Category: Blog

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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!

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Following up on data storage issues

There were lots of helpful comments on my previous post as well as some commiseration from Peter Murray-Rust. Also Jean-Claude Bradley’s group is starting to face some similar issues with the combi-Ugi project ramping up. All in the week that the Science Commons Open Data protocol is launched. I just wanted to bring out a few quick points:

The ease with which new data types can be incorporated into UsefulChem, such as the recent incorporation of a crystal structure (see also JC’s Blog Post), shows the flexibility and ease provided by an open ended and free form system in the context of the Wiki. The theory is that our slightly more structured approach provides more implicit metadata, but I am conscious that we have yet to demonstrate the extraction of the metadata back out in a useful form.

Bill comments:

…I think perhaps the very first goal is just getting the data out there with metadata all over it saying “here I am, come get me”.

I agree that the first thing is to simply get the data up there but the next question out of this comment must be how good is our metadata in practise? So for instance, can anyone make any sense out of this in isolation? Remember you will need to track back through links to the post where this was ‘made’. Nonetheless I think we need to see this process through to its end. The comparison with UsefulChem is helpful because we can decide whether the benefits of our system outweigh the extra fiddling invovled, or conversely how much do we have to make the fiddling less challenging to make it worthwhile. At the end of the day, these are experiments in the best approaches to doing ONS.

Things that do make our life easier are an automatic catalogue of input materials. This, and the ability to label things precisely for storage is making a contribution to the way the lab is running. In principal something similar can be achieved for data files. The main distinction at the moment is that we generate a lot more data files than samples so handling them is more logistically difficult.

Jean-Claude and Jeremiah have commented further on Jeremiah’s Blog on some of the fault lines between computational and experimental scientists. I just wanted to bring up a comment made by Jeremiah;

It would be easier to understand however, if you used more common command-based plotting programs like gnuplot, R, and matlab.

This is quite a common perception. ‘If you just used a command line system you could simply export the text file’. The thing is that, and I think I speak for a lot of wet biologists and indeed chemists, that we simply can’t be bothered. It is too much work to learn these packages and fighting with command lines isn’t generally something we are interested in doing – we’d rather be in the lab.

One of the very nice things about the data analysis package I use, Igor Pro, is that it has a GUI built but it also translates menu choices and mouse actions into a command line at the bottom of the screen. What is more it has a quite powerful programming language which uses exactly the same commands. You start using it by playing with the mouse, you become more adept at repeating actions by cutting and pasting stuff in the command line and then you can (almost) write a procedure by pasting a bunch of lines into a procedure file. It is, in my view, the outstanding example of a user interface that not only provides functionality for the novice and expert user in a easily accesible way, it also guides the novice into becoming a power user.

But for most applications we can’t be bothered (or more charitably don’t have the time) to learn MatLab or Perl or R or GnuPlot (and certainly not Tex!). Perhaps the fault line lies on the division between those who prefer to use Word rather than Tex. One consequence of this is that we use programs that have an irritating tendency to have proprietary file systems. Usually we can export a text file or something a bit more open. But sometimes this is not possible. It is almost always an extra step, an extra file to upload, so even more work. Open document formats are definitely a great step forward and XML file types are even better. But we are a bit stuck in the middle of slowly changing process.

None of this is to say that I think we shouldn’t put the effort in, but more to say, that from the perspective of those of us who really don’t like to code, and particularly those of us generating data from ‘beige box’ instruments the challenge of ‘No insider information’ is even harder. As Peter M-R says, the glueware is both critical, and the hardest bit to get right. The problem is, I can’t write glueware, at least not without sticking my fingers to each other.

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The problem with data…

Our laboratory blog system has been doing a reasonable job of handling protocols and simple pieces of analysis thus far. While more automation in the posting would be a big benefit, this is more a mechanical issue than a fundamental problem. To re-cap our system is that every “item” has its own post. Until now these items have been samples, or materials. The items are linked by posts that describe procedures. This system provides a crude kind of triple; Sample X was generated using Procedure A from Material Z. Where we have some analytical data, like a gel, it was generally enough to drop that in at the bottom of the procedure post. I blithely assumed that when we had more complicated data, that might for instance need re-processing, we could treat it the same way as a product or sample.

By co-incidence both Jenny and I have generated quite a bit of data over the last few weeks. I did a Small Angle Neutron Scattering (SANS) experiment at the ILL on Sunday 10 December, and Jenny has been doing quite a lot of DNA sequencing for her project. To deal with the SANS data first; the raw data is a non-standard image format. This image needs a significant quantity of processing which uses at least three different background measurements. I did a contrast variation series, which means essentially repeating the experiment with different proportions of H2O and D2O, each of which require their own set of backgrounds.

Problem one is just that this creates a lot of files. Given that I am uploading these by hand you can see here, here and here (and bearing mind that I still have these ones and five others to do), that this is going to get a bit tiring. Ok, so this is an argument for some scripting. However what I need to do is create a separate post for all 50-odd data files. Then I need to describe the data reduction, involving all of these files, down to the relatively small number of twelve independent data files (each with their own post). All of this ‘data reduction’ is done on specially written software, and is generally done by the instrument scientist supporting the experiment so describing it is quite difficult.

Then I need to actually start on the data analysis. Describing this is not straightforward. But it is a crucial part of the Open Notebook Science programme. Data is generally what it is – there is not much argument about it. It is the analysis where the disagreement comes in – is it valid, was it done properly, was the data appropriate? Recording the detail of the analysis is therefore crucial. The problem is that the data analysis for this involves fiddling. Michael Barton put it rather well in a post a week or so ago;

It would be great, every week, to write “Hurrah! I’ve discovered to this new thing to do with protein cost. Isn’t it wonderful?”. However, in the real world it’s “I spent three days arguing with R to get it to order the bars in my chart how I want”.

Data analysis is largely about fiddling until we get something right. In my case I will be writing some code (desperate times call for desperate measures) to deconvolute the contributions from various things in my data. I will be battling, not with R but with a package called Igor Pro. How do I, or should I, record this process? SVN/Sourceforge/Google Code might be a good plan but I’m no proper coder – I wouldn’t really know what to do with these things. And actually this is a minor part of the problem, I can at least record the version of the code whenever I actually use it.

The bigger problem is actually capturing the data analysis itself. As I said, this is basically fiddling with parameters until they look right. Should I attempt to capture the process by which I refine the paramaters? Or just the final values? How important is it to capture the process. I think there is at core here the issue that divides the experimental scientists from the computational scientist. I’ve never met a primarily computer based scientists that kept a notebook in a form that I recognised. Generally there is a list of files, perhaps some rough notes on what they are, but there is a sense that the record is already there in those files and that all that is really required is a proper index. I think this difference was at the core of the disagreement over whether the Open NMR project is ONS – we have very different views of what we mean by notebook and what it records. All in all I think I will try to output log files of everything I do and at least put those up.

In the short term I think we just need to swallow hard and follow our system to its logical conclusion. The data we are generating makes this a right pain to do it manually but I don’t think we have actually broken the system per se. We desperately need two things to make this easier. Some sort of partly automated posting process, probably just a script, maybe even something I could figure out myself. But for the future we need to be able to run programs that will grab data themselves and then post back to blog. Essentially we need a web service framework that is easy for users to integrate into their own analysis system. Workflow engines have a lot of potential here but I am not convinced they are sufficiently useable yet. I haven’t managed to get Taverna onto my laptop yet – but before anyone jumps on me I will admit I haven’t tried very hard. On the other hand that’s the point. I shouldn’t have to.

If I have time I will get on to Jenny’s problem in another post. Here the issue is what format to save the data in and how much do we need to divide this process up?

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Seeking advice and resources on Open Notebook Science

The following comment was posted to the ‘About‘ page by Sharon Sonenblum from Georgia Tech. Rather than leave it there where people might not see it I thought I would bring it to the front for everyone’s attention.

‘I’m looking for some resources or direction for diving into open notebook science. I have been interested in the concept for quite some time and recently began following this blog and a few others. I am excited to see that ONS is real and growing, but I’m not sure the best places to start. I want to find out what other folks are doing, what software they are using and what has and has not worked. I also would love to chat with anyone doing research with human subjects to figure out how IRB restrictions play out in ONS.’

Hi Sharon, great to see people interested in ONS! I am sure others will offer comments and suggestions but I will put my tuppence in first. My main suggestion would be to dive in and see what works for you, within the limitations of what you can do. Depending on the kind of work you are doing and how you are already recording it there are a range of options. As I mentioned in yesterday’s post there are as many different approaches to ONS as there are people doing it. We are definitely at the stage of exploring what is possible, what works, and there is plenty of discussion and indeed disagreement over what the best approach is.

There are really two places you could start. The easiest, and possibly the safest way to dip your toes into the water, is to start up a blog that discusses your lab work in general. There are good examples of this kind of approach with Rosie Redfield’s lab being one of the main proponents (see also Michael Barton’s blog). This can be, but is not necessarily, Open Notebook Science as defined by Jean-Claude Bradley. From what you say there may be real issues with you making your primary data available. If it involves human subjects then I would imagine it will be very difficult, if not impossible, to make the raw data available due to ethical considerations. Certainly I would expect that any review board would require that any data that was released was anonymised and that subjects understood exactly what the release conditions would be. I am no expert in ethics and we don’t (as far as I know) have anyone in the ONS community who is dealing with either human or animal subjects. This is an area that I think is important and that we have yet to explore in detail; if we believe that some science (say chemistry) should be fully open but that some (e.g small scale drug trials) cannot be then can we draw clear boundaries? I don’t know the answer but clearly some care is required with this.

If you can get clearance to go fully to ONS then there are a range of options. I would say it depends a lot on what sort of data you are dealing with. Take a look at your existing lab book and see what it looks like. Is it an electronic document already? Could you simply put that online? Is it an index to a set of data files, spreadsheets, graphs, analysis? If so a Wiki may be the best approach and using a free hosted service, either Wikispaces as used by UsefulChem, or OpenWetWare, could be a good option. Here you can add data files and then add pages that describe, and index them, as well as pages for analysing and discussing the results. Is your lab book more of a journal? Then a Blog may be the best approach, although you need to be careful here about date stamps as many blog engines allow you to change the datestamp. We use an in house developed blog at Southampton that gets around some of these problems but this is definitely an alpha to beta stage product.

Finally, make sure you discuss it with the people around you. Many scientists are deeply uncomfortable with the whole idea of making the lab notebook available. Be sure that you understand and take into account any concerns. In some cases they may not be valid concerns but as with anything there are real risks with the open notebook approach. Take the opportunity to understand any concerns and be prepared to argue where you think they are unjustified, but in a constructive way. Hopefully you can find good discussion points on this blog, at UsefulChem, Open Reading Frames (see also Bill’s excellent three part series at 3 Quark’s Daily), petermr’s blog, Jeremiah Faith’s blog, Michael Barton’s blog, What you’re doing is rather desperate, Public Ramblings, BBGM…who have I missed?

Good luck and keep us updated! The best thing about ONS is the conversations that can get started.

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A big few weeks for open (notebook) science

So while I have been buried in the paper- and lab-work there has been quite a lot of interesting stuff going on. Pedro Beltrao has started an Open Notebook style project at Google Code which he describes in a post on Public Ramblings. This in interesting, because once again someone is using a different system as an Open Notebook. We have Wiki’s, Blogs, TeX based documents, and now, software version repositories being used. As Jean-Claude Bradley has said and we have discussed we have a lot to learn from exploring different systems, both in terms of understanding the benefits and limitations of specific systems on the way to designing and implementing better ones, but also from the perspective of what this tells us about how we do our science, and how this differs from discipline to discipline. Indeed, there already seems to be a place where this discussion has started in Pedro’s system. It is great to see this going forward and also great to see other members of the community, including Bill Hooker and Michael Barton already getting in and getting their hands dirty. I only wish I could contribute a bit more on the science itself.

Also good is the publicity that Open Notebooks and Open Notebook Science are getting. An article in Chemistry World, the member’s journal of the Royal Society of Chemistry, features UsefulChem, and discussion from Peter Murray-Rust, Steve Bachrach and others. Our efforts at Southampton even get a mention! What is good about this is not so much the personal publicity but that the mainstream ‘industry’ journals are increasingly starting to pick up the story. Not so long ago there was the article in Wired; Chemistry World has also recently discussed the issues associated with openness in a reasonably balanced manner (see also Peter Suber and Peter Murray-Rust’s commentaries).

In addition there is good coverage on the web. Rosie Redfield’s lab pages got featured by David Ng on World’s Fair on Science Blogs which was also picked up at BoingBoing (thanks to Neil Saunders for bringing this to my attention). Momentum is building as Neil says. The issues are becoming mainstream and the benefits are starting to flow through in specific cases. This is how things start to change. The challenge is in maintaining this forward momentum as it builds.

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The OPEN Research Network Proposal – update and reflections

Despite all evidence to the contrary, I have not in fact fallen off the end of the world. I have just been a little run off my feet over the last week or so. A quick weekend trip to the south of France (see here for probably rather too much detail) and a lot of other things, not least some wrangling over allowed costs for the grant, have been keeping me busy.

The research network proposal was successfully submitted on Tuesday 27th November, some six days after I proposed here the possibility of applying for this grant. To echo what Mat Todd said, I haven’t ever been involved with a grant proposal that came together so fast, and while it still involved several days with very little sleep on my part it could not have been put together without a great deal of assistance from a large number of people. The final version of the proposal is here and I will try to put up a page on OpenWetWare for further discussion. The text of the case for support is also available at Nature Precedings. Precedings were uncomfortable about hosting the financial details of the proposal and I think this is interesting in its own right and will write on it later. Here, however, I want to reflect on the process of preparing the grant and what worked well and what didn’t.

Finding the community

The use of this Blog and the subsequent diffusion of the request for help through a number of other blogs was very effective and quite rapid. Diffusion was important and the proposal was featured on a wide range of blogs (1, 2, 3, 4, 5…others?). Given the very short time scale the number of people that became involved was really very high. People are able to move much faster than organisations so on the timescale that we were working it wasn’t possible to get organisations such as PLoS, Nature Publishing Group, BioMedCentral etc. formally involved by the time of the grant submission. I am still very keen to get the involvement of organisations like these and others and it isn’t too late to send a letter of support as I can update these at any time.

It is interesting to contrast this with the response I received to my earlier request for collaborators on the protein-DNA ligation project. In the case of the network proposal I was very rapidly swamped with support whereas for the actual science based project I haven’t had a response as yet. I think this is a good demonstration that while the Open and Connected approach can be effective, it is currently working best for development and networking projects associated with open and connected practises. As a research community we work very well on our common interests, where we have critical mass. However beyond this, in the areas of our ‘real research’, we are not yet seeing the potential benefits to anywhere near the same extent. I believe this is because we don’t yet have either critical mass nor a sufficiently connected network of researchers. In my view a central aim of the Research Network should be to break out of the ghetto and start to enable and demonstrate the benefits we know and have seen in the context of a wider range of scientific disciplines.

Writing the grant

In the process of writing and editing the grant it became clear that contributors have very different ‘contribution styles’ and that different types of contribution had higher or lower chances of making it into the final document. The proposal was written in GoogleDocs based on a first draft that I put together rather rapidly. The structure changed significantly over the course of the six days. Some contributors preferred to email specific comments whereas some got right in and hacked away at the text. At times there were six or ten people simultaneously editing the document. I am particularly grateful to those who spent the last night before submission going through and finding typos (although there are still quite a few I am embarrased to admit). This made the final stages of ‘cleaning up’ much easier.

Those who directly edited the document saw a much higher chance of their changes making it into the final document. Email comments were also valuable and were included or taken account of in many cases but because they were less immediate there was a greater tendency for them to be passed over or simply lost in the rush. At all times I took the arbitrary decision that I would delete, adapt, or add text as I saw fit. While a concensus approach may have worked, if more time was available, with the time restraints imposed it seemed to me that strong ‘editorial’ guidance was required to hit the final target.

Overall, this was a relatively pleasant way to write a proposal. The fact that many eyes went over the text was a great help and made me much more confident, even when I took a final decision to remove something, that a range of views had been explored, and that there was less chance of us missing important details. The full editing record is available in GoogleDocs if you have editing rights to the document. At the moment I don’t think I can expose the history. I considered doing the writing on OpenWetWare but that would have required people getting accounts, and the extra 24 hours involved there may have meant we didn’t make it. A wiki is nonetheless probably a better framework for this kind of writing.

Submitting the grant

The mechanics of the submission process meant that essentially no-one else had access to the financial details and there was little point discussing these. I wrote the justification of resources and Workplan on my own simply due to time contraints. The logistics meant that the text had to be closed off from the GoogleDoc at a specific time and then adapated to fit the available space. You can see what was done by comparing the final GoogleDoc version with the submitted version.

Would this work for a ‘real’ grant application?

As far as I am aware this is the first time a grant application has been written ‘in the open’ like this. However this is not a conventional research project. It is not clear at the moment whether the same benefits would be seen for a conventional project. Part of the reason people contributed was that they could be directly involved in the network. This would not be the case for a conventional project – would be people who would see no personal benefit be prepared to contribute as much? Having said that, the benefits of having many eyes on the proposal were clear, and made it possible to turn around the submission much faster than would otherwise have been the case. Perhaps the question is not so much; would people contribute? as; what is the best way to encourage people to contribute?

Thanks for everyone who helped and all those who offered support. It wouldn’t have happened without the contributions and support of a lot of people. You know, this Open Science thing actually works!

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Proposal submitted…

Enough said. Thanks to everyone who helped. I will reflect on the process at a later stage and will put the complete proposal up as soon as I can. If anyone wants to send letters of support or get involved don’t feel that you’ve missed the boat. Whether the money comes up or not we ought to be doing something along these lines and I can always include more material when we reply to referee’s comments.

Cheers

Cameron