Partially Attended

an irregularly updated blog by Ian Mulvany

blog posts about science

Prakash lab - frugal science and the future of research

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)

blockchain in STEM - part 3

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)

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

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)

Some thoughts on FORCE2015, science trust and ethics.

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)

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

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)

WriteLateX/Overleaf launch event at the British Library

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)

advice on publishing research online

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)

EC consultation on Open Data - a report.

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)

EC consultation on Open Data - my presentation.

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)

The new food.

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)

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

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)


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)

Science Online London Keynote, Michael Nielson on Open Sciecne

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)

SOLO11, day1, morning sessions.

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)

Talkfest, science and community

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)

Robert Bunsen's Birthday

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)

Slides from APS Talk, August, 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)

science scraping with YQL

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)

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

Probabilistic language models, auto-correction tools and scientific discovery. "Durgesh Kumar Dwivedi": 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)

World War II, Science and Springer Authors

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)

BarCamp Cambridge - teacking computers to understand text, Peter Corbett

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)

live blogging from BarCamp Cambridge, Matt's talk

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)

Open Reviewing

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)

open science

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)

The Laboratory Website and Video Awards

Attila Csordas sent along links about these awards, looks nice, and a blog link about them: tags: science ... (more)

Today at lunch duplicators and instantiators

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)

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

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)