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An abstract for the International Meeting on E-social Sciences

I have said before that I think we could benefit from the involvement of social scientists in understanding the possible cultural issues involved in the move towards more open practises. To this end we are submitting an abstract for the 4th International Meeting on e-social Science to present a ‘short paper’. I’ve put the abstract below: the deadline is next Monday (4th February). If you have any comments and/or would like to be included as an author on the paper. I am a bit pressed for time this week and google services seem slow this morning so I will probably stick to using comments from here rather than using Google Docs. Any/all comments welcome.

The Effect of Network Size and Connectivity on Open Notebook Approaches to Scientific Research: The view from the inside

Cameron Neylon with contributions from the Open Notebook Science Collective

A small but growing group of researchers in the physical and biological scientists are interested in developing and applying open approaches to their research practise. The logical extreme of this approach is ‘Open Notebook Science’ a term coined by Jean-Claude Bradley to refer to the practise of making the raw data from an experimental laboratory available as soon as practicable after it is generated. The promise of such open approaches is that loose coalitions of scientists can aggregate around specific problems according to interest, expertise, and resource availability and that such an approach can allow significantly more rapid solutions to problems to be developed. Specific recent examples of such approaches include the aggregation of a group of significant size to rapidly (five days) prepare a full scale grant application, attempts, successful and unsuccessful to identify collaborators to provide specific experimental capabilities to allow the completion of experimental results, and requests for experts to examine specific chemical datasets to identify potential errors. We will describe the experience of these different examples from the inside as well as the tools and resources used; their usefulness and limitation. The key observation is that successful application of these approaches requires a critical mass of interested scientists with sufficient times to provide a large enough pool of resources to solve the problem and that the network be sufficiently well connected for requests to be routed to the those best suited to help. In most cases the record of these efforts are fully publically available and may provide useful data for social science research in this area.

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Sharing is caring…and not sharing can be reprehensible

Sometimes you read things that just make you angry. I’m not sure I can add much to this eloquent article written by Andrew Vickers in the New York Times (via Neil Saunders and the 23andme blog).

Shirley Wu has recently written on the fears and issues of being scooped and whether this is field dependent or not. Her discussion, and the NYT article seems to suggest that these fears are greatest in precisely those disciplines where sharing could lead to advances with direct implications for people, their survival, and their quality of life.

I, to be honest, have been getting more and more depressed about the fact that this keeps coming back as the focus of any discussion about Open Notebooks or Open Science. Why is the assumption that by sharing we are going to be cheated? Surely we should be debating about the balance between benefits and risks. And about how this compares to the balance of  benefits and risks in not being open. Particularly when those risks relate to people’s chance of survival.

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Picture this…

There has been a bit of discussion recently about identifying and promoting ‘wins’ for Open Science and Open Notebook Science. I was particularly struck by a comment made by Hemai Parthasarathy at the ScienceBlogging Meeting that she wasn’t aware of any really good examples that illustrate the power of open approches. I think sometimes we miss the most powerful examples right under our nose because they are such a familiar part of the landscape that we have forgotten they are there. So let us imagine two alternate histories; I have to admit I am very ignorant of the actual history of these resources but I am not sure that matters in making my point.

History the first…

In the second half of the twentieth century scientists developed methods for sequencing proteins and DNA. Not long after this the decades of hard work on developing methods for macromolecular structure determination started to bear fruit and the science of protein crystallography was born. There was a great feeling that in understanding the molecular detail of biological systems that disease was a beatable problem, that it was simply a matter of understanding the systems, to know how to treat any disease. Scientists, their funders, pharmaceutical companies, and publishers could see this was an important area for development, both in terms of the science and also with significant commercial potential.

There was huge excitement and a wide range of proprietary databases containing this information proliferated. Later there came suggestions that the NIH and EMBL should fund public databases with mandated deposition of data but a broad coalition of scientists, pharmaceutical companies, and publishers objected saying that this would hamper their ability to exploit their research effort and would reduce their ability to turn research into new drugs. Besides, the publishers said, all he important information is in the papers…By the mid-noughties a small group of scientists calling themselves ‘bioinformaticians’ started to appear and began to look at evolution of genetic sequences using those pieces of information they could legally scrape from the, now electronically available, published literature. One scientist was threatened with legal action for taking seven short DNA sequences from a published paper…

Imagine a world with no GenBank, no PDB, no SwissProt, and no culture growing out of these of publically funded freely available databases of biological information like Brenda, KEGG, etc etc. Would we still be living in the 90s, the 80s, or even the 70s compared to where we have got to?

History the second…

In the second half of the twentieth century synthetic organic chemistry went through an enormous technical revolution. The availability of modern NMR and Mass spectrometry radically changed the whole approach to synthesis. Previously the challenging problem had been figuring out what it was you had made. Careful degradation, analysis, and induction was required to understand what a synthetic procedure had generated. NMR and MS made this part of the process much easier shifting the problem to developing new synthetic methdology. Organic chemistry experienced a flowering as creative scientists flocked to develop new approaches that might bear their names if they were lucky.

There was tremendous excitement as people realised that virtually any molecule could be made, if only the methodology could be figured out. Diseases could be expected to fall as the synthetic methodology was developed to match the advances in the biological understanding. The new biological databases were providing huge quantities of information that could aid in the targeting of synthetic approaches. However it was clear that quality control was critical and sharing of quality control data was going to make a huge difference to the rate of advance. So many new compounds were being generated that it was impossible for anyone to check on the quality and accuracy of characterisation data. So, in the early 80s, taking inspiration from the biological community a coalition of scientists, publishers, government funders, and pharmaceutical companies developed public databases of chemical characterisation data with mandatory deposition policies for any published work. Agreed data formats were a problem but relatively simple solutions were found fast enough to solve these problems.

The availability of this data kick started the development of a ‘chemoinformatics’ community in the mid 80s leading to the development of sophisticated prediction tools that aided the synthetic chemists in identifying and optimising new methodology. By 1990, large natural products were falling to the synthetic chemists with such regularity that new academics moved into developing radically different methodologies targeted at entirely new classes of molecules. New databases containing information on the activity of compounds as substrates, inhibitors, and activators (with mandatory deposition policies for published data) provided the underlying datasets for validation that meant by the mid 90s structure based drug discovery was a solved problem. By the late 90s the chemoinformatic tools available made the development of tools for identifying test sets of small molecules to selectively target any biological process relatively straightforward.

Ok. Possibly a little utopian, but my point is this. Imagine how far behind we would be without Genbank, PDB, and without the culture of publically available databases that this embedded in the biological sciences. And now imagine how much further ahead chemical biology, organic synthesis, and drug discovery might have been with NMRBank, the Inhibitor Data Bank…

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More on the PSB proposal

Shirley Wu has followed up on her original proposal to submit a session proposal for PSB. She asks a series of important questions about going forward on this and I thought I would reply to these here to widen exposure.

I think it is worth going for a session and I am happy to lead the application but there may well be better people; Jean-Claude, Antony Williams, Peter Murray-Rust, Egon Willighagen to get to lead it depending on focus. I think the important question to ask is whether we can generate enough research papers to justify a session. I believe we can and should and I will commit to generating one if we go ahead, but we need at least another 3-4 to go ahead I think.

So, to answer Shirley’s questions:

1. What should be the focus of this session on Open Science? (first, frame it as a traditional PSB session, then perhaps as a “creative” session)
2. What kind of substantial/technical/research papers can be written about Open Science?
3. Who are the major players in the field? Who would the session chair invite to submit a paper?
4. Who is willing to help write/organize the actual proposal and session?

Given it is a computing symposium I would say that it should focus on tools and standards and how they effect what we can, or would like to do. This also gives us a chance to provide research type papers describing such tools and standards and investigating their implementation. So we could write papers describing different implementations of Open Notebooks and critical analysis of the differences, the organisation of Open Data, standards for describing data, and social and cultural aspects of what is happening etc etc.

People to invite to write papers include Jean-Claude Bradley, OpenWetWare group, Egon, Peter MR, Deepak Singh (willing to write a review/scoping type paper?), Antony Williams (ChemSpider), Simile Group (www.simile.mit.edu), other repository, data archival groups, Nature Publishing/PLoS/PMC/UK-PMC to describe systems, Heather Piwowar to analyse what happens, and social sciences groups that are becoming interested in what is going on.

Finally, as I say, I am willing to help, but as you can see time becomes a constraint for me and things have a habit if getting left to the last minute. If anyone else would like to step in to lead then I am more than happy to be a co-chair.  If no one else is available I am happy to lead. I at least have the advantage that I can probably source the resources so that I can get there!

I am going to tag this “Open Science PSB09” if that seems a good tag to aggregate around.

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Open Science Session at PSB 2009?

Shirley Wu from Stanford left a comment on my New Years Resolutions post suggesting the possibility of a session on Open Science at the PSB meeting in Hawaii in 2009 which I wanted to bring to front for peoples attention.

[…] Since you mentioned organizing an international meeting on the subject and publicizing open science, I’m curious what your thoughts (and anyone else’s who reads this!) would be on participating in a session on Open Science at the Pacific Symposium on Biocomputing at PSB. They don’t traditionally cover non-primary research/methods tracks, but they do pride themselves on being at the cutting edge of biology and biocomputing, so I am hoping they will be amenable to the idea. If there was support from, shall we say, the founders of this movement, I think it would help a great deal towards making it happen. […]

She also has a post on her new blog One Big Lab where she fleshes out the idea in a bit more detail and which is probably the best place to continue the discussion.

Hi Shirley! Great to have more people out there blogging and commenting. I am not sure whether I really qualify as a ‘founder of the movement’. I know things are moving fast, but I don’t think having been around for nine months or so makes me that venerable!

This sounds broadly like a good idea to me. I was considering trying to organise a meeting in the UK towards October – November this year but the timelines are tight and really dependent on money coming through. I would be happy to push back to Jan 2009 in Hawaii if people felt this was a good idea; if the grant comes through we could use this as the first annual meeting. My only concern is that Hawaii probably increases average costs for people as more people have to come further and book accomodation than if it is either Western Europe or East Coast US. The other issues is how and whether to focus such a session. I also don’t see a problem with having two meetings ~6 months apart. What do people think?

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Biosciences Federation Survey on Open Access – Please do this survey!

Ok, having flagged up two surveys in my previous post I have now done the second one. It seems to be for anyone worldwide but I wanted to bring it to people’s attention because it further clouds the definition of Open Access, whether deliberately or through ignorance I can’t say.

Fairly early on we have the following question:

6. What do you understand by the term ‘Open Access’? (Tick all those that apply)

  • Journals that are free to the reader
  • Journals that are free to the author
  • Journals that charge the author
  • Copies of journal articles freely available online (other than in the journal itself)
  • Not sure
  • Never heard the term
  • Other (please give details)

BBB doesn’t seem to even exist as an option!
And then in the following panel;

Full Open Access (OA) journals are generally defined as journals that are free for everyone to read immediately on publication, whether the costs of publication are defrayed through author-side charges, or in some other way

Now, we can (and have) argued for a long time over definitions of OA and the role of BBB etc. But to not mention it at all does not seem helpful. Might I humbly suggest that all those who feel it appropriate do the survey and put something in the ‘Other’ box for Question 6?

The survey is at: http://www.surveymonkey.com/s.aspx?sm=O8NxxhwFB2DQwDUvW183nw_3d_3d

I am assuming fair use for the purpose of criticism (this is significantly less than 5% of the full text of the survey).

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Some surveys you may wish to fill out

UK PubMedCentral, a UK mirror of PMC and a growing project at the British Library is soliciting responses to a survey:

Dear Colleague,

As you will know, UKPMC provides free access to an extensive repository of biomedical research literature, as well as an easy way for researchers to submit newly published work to meet the UKPMC Funders Group members’ Open Access requirements. The vision is for UKPMC to be much more than that!

As we enter the next stage of developing UKPMC into an innovative and useful resource for UK researchers we want to ensure that your needs and ideas are heard and incorporated at the outset. Please help us by completing our online questionnaire.

It should only take a few minutes and, as our way of saying thank you, all respondents will be entered into a prize draw to win an all-expenses paid weekend for two in London.

Click here to be taken straight to the survey page:

http://www.bl.uk/surveys/ukpmc/ukpmc.htm

Much of the survey asks questions about what additional tools you use for scientific search etc and what features you would like to see in UK PMC. This worries me as it seems like duplication both of effort and the creation of yet another del.icio.us/Facebook/Google/whatever for scientists. We don’t need another one, we need integration between the existing ones and improvement of user interfaces, interoperability, and useability. This wonderful video on the data portability initiative, which I saw featured on Deepak’s blog, tells the story. That’s my view anyway. Feel free to take the survey and disagree with me!

In addition the UK Biochemical Society has also commissioned some research and is looking for people to fill out another survey;

The Biochemical Society, in collaboration with other members of the Biosciences Federation (www.bsf.ac.uk), is conducting research into your experience of Open Access; I am writing to ask you to participate in this, by completing a brief questionnaire that should take no longer than 15 minutes.

The survey can be found here and the deadline is 1 February.

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Open Science and the developing world: Good intentions, bad implementation?

I spent last week in Cuba. I was there on holiday but my wife (who is a chemistry academic) was on a work trip to visit collaborators. This meant I had the opportunity to talk to a range of scientists and to see the conditions they work under. One of the strong arguments for Open Science (literature access, data, methods, notebooks) is that it provides access to scientists in less priviledged countries to both peer reviewed research as well as to the details of methodology that can enable them to carry out their science. I was therefore interested to see both what was available to them and whether they viewed our efforts in this area as useful or helpful. I want to emphasise that these people were doing good science in difficult circumstances by playing to their strengths and focussing on achievable goals. This is not second rate science, just science that is limited by access to facilities, reagents, and information.

Access to the literature

There is essentially no access to the subscriber-only literature.  Odd copies of journal issues are highly valued and many people get by by having visiting positions at institutes in the developed world. I talked to a few people about our protein ligation work and they were immensely grateful that this was published in an open access journal. However they were uncertain about publishing in open access journals due to the perceived costs.  While it is likely that they could get such costs waived I believe there is an issue of pride here in not wishing to take ‘charity’. Indeed, in the case of Cuba it may be illegal for US based open access publishers to provide such assistance. It would be interesting to know whether this is the case.

Overall though, it is clear that acccess to the peer reviewed literature is a serious problem for these people.  Open Access publishing provides a partial solution to this problem. I think to be effective it is important that this not be limited to self archving, as for reasons I will come back to, it is difficult for them to find such self archived papers. It is clear that mandating archival on a free access repository can help.

Access to primary data

Of more immediate interest to me was whether people with limited access to the literature saw value in having free access to the primary data in open notebooks. Again, people were grateful for the provision of access to information as this has the potential to make their life easier. When you have limited resources it is important to make sure that things work and that they produce publishable results. Getting details information on methodology of interest is therefore very valuable. Often the data that we take for granted is not available (fluorescence spectra, NMR, mass spectrometry) but details like melting points, colours, retention times can be very valuable.

There were two major concerns; one is a concern we regularly see, that of information overload. I think this is less of a concern as long as search engines make it possible to find information that is of interest. Work needs to be done on this but I think it is clear that some sort of cross between Google Scholar and Amazon’s recommendation system/Delicious etc. (original concept suggested by Neil Saunders) can deal with this.  The other concern, relating to them adopting  such approaches, was one that we have seen over and over again, that of ‘getting scooped’. Here though the context is subtley different and there is a measure of first world-developing world politics thrown in. These scientists are, understandably, very reluctant to publicise initial results because the way they work is methodical and slow. Very often the key piece of data required to make up a paper can only be obtained on apparatus that is not available in house or requires lengthy negotiations with potential overseas collaborators. By comparison it would often be trivially easy for a developed world laboratory to take the initial results and turn out the paper.

The usual flip side argument holds here; by placing an initial result in the public domain it may be easier for them to find a collaborator who can finish of the paper but I can understand their perspective. These are people struggling against enormous odds to stake out a place for themselves in the scientific community. The first world does not exactly have an outstanding record on acknowledging or even valuing work in developing countries so I can appreciate a degree of scepticism on their part. I hope that this may be overcome eventually but given that the assumption of most people in my own community is that by being open we are bound to be shafted I suspect we need to get our own house in order first.

The catch…

All of this is well and good. There are many real and potential benefits for scientists in the developing world if we move to more open styles of science communication. This is great, and I think it is a good argument for more openness. However there is a serious problem with the way we present this information and our reliance on modern web tools to do it. Its a very simple problem: bandwidth.

All of our blogs, our data, and indeed the open access literature is very graphics heavy. I actually tried to load up the front page of openwetware.org while sitting at the computer of the head of the department my wife was visiting (the department has two networked computers). Fifteen minutes later it was still loading.  The PLoS One front page was similarly sluggish. I get irritated if my download speeds drop below 500K/second, at home, and I will give up if they go down to 100K. We were seeing download rates of 44 bytes/second at the worst point. In some cases this can even make search engines unuseable making it near impossible to track down the self-archived versions of papers. Cuba is perhaps a special case because the US embargo means they have no access to the main transatlantic and North American cables, in effect the whole country is on a couple of bundles of phone lines, but I suspect that even while access is becoming more pervasive the penetration of reasonable levels of bandwidth is limited in the developing world.

The point of this is that access is about more than just putting stuff up, it is also about making it accessible. If we are serious about providing access, and expanding our networks to include scientists who do not have the advantages that we have, then this necessarily includes thinking about low bandwidth versions of the pages that provide information. I looked through PLoS One, openwetware, BioMedCentral, and couldn’t find a ‘text only version’ button on any of them (to be fair there isn’t one on our lab blog either).  I appreciate the need to present things in an appealling and useful format, and indeed the need to place advertising to diversify revenue streams. I guess the main point is not to assume that by making it available, that you are necessarily making it accessible. If universal accessibility is an important goal then some thought needs to go into alternative presentations.

Overall I think there are real benefits for these scientists when we make things available. The challenges shouldn’t put us off doing it but perhaps it is advisable to bear in mind the old saw; If you want to help people, make sure you find out what they need first.

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Some New Year’s resolutions

I don’t usually do New Year’s resolutions. But in the spirit of the several posts from people looking back and looking forwards I thought I would offer a few. This being an open process there will be people to hold me to these so there will be a bit of encouragement there. This promises to be a year in which Open issues move much further up the agenda. These things are little ways that we can take this forward and help to build the momentum.

  1. I will adopt the NIH Open Access Mandate as a minimum standard for papers submitted in 2008. Where possible we will submit to fully Open Access journals but where there is not an appropriate journal in terms of subject area or status we will only submit to journals that allow us to submit a complete version of the paper to PubMed Central within 12 months.
  2. I will get more of our existing (non-ONS) data online and freely available.
  3. Going forward all members of my group will be committed to an Open Notebook Science approach unless this is prohibited or made impractical by the research funders. Where this is the case these projects will be publically flagged as non-ONS and I will apply the principle of the NIH OA Mandate (12 months maximum embargo) wherever possible.
  4. I will do more to publicise Open Notebook Science. Specifically I will give ONS a mention in every scientific talk and presentation I give.
  5. Regardless of the outcome of the funding application I will attempt to get funding to support an international meeting focussed on developing Open Approaches in Research.

Beyond the usual (write more papers, write more grants) I think that covers things. These should even be practical.

I hope all of those who have had a holiday have enjoyed it and that all those who have not are looking forward to one in the near future. I am looking forward to the New (Western, Calendar) Year. It promises to be an exciting one!

I am now off to cook lots of lovely Chinese food (and yes I know that is calendarically inappropriate – but it will still taste good!). Happy New Year!