhone?

December 21, 2008

Well, I just read through the engadget report on the iPhone SDK and it's looking pretty good. I'm in the middle of downloading the free SDK, mainly so that I can have a virtual iPhone to play around with, but last night I got to thinking about what kind of applications I personally would like to see on the device. I live in London, but I frequently travel to Europe. ... (more)

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21 Dec 2008

Why the LHC is not really that impressive

December 21, 2008

Yesterday the Guardian had a special pull out section dedicated to the LHC. If you browse through the articles you find lots of comments along the lines of "temple to mystery and imagination", "a journey to the edge of understanding". "a modern cathedral to our relationship with the universe", and so on. From the superlatives that are being written one would think that the LHC is the best thing to happen to enlightenment ... (more)

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21 Dec 2008

Your Brightkite Invite

December 21, 2008

I just got the following Yay! "Hi, Somebody has sent you a Brightkite invite. Brightkite is a location-based social network, currently in private beta. Personal message: The wait is over! Here's your Brightkite beta invite. Enjoy!" Then on sign up discovered that it is only supported by a number of US carriers, boo. Read and post comments | Send to a friend ... (more)

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14 Jul 2008

agile programming

July 14, 2008

I work for a department where we try to do agile development. I liked thisDilbertabout the subject. ... (more)

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14 Jul 2008

An idea for an interface for picture search

July 14, 2008

A few weeks ago I was a beer festival in Munich, and I was talking tosomeone who was working on something, hey it was a beer festival, but then Ihad an idea about the type of interface that might be really useful fordoing search. We now search for images using text, so somewhere someone hasto build the text to image representation of the images in their database.Arguably this is one area where tagging has made an enormous improvement,ala flickr, but it seems to me that if you could make an interface thatwould allow a user to either draw or assemble a rough draft of the imagethey were searching for then this might offer a powerful and complimentaryapproach. ... (more)

Tags: cool, munich, image, flickr, tech, search, picture, presentation, talk

14 Jul 2008

and while we are at it here are the references from that article

July 14, 2008

References - "Python Objects", Fredrik Lundh, http://www.effbot.org/zone/python-objects.htm - "How to think like a Pythonista", Mark Hammond, http://python.net/crew/mwh/hacks/objectthink.html - "Python main() functions", Guido van Rossum, http://www.artima.com/weblogs/viewpost.jsp?thread=4829 - "Python Idioms and Efficiency", http://jaynes.colorado.edu/PythonIdioms.html - "Python track: python idioms", http://www.cs.caltech.edu/courses/cs11/material/python/misc/python_idioms.html - "Be Pythonic", Shalabh Chaturvedi, http://shalabh.infogami.com/Be_Pythonic2 - "Python Is Not Java", Phillip J. Eby, http://dirtsimple.org/2004/12/python-is-not-java.html - "What is Pythonic?", Martijn Faassen, http://faassen.n--tree.net/blog/view/weblog/2005/08/06/0 - "Sorting Mini-HOWTO", Andrew Dalke, http://wiki.python.org/moin/HowTo/Sorting - "Python Idioms", http://www. ... (more)

Tags: blog, python, web

14 Jul 2008

Are Academics Prostitutes

July 14, 2008

A blog post from AcademicProductivity trundled across my reader this morning in which the blogpoints to a paper in which the author claims that academicsare prostitutes because they modify their papers in response to thedemands of reviewers. I got a sense frisson when I read the blog post andsome of the text that is quoted there from the paper, but then I read thecomments to the blog post, and they are very good at, if you like, pointingout that the paper is a bit weak in it's premise. ... (more)

Tags: blog

14 Jul 2008

BarCamp Cambridge - James Smith talking about Ensemble, head of the internet team for Ensemble

July 14, 2008

Ensemble came out of the human genome project about 8 years ago to preventcommercialization of genomic data. the idea was to have an open source human genome companies would have to do some work before they could make money off ofsequences. the ensemble projects takes the raw data from the genes and adds other datato this, such as reference data from other experiments there is enemble codeand there is the data ... (more)

Tags: cambridge, barcamp, mac, perl, web, rss, talk

14 Jul 2008

BarCamp Cambridge - James talking about HTML5

July 14, 2008

James is just an interested bysander on the HTML 5 mailing list, hey, it's abarcamp html5 is th enew verison of html applemozillaoperaanyone who joins the mailing list and w3c (which means MS, which means this is going to work in IE) if you have ideas, then you can joing hte mailing list and put ideasforwards for the specification why should we? lots of information is locked up in HTML, not XML, not SVGL ... (more)

Tags: cambridge, python, barcamp, web, talk

14 Jul 2008

BarCamp Cambridge - teacking computers to understand text, Peter Corbett

July 14, 2008

a desk at the computer lab and at the chemistry lab. computationl lingustic chemistryauto-detect language in chemistry papers to try to recognics chemical andmarkup. suppliment the mark-up from publishers. can draw the chemical and annotating them overlayed over the paper some problems are that there can be new names in papers,comapct names, include extra hyphens, this program can deal with these kindsof things. also can use systematics parsing. ... (more)

Tags: cambridge, network, barcamp, science

14 Jul 2008

BarCamp Cambridge Jeff Fates, Drupal

July 14, 2008

OS CMS systems beat the crap out of the free ones for what you get for your money, including support. If you have a budget then you can get in touch with the authors of the OS systems easily the only thing they sometimes don't win on is polish it is someone's job to look at each piece and make sure that it is slick Drupal is free, It upgrades about twice a year, one major one minor ... (more)

Tags: cambridge, blog, barcamp

14 Jul 2008

BarCamp Cambridge, ARM microcontroler

July 14, 2008

ARM microcontroler dev guy. hard to use these processors, whanted to make something like this availableto normal peoplewant internet bluetooth connected devices so they built something he just plugged in a microcontoler with a wireless sensorhis machine things that it's a flash drive he dregged over a binarythe device started blinking, this is the hello world of hardware hacking,cool what can you do now? well cool stuff obviously! ... (more)

Tags: cool, cambridge, barcamp, mac, web, talk

14 Jul 2008

BarCamp Cambridge, Tom Morris, Semantic Web for hackers

July 14, 2008

what's cool about microformats web? is it the stickers?the t-shirtsthe community process urlb.at/2f personal information disastertravel airlines don't talk to railroads microformats say, what problem does it solve? perhaps there is no problem at all what problem does blogging solve?Twitter for christ's sake? no one knows what they do until they are popular e.g. yahoo pipes is not practical yetit is a user experience nightmareand it doesn't have a clear defined purpose ... (more)

Tags: cool, cambridge, blog, travel, python, blogging, barcamp, twitter, mac, web, rss, talk

14 Jul 2008

comment on climbing goals

July 14, 2008

I find that having a cool trip planned every now and again is key forkeeping me motivated. I've been doing a lot of job and country hopping overthe past 10 years, and this has had a signifigant detrimental impact on theamount of climbing that I could do, but hey, I'm doing a job that I love,and those are the rolls we choose to take. One thing that has kept me motivated to get of my arse and actually try abit harder when I am down in the gym is having a few cool trips planned inthe year. ... (more)

Tags: cool, climbing

14 Jul 2008

CPANPLUS and Mac OSX

July 14, 2008

OK, so I'm interested in installing the Connotea code base on my mac fordevelopment reasons. It will be the first time that I am going to startplaying around with a largish perl installation on my macine and there are alot of perl dependencies to be installed. Rather than going through CPANmodule by module, and rather than writing a bundle file for the connoteadependancies (because I don't know how to do that yet) I decided to try touse CPANPLUS, due to the tips on perl administration withCPANPLUS ... (more)

Tags: osx, mac, perl

14 Jul 2008

friends of mine of TV

July 14, 2008

A friend of mine set up her own business a few years ago, at the same timeas having a baby. It was really tough for Ais for the first couple of years,but it is looking like things are really working out for her now. She wasrecently featured on TV in Ireland, and she has posted a link to the clipfrom her blog. For a really inspirational view on managing business withchildcare have a loot at the vid: ... (more)

Tags: cool, blog, inspirational, ireland, business

14 Jul 2008

get addicted, feed the world

July 14, 2008

at http://www.freerice.org ... (more)

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14 Jul 2008

Get Slimmer Pets

July 14, 2008

12/01/2008 Originally uploaded by Ian Mulvany I was shopping at Lidl last weekend and saw this for sale. It might be a bit of a drastic measure, but I think it would work. ... (more)

Tags: flickr

14 Jul 2008

Getting motivated for climbing

July 14, 2008

A good friend of mine has just hit the 8a mark in climbing. Dave is a greatclimber, and a really nice guy, but what really blew me away is that hisfiancee Caroline led 7b on her first sports climbing trip. One thing know about both of them is that they do a lot of running,something like 10 - 15 miles evrey morning. If this isn't motivation for me to pick up running then I don't know whatis. ... (more)

Tags: climbing, training

14 Jul 2008

getting started

July 14, 2008

Well, i'm starting out my mob-blogging life waiting in que for a flight to milan, and i discover that my predictive text thinks i'm a clogger! An interesting, if somewhat disturbing begining. Tags: moblog, txt, travel ... (more)

Tags: txt, blog, moblog, travel, blogging

14 Jul 2008

google reader now has search

July 14, 2008

Well, OK, this is probably not news, but I guess what is interesting for meis that this is a feature that I didn't really notice until today when Iwent looking for it, and hey, though that little search box had probablybeen there for weeks now, I only "saw" it today when I looked for it. ... (more)

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14 Jul 2008

Great places to hang out in Den Haag

July 14, 2008

I have a good friend who lives in Den Haag and passed on the followingadvice about places to go and eat if you have a small child. This is reallygreat advice so I thought I should post it here: Hi Victoria, Very sad to hear your friend has such a lousy experience in my country. AsIan can confirm, it's not a very easy place for 'outsiders'... The upside isthat if you are not at fancy free and footloose as my friend Ian is- andwith a little boy that age she will have moderated her dancing ambitions-The Hague can be quite a nice place to hang out. ... (more)

Tags: restaurant, food

14 Jul 2008

If programming is magic, then the old languages are strong

July 14, 2008

The similarity between magic and programming is never more apparent thanwhen you sit down and watch someone who is truly good on the command line.By virtue of having secret knowledge they can quickly accomplish theapparently impossible. If you start out in the unix world you begin bylearning some simple incantations such as 'cd', 'ls' and 'top' and 'kill'.If you persevere with the art eventually you may master the hidden runesthat bring 'sed' and 'awk' to life. ... (more)

Tags: programming, magic

14 Jul 2008

Installing Python Image Library on a Mac

July 14, 2008

I spent about half an hour trying to install the excellent Python ImageLibrary on my mac. It's one of those things that is more annying than itshould be. You get libjpeg from herehttp://www.ijg.org/files/jpegsrc.v6b.tar.gz follow the instructions here onhow to patch the makefile and how to install libjpeg:http://www.kyngchaos.com/macosx/install/libjpeg (all this after installingthe developer tools on mac), only to fail and then discover that there is aprebuilt binary package here:http://pythonmac.org/packages/py25-fat/index.html which works perfectly. ... (more)

Tags: python, osx, mac

14 Jul 2008

Liam dropping by london

July 14, 2008

10072007136 ... (more)

Tags: london

14 Jul 2008

live blogging from BarCamp Cambridge,

July 14, 2008

I am at Bar Camp Cambridge, We have had the three word introductions and are just running through themorning talks now. It's pretty cool. The coffee is good, and cookies are great. Let's see how the day goes. ... (more)

Tags: cool, cambridge, blog, blogging, barcamp, talk

14 Jul 2008

live blogging from BarCamp Cambridge, Laura James

July 14, 2008

Laura JamesAlert Me.Com might get too corporate. trying to do the internet of things, internet access to small devicesthey are implimetning today, and will be shipping later this year.comes from R&D, but working in a shipping they are going to ship a home security system, but they are actuallybuilding a platofrmthat can connect anything that does not require full audio and video using a mesh network that connect to a hub using a 'zigby'output can be things like a lamp that has a color dependant state ... (more)

Tags: cool, cambridge, blog, network, python, blogging, barcamp, twitter, mac, web, talk

14 Jul 2008

live blogging from BarCamp Cambridge, Matt's discussion

July 14, 2008

discussionQ Gridle is raised along with RDFa if you don't like the way that the xslt is workin you can make your own.however most domain exprts can't write xslt if you just let the domain experts create microformats you may leave theontologicaldefinitions to people who are creating the xslt AG says that there may be two different problems, address to addressbookfrom page vs data harvesting ... (more)

Tags: cambridge, blog, blogging, barcamp, book

14 Jul 2008

live blogging from BarCamp Cambridge, Matt's talk

July 14, 2008

Matt talking about semanitic web for science, an introductionXML, URI, namespaces, RDL OWL,standards are often argued about but it;s just XML we are supposed to be able to publish semantis data easily,at the moment it's not just an extension but a whole other world,people won't learn sapqrl Matt believes that we can get the benifits of semantic now, but withoutin any case, it's hard to get funding ... (more)

Tags: cambridge, blog, flickr, blogging, barcamp, web, science, talk

14 Jul 2008

Mining social data, what Flickr tells us about place

July 14, 2008

toscany activity spikes with R Originally uploaded by fgirardin Web 2.0 is a buz word. At a conference that I attended last week it came up frequently as being one of the most over-hyped terms around at the moment, but there is substance behind it, and how that substance appears is fully up to the creativity of people who are willing to get their hands dirty with the actual data that is being produced by social web sites. ... (more)

Tags: flickr, picture, web

14 Jul 2008

Money Saving Web Sites for Living in the UK

July 14, 2008

The Guardian ran an article this week listing 10. As a placeholder here aresome of them that I might find useful: https://www.mysupermarket.co.uk/ http://www.saynoto0870.com/ http://www.quidco.com/ http://www.energysavingtrust.org.uk/ ... (more)

Tags: web

14 Jul 2008

mozy backup service

July 14, 2008

I've been trying the free account this week. I've backed up 1.6 GB of data.It took, with given interruptions of a normal work day, about 4 days tobackup this amount of Data. I am beginning to think that the world of offline remote backups is still alittle bit away! ... (more)

Tags:

14 Jul 2008

New terminal in Mac OS 10.5 is nice

July 14, 2008

The new terminal is very nice, but I did a wipe and re-install and waswondering what had happened to my old terminal settings. Of course thedefault .bash_profile file was being used as the settings file, so I deletedit and now the terminal works as expected. ... (more)

Tags:

14 Jul 2008

Open Reviewing

July 14, 2008

Arecent blog post on Action Potential pointed me towards the neuroscience peer review consortium. Theyhave a description here about theconsortium and a list ofparticipating journals. I have no doubt that this is the future of peerreview. At the moment the peer review system is horribly inefficient forpapers that get rejected. Rejection from a journal can occur because a paperis crap, but often it happens for many other reasons, because the journalhas already met it's pagequota, the journal is publishing a set of special issues on another topic,the editors of the journal are interested in shifting the focus of thejournal, the topic of the paper is slightly away from the main interests ofthe editorial board, the paper is good, but just gets edged out by a set ofbetter papers that come in. ... (more)

Tags: peer, blog, nature, science

14 Jul 2008

open science

July 14, 2008

I just posted the below as a comment on a blog, but it was good so I thoughtI'd repost here What is open science and what is the system? Well I am sure that there aremany viewpoints on this, so I am going to just put forward one here. At a fundamental level 'the system' is how we ascribe credit toparticipation in science. The credit is converted to grant money, thedollars keep the food on the plate. ... (more)

Tags: science2.0, blog, science, open science, talk, food

14 Jul 2008

Patents and Peer Review, kissing cousins?

July 14, 2008

Below follows a long comment that I posted to an article on O'Reilly Radar about patents. The original blog post is here There is an interesting compliment to the patent system in the domain of assigning credit to ideas, which is the academic peer-review system. The inventor of the idea in the case of academia is the author. The equivalent to the patent office is the editorial board of the academic journal that the author submits to. ... (more)

Tags: blog, patents, peer review

14 Jul 2008

Potter prediction

July 14, 2008

I wonder how long it's going to be before we see a children's TV series setat Hogwarts. I predict within the next 5 years. tags: Harry Potter, TV ... (more)

Tags: tv, harry potter

14 Jul 2008

pythonic is a way of thinking

July 14, 2008

Thistutorial delves into pythonic ways of coding. I'm learning from it. tags: python, hoto, tutorial ... (more)

Tags: tutorial, python, hoto

14 Jul 2008

restaurant BAYOU Berlin

July 14, 2008

I got the email below a few days ago: Hello to you all,Please forgive the bulk email! We hope all is well with you.We will be opening our new restaurant on December 1st. Please visit our newwebsite at www.bayou-berlin.com You are able to book hotel reservations onour site using our corporate discount rate. We hope to see you sometimesoon,All the best,Steve and Brandon Earlier this year I was on holiday in Nerja in the south of Spain. ... (more)

Tags: restaurant, germany, web, food, book

14 Jul 2008

Sci - foo lurking

July 14, 2008

I'm a Sci-Foo lurker, as I didn't make the cut to go this year, but I'vebeen lapping up the news seeping out of the meeting. So far my favoriteTwitter post about the meeting comes from Richard Ackerman's feed: "Timo and Tim are trying to kill us. Doesn't cult brainwashing start withsleep deprivation? Fun so far, anyway" ... (more)

Tags: twitter

14 Jul 2008

Simpsian

July 14, 2008

Yesterday one of the guy's at the office interviewed the producer of TheSimpsons. As a result he had to do quite a lot of research yesterday onSimsonalia, and decided to use the make your own simpson avatar tool on theSimpsons movie page to make all of us our own simpson character, this iswhat I would look like if I were a simpson. Tags: simpsons, avatar IansSimpson. ... (more)

Tags: avatar, simpsons

14 Jul 2008

sometimes, just sometimes a piece of news makes me smile

July 14, 2008

From the Guardian today, a group of ultra-right wing MEP's were unable toform a group within the European Parliament owing to internal xenophobia. http://www.guardian.co.uk/farright/story/0,,2211167,00.html?gusrc=rss&feed=12 ... (more)

Tags: rss

14 Jul 2008

spreading of meme's behavior driven transmission of an idea

July 14, 2008

Thistech blog article is a charming description of how human behaviour seemsto have spread the name of a particular wireless node across america. Ithink it is a lovely example of the spread of an idea driven by simpleself-interest. ... (more)

Tags: blog

14 Jul 2008

The fruitcakes have a talking form

July 14, 2008

A new creationisim journal ARJ.GRRRRRRRR ... (more)

Tags: talk

14 Jul 2008

The Laboratory Website and Video Awards

July 14, 2008

Attila Csordas sent along links about these awards, looks nice, http://www.the-scientist.com/lawva/ and a blog link about them: http://pimm.wordpress.com/2007/10/09/the-laboratory-website-and-video-awards-by-the-scientist tags: science ... (more)

Tags: blog, web, science

14 Jul 2008

Tips for switching from Windows to Mac

July 14, 2008

I've written up the short answers to some questions that you might have if this is the first time to use a mac, read through this and if you followthe suggestions you should have the hang to the system pretty quickly. If it turns out you don't like it, then at least you will have made an informeddecision! -- Where is the right mouse button? This is the biggest obvious first difference. ... (more)

Tags: cool, nature, mac, picture, web

14 Jul 2008

Today at lunch duplicators and instantiators

July 14, 2008

I work at a pretty innovative place and the discussions that we have atlunch time are pretty mind bending. The last time I can recall having somany interesting discussions over lunch and breaks was way back when I wasin my first undergraduate degree, but the topics of conversation that tendto come up at my current place of employment are really worth trying torecord. Today we started off having a couple of split conversation, Euan describingchatting to Martha at Sci-Foo and Euan and I talking about Euler, as you do. ... (more)

Tags: replicator, books, science, lunch, talk, book

14 Jul 2008

Weddings make you fat

July 14, 2008

I just got back from a wedding and bier festival thing in Munich. I've been tracking my weight on and off for the past year and a half with the ultimate goal of getting back to my climbing fit weight of about 80kgs. From the graph below you can see the spike that was caused by the extertions at the wedding! (OK, in the vox rendering you can't really see the spike on the right hand side of the graph, but if you are bothered then click through and you'll see the original graph. ... (more)

Tags: munich, wedding, climbing, weight

14 Jul 2008

weekend grill

July 14, 2008

I visited my girlfriend in Germany this weekend, and her father wascelebrating his 60th birthday. A friend of his arranged a full wild boarfrom the German forests. The spit it and slow cooked it for 7 hours, ittasted amazing. I can quite see why Asterix and friends got so excited aboutthis. 13102007410.jpg 13102007409.jpg ... (more)

Tags: germany

14 Jul 2008

Why do all of the science fiction authors have all of the really good ideas already?

July 14, 2008

My friend Gavin has been increasingly interested in the singularity, wherebythe quiddity of humanness is uploaded into a computer, to reside there. Ithink the definition of the singularity has something to do reaching themoment where the boundary between a human individual entity and thetechnology that surrounds them becomes transparent, or disappearsaltogether. It struck me this weekend that if you can upload an intelligence , a person,a being, a soul, into a peice of technology, then you would probably beliving at a moment when technology was advanced enough to be able to build abody from the amino acid's up. ... (more)

Tags: travel, science

29 Jun 2006

Volvox

June 29, 2006

“Volvox”:img:img:http://www.mulvany.net/photo/blogPics/volvox The very first thing to die on it’s own, without the intervention of an outside agent, was an organism called Volvox. The first life that we know of whose cells perish from old age, rather than misfortune. Before humble Volvox all other living things would go on forever, the immortal bacteria, the barely describable virus. Volvox introduced death by natural causes to the world, and all living things that came after that were as complex, or more so, followed suit, and found programmed within them some pace maker, set to expire after they had done their duty on the earth. ... (more)

Tags: test, git, jekyll

26 Jun 2006

Economics and The New World Order,

June 26, 2006

Economics and The New World Order, I had a rather detailed and engaging conversation on Friday night with a couple of good friends of mine about Economics, and it's explanatory power. My friend Brain holds that economics explains everything, except perhaps for the laws of physics. Now I am also tempted to buy into his arguments, he is quite a persuasive fellow, however I intrinsically feel some caution in doing so, and I have been trying to figure out why. ... (more)

Tags: economics

26 Jun 2006

Economics and The New World Order,

June 26, 2006

Economics and The New World Order, I had a rather detailed and engaging conversation on Friday night with a couple of good friends of mine about Economics, and it's explanatory power. My friend Brain holds that economics explains everything, except perhaps for the laws of physics. Now I am also tempted to buy into his arguments, he is quite a persuasive fellow, however I intrinsically feel some caution in doing so, and I have been trying to figure out why. ... (more)

Tags: economics

Posts

12 week lattice training plan - review

Prakash lab - frugal science and the future of research

Profit Trees and making business cases

CODECHECK - reviewing code in publications

Using Datasette to publish data

Goodbye SAGE, hello BMJ!

thoughts on GetFTR

Some brief thoughts on scholarly publishing and climate change.

STM Research data workshop.

STM Research data workshop.

Google data set search.

rescognito - a route towards a weighted scholarly graph.

Where is research going - a Kudos report

Rave tech conference 2019

Unpaywall Journals - possibly the most interesting thing to happen this year in library subscription land.

Responsible metrics - the state of the art - Elizabeth Gadd at Force2019

Responsible metrics, the state of the art, Elizabeth Gadd at Force2019

Things holding back your analytics.

Book review - Tiamat’s wrath - book nine of the expanse series.

The three body problem.

Are scholarly publishers technology companies?

Strategies to reduce cognitive load, and make systems more robust whilst doing so, and why that’s important for product development.

key questions about AI in the publishing knowledge industry

test blog post

AGILE or agile?

Some ruminations on software architecture and diagramming

The state of retractions in the research literature.

RAVE publishing technology conference 2018

Belmont Forum Round Table - data accessibility statements

One Two Four All - a technique for getting insights from groups

One Two Four All - a technique for getting insights from groups.

blockchain in STEM - part 3

testing a new form of peer review - again

notes on notes on “crossing the chasam”

Distill is dedicated to making machine learning clear and dynamic

Grants for Nonprofits | Grants for Researchers | Instrumentl

JavaScript End to End Testing Framework | Cypress.io

Jobs to be Done A Case Study in the NHS | Digital transformation blog

Narrative Science | Natural Language Generation Technology

Reaktor Breakpoint 2018 Ben Sauer, The rise of voice, and how to design for it - YouTube

Sentry | Error Tracking Software — JavaScript, Python, PHP, Ruby, more

Voice Principles | Clearleft

blockchain in STEM - part 2

Architect, The Killer Serverless Framework – Reify

Limiting “Software Infant mortality” rate — decoding GO-JEK’s Deployment Checklist

Model Zoo - Pretrained deep learning models for transfer learning, educational purposes, and more

OA negotiation manifesto from university of California.

Ongoing experiment in ‘Extreme Open Science’ announced at Structural Genomics Consortium - HBGDki

Preprints growth rate ten times higher than journal articles - Crossref

Research Software Engineering conference 2018 workshop abstract

Scholia

Unsupervised Extraction of Epidemic Syndromes from Participatory Influenza Surveillance Self-reported Symptoms | bioRxiv

Blockchain in STEM - part 1

Adequate statistical power in clinical trials is associated with the combination of a male first author and a female last author.

Advanced computing with IPython

After 5 years and $3M, here's everything we've learned from building Ghost

Digital Radar - STM landscape

Internet Archive, Code for Science and Society, and California Digital Library to Partner on a Data Sharing and Preservation Pilot Project

Open Knowledge Maps - social science map

Strategy in a Lean Enterprise - lean value tree.

The Cost of Developers – by Ben Thompson

VIPER - The Visual Project Explorer

About Backyard Brains

Cool slide deck about the advantages of using the shell for data science.

How to Visualize an XML Sitemap Using Python - Ayima

Impact of Social Sciences – The academic papers researchers regard as significant are not those that are highly cited

Mindcontrol A web application for brain segmentation quality control - ScienceDirect

The Guardian view on digitising culture make manuscripts more illuminating | Editorial | Opinion | The Guardian

eLife Innovation Sprint - appstract.pub

A new new way to make biological data more easily citable

Alexa is becoming less popular as a baby name since the Amazon service launched.

Computer replaces workers, workers ty to turn into data scientists.

Google employees resigning in protest at potential militarisation of AI

Is caution justified when thinking about docker?