Author: Cameron Neylon

Posted on

How best to do the open notebook thing…a nice specific example

Peter Murray-Rust is going to take an Open Notebook Science approach to a project on checking whether NMR spectra match up with the molecules they are asserted to represent. The question he poses is how best to organise this. The form of an open notebook seems to be a theme at the moment with both discussions between myself and Jean-Claude Bradley (see also the ONS session at SFLO and associated comments) as well as an initiative on OpenWetWare to develop their Wiki notebook platform with more features. There are many ideas around at the moment so Peter’s question is a good specific example to think about.

As I understand Peter’s project the plan is as follows;

  1. Obtain NMR spectra from a public database and carry out a high level QM calculation to see whether this appears consistent with the molecule that the spectra is supposed to represent.
  2. Expose the results of this analysis useful form.
  3. Identify and prioritise examples where the spectrum appears to be ‘wrong’. The spectrum could be misassigned, the actual molecule could be wrong, or the calculation could be wrong.
  4. Obtain feedback on the ‘wrong’ cases and attempt to correct them through a process of discussion and refinement

So there are several requirements. The raw data needs to be presented in a coherent and organised fashion. Specific examples need to be ‘pushed out’ or ‘alerted’ so that knowledgeable and interested people are made aware and can comment and (and this is separate from commenting) further detailed discussion is enabled and recorded for the record. In addition there are the usual requirements for a notebook or a scientific record. The raw data must remain inviolate and any modifications must be recorded along with the process that generated the data. There will also presumably be a requirement to record thought processes and realisations as the process goes forward.

My suggestion is as follows:

  • The raw data is generated by a computational and repititive process so I imagine it is highly structured. I would use a template web page, possibly sitting within a Wiki but not editable, to expose these. This would include details of what was run and how and when. This would be machine generated as part of the analysis. Obviously appropriate tagging will play an important role in allowing people to parse this data.
  • A blog to provide two things. An informal running commentary of what is going on, what the current thought processes are, and what is being run and ‘alerts’ of specific examples which are interesting (or ‘wrong’). This is largely human generated, although the ‘alerts’ could be automated.
  • A wiki to enable discussion of specific examples and detailed comparisons by outside and inside observers. As Peter suggests in his draft paper, specific groups, both functional and academic, may show up as problems but predicting these in advance is challenging. A wiki provides a free form way of letting people identify and collate these. It may be appropriate to (automatically or manually) post comments from the blog into the wiki (which would also provide reliable time stamps and histories, not available in most standard blog engines).

So my answer to Peter’s question which might have been paraphrased as ‘Which engine is the best to use?’ is all of them. They all provide functionality that is important for the project as I understand it but none of them provide enough functionality on their own. An interesting question which would arise from this combination of approaches is ‘where is the notebook?’ to which I will admit I don’t have an answer. But I’m not sure that it matters.

This doubling up mirrors current practise both in Jean-Claude’s group where the UsefulChem wiki is the core notebook but the Blog is used for high level discussion. Similarly I am moving towards using this Blog for higher level discussion of results but the chemtools blog as more of a data repository. At Southampton we are thinking about the notion of ‘publishing’ from the Blog to a Wiki once a protocol or set of results is sufficiently established as Step 1 on the way to the paper.

Finally a throw away suggestion. Peter, if you want to get a lot of spectra with a lot of associated molecules, without any concerns about publisher copyrights, then consider opening this up as a service for graduate students to check their NMR assignments. I bet you get inundated…

Posted on

Why and where we search…

This quote is grabbed from a comment by Jean-Claude Bradley at bbgm in reply to my comment on Deepak’s post on my post on…. anyway my original comment was that our Wiki review would not be indexed on Google Scholar which is where people might go for literature searches

Jean-Claude:

Getting on Google Scholar is something on my list to look into – if anyone knows how to do it please let us know. But from our Sitemeter tracking on UsefulChem it is clear that scientists are using Google to search for (and find) actionable scientific information.

Now this is an interesting point and it mirrors what I do. Jean-Claude has established that a lot of the ‘new’ traffic coming to UsefulChem comes from Google searches for specific information. Specific molecules in many cases but also spectra and other experimental data. If I’m looking for information, or a resource, scientific or otherwise, I will do a generic Google search for the most part (the most successful recent one was for ‘sticky apple pudding‘ – the result was very good indeed – see the Waitrose.com link).

But if I’m looking for scientific literature I will go to PubMed or sometimes to Google Scholar if I’m getting frustrated. I only ever use WOK for citation based searching (i.e. who cited a paper) or on the rare occasions when I’m looking for material that is not indexed in PubMed. Partly this is because I really like the ‘related items’ tab in PubMed. But what strikes me is that in my mind I have obviously divided these classes of searches up into two different things: ‘information/resources’ and ‘literature’. I bet this correlates quite strongly with both age and with scientific field. Do others out there think of these things as different or as all part of a continuum of information?

I recently saw a talk on a ‘Research Information Centre’ being developed by Microsoft, a sort of portal for handling research projects and all the associated information. This is at an early stage of development but one of the features they were working on was an integrated search where you could add and subtract various items (PubMed, WOK, Google, GoogleScholar, and various toll access info sources as well). GoogleScholar could do this well. So as Jean-Claude says above. Anybody got any contacts with the developers? We could just talk to them…

Posted on

The Directed evolution library construction Wiki Review

I and a few others have been working for some time on converting a review I wrote some time ago for publication on OpenWetWare. Jason Kelly put the initial work in in developing an area for reviews and it was from him that I had the idea of taking this forward.

The traditional review is a cornerstone of the research literature. The first port of call for virtually any researcher on moving into an unfamiliar area is to find a good review. These vary vastly in length, specificity, and usefulness. The one thing that all traditional reviews have in common is that they are out of date as soon as they are printed.

On the other hand collaborative tools on the web make it straightforward to update and maintain, or even correct the text of a review. This is an area where community support can provide real added value in generating a useful and useable resource that can be maintained. By placing a review within the framework of a Wiki it would be possible for regular updates, and links to the current literature to be made available and for an open discussion of differences of opinion to take place. Unlike e-notebooks there are less technical and user interface issues to be worked out. This really ought to be an easy win.

There are many details that remain to be worked out. Should these be moderated, who can be trusted to maintain them, and more practically how can the regular maintainance of such reviews be guaranteed. On OpenWetWare anyone with an account can edit and anyone can view. The best practise for maintaining these reviews remains to be worked. The first step is to get a community of people involved in doing this.

So the review is now in a reasonable state, and certainly more up to date than it was. Any comments are welcome, either here, or on the review itself. We are also starting to write a paper on the review which we hope to get published. I think this is necessary so as to provide a pointer from the traditional literature to the review. As it happens the review is one of the top hits on Google but this is not where people go to find literature. It doesn’t appear on a Google Scholar search (that top hit is the original review) and is obviously not on PubMed or WOK. Whether we can get the paper published remains to be seen. Time to start emailing journal editors…

Posted on

Variations in reproduction charges – the results are in!

I blogged the other day about the way charges for reproducing figures in review articles appear to have gone ballistic. At that stage I only had the cost for J Biol Chem which was a whopping $USD73 to reproduce a figure. I had three other images I was using and was expecting around $20 for them, based on the website that Science Direct points you at for permissions. Well I was wrong, they have now come back at $USD3 each. So J Biol Chem, $73, Structure and J Mol Biol $3. Question is, what am I paying for from J Biol Chem (apart from my own lack of organisation in getting similar but copyright free figures). The other question is why through one website is it $3 whereas the one at Science Direct said it would be $20. Especially seeing as they both seem to be run by the Copyright Clearance Center!

Posted on

Joint NSF-EPSRC programme in Chemistry – an opportunity for ONS?

Looking at the EPSRC website I came across the following call for proposals involving collaboration between a US and UK programme:

http://www.epsrc.ac.uk/CallsForProposals/NSF-EPSRCChemistryProposals07.htm

Now, being an academic I’m up for any method of trying to get money out the system, especially special programmes. But is there an opportunity here to do something quite exciting in the area of Open Notebooks for chemistry where we take Jean-Claude’s experience and our Lab Blogbook system and try to build something that combines the best of both or possibly better, something which is a superset of both? Biggest issue I can see is that it might not be seen as chemistry, but if we focus on the idea of getting the chemical data both in and back out again it might fly.

Deadline for outline applications is November 6th…

Posted on

UK research council policies on open data

I was looking through the website of the Biotechnology and Biological Sciences Research Council the other day looking for policies on data sharing and open access. You can find the whole policy here but here are the edited highlights;

…BBSRC is committed to getting the best value for the funds we invest and believes that helping to make research data more readily available will reinforce open scientific enquiry and stimulate new investigations and analyses…

…BBSRC expects research data generated as a result of BBSRC support to be made available with as few restrictions as possible in a timely and responsible manner to the scientific community for subsequent research…In line with the BBSRC Statement on Safeguarding Good Scientific Practice, data should also be retained for a period of ten years after completion of a research project…

Ten years? I wonder how many UK scientists really work to that standard in practise (and I don’t include ‘I know its around here somewhere…’)?

…BBSRC supports the view that those enabling sharing should receive full and appropriate recognition by funders, their academic institutions and new users for promoting secondary research…

…BBSRC reserves the right to implement a more prescriptive approach to data sharing for research initiatives…

There are also detailed guidance notes and a FAQ for those who want to follow up.

The focus here is really on large coherent data sets rather than aggregating or indexing diffuse sets of online notebooks that I am more interested in. However I am in the process of writing some proposals that I want to embed an Open Notebook Science approach into so it will be interesting to see what the referees comments come back looking like on those. All proposals to BBSRC since April this year have had to have a section on ‘Data Sharing’ that explicitly includes published and unpublished data.

Posted on

The need for open data is getting more mainstream

Via Jean-Claude Bradley on UsefulChem, an article in Wired on making more of the ‘Dark Data’ out there available. As Jean-Claude notes this is focussed mainly on the notion of ‘failed experiments’ and ‘positive bias’ but there is much more background data out there. Experiments that don’t quite make the grade for inclusion in the paper or are just one of many that may be useful from a statistical perspective. How many synthetic chemistry papers give the range of yields achieved for a reaction? Or for a PCR reaction.

But its good to see more of this happening in the mainstream media and especially that Jean-Claude is getting the kudos for pushing the Open Notebook Science agenda. As this gets more mainstream it will filter through to the funders and other bodies.

Postscript: The article was originally commented on by Attilla at Pimm where there are more thoughtful comments on this.

Posted on

Limits to openness – where is the boundary?

I’ve been fiddling with this post for a while and I’m not sure where its going but I think other people’s views might make the whole thing clearer. This is after all why we believe in being open. So here it is in its unfinished and certainly unclarified form. All comments gratefully received.

One issue that got a lot of people talking at the Scifoo lives on session on Monday (transcript here) was the question of where the boundaries between what should and should not be open lie. At one level it seems obvious: the structure of a molecule can’t really have privacy issues whereas it is clear that a patient’s medical data should remain private. The issue came up a lot at the recent All Hands UK E-science meeting where the issues were often about census data or geographical data that could pinpoint specific people. It seems obvious that people’s personal data should be private but where do we draw the line? I am uncomfortable with a position where it is ‘obvious’ that my data should be open but ‘obvious’ that personal medical or geographical data should not be. Ideally I would like to find a clear logical distinction.

Continue reading “Limits to openness – where is the boundary?”

Posted on

Variations in reproduction charges for figures in a review article

Interesting morning negotiating the problems of getting permission to re-produce figures in a review I am currently writing. I wanted to reproduce figures from four papers, two from J Mol Biol (Elsevier), one from Structure (Cell Press), one from J Biol Chem (ASBMB). I could request permission for all three journals from copyright.com and as I’m in a rush I did this. Looking back at the journal websites now it appears that I should have gone to copyright clearance centre for the J Mol Biol ones and for the article in Structure.

At copyright.com the JBC article was charged at USD73 to reproduce a figure and at the copyright clearance centre it seems that the others are around USD23. Putting aside the issues of the price differential here I am wondering when these charges came in. The last time I wrote a review like this there was an administrative charge of $1.50 (I think) on one of the images I borrowed. Admittedly that was a couple of years ago. These are mostly representations of the structure of biological macromolecules so there is a clear creative aspect in generating the original figures.

Anyway, I’m tied in now, so will report back what the final charges are. I did consider asking the authors of the original papers for different, non-copyright, versions of the pictures but for most of these I feel I am reviewing the paper and should therefore reproduce the image. Anybody got an alternative view on this? I already took the decision that I woudn’t refer to any papers that I couldn’t view from my desktop (if I restricted myself to open access I wouldn’t have had anything to write about) but would I be better off leaving the pictures out?

Posted on

Scifoo Lives On session: Open notebook science case studies

Yesterday afternoon the Open Notebook Science case studies session was held as part of the Scifoo lives on sessions at Nature Island, Second Life. Jean-Claude Bradley organised, moderated and spoke first followed by me and Jeremiah Faith. We all spoke about experiences and implementation of different approaches to open notebook science.

Jean-Claude has put the transcript up here.

There was an active discussion about the need for more fun in science and the way in which science has become secretive has taken a lot of the fun out of it. CW Underwood talked about being sick of the ‘Secret Squirrel’ nature of science. One thing that was very encouraging was that Jeremiah said that in his search for his next post he had raised the issue as to whether the possible PI objected to him keeping his notebook open. So far he had had no objections.

Other issues that came up:

Open notebook science takes work and discipline.

It does involve some effort to get set up and to keep systems running as well as to maintain the observation that makes sure that things are running properly. CW pointed out that his PI would regard this as a waste of time. I can see this perspective being quite a strong one and a slow one to counter. Arguably the benefits of putting the effort in are not yet tangible enough to be convincing to people who are happy with the way their science works as it is.

What is the best system for holding the notebook?

Three different systems were presented. The UsefulChem Wiki by Jean-Claude using publically available hosted services. Our Blog based notebook which is a custom built and somewhat closed system. And Jeremiah uses Tex to generate a PDF of the whole thing. Jeremiah’s presentation included the comment that he had shown several people both a Wiki and the Tex based system and they had all preferred the Tex based one. This is the opposite of my experience where people seem to prefer whatever is closest to Word. This may be different communities or maybe just different people we have had contact with.

My feeling is that the three groups have evolved different systems because of three main things. Firstly a different initial aim, my initial aim for instance was not really an open notebook but an effective means of capturing data and procedures. Secondly differences in the procedures being carried out and the culture we work within. I am still slowly working my way through putting up Exp098 from UsefulChem in our blog system and this is certainly showing up some differences but I’m not sure I know what they mean yet.

Finally I think we have a different view of what the lab book is and what the ‘ideal’ lab book would look like. Jeremiah’s point was that he, and others, wanted it to ‘look like a lab book’, which is fair enough. I think my group is somewhere in the middle and Jean-Claude has pushed the idea of what a lab book is one step further. The finished product is a summary of the experiment – not precisely a point by point record of everything that happened along the way, that is all in the history tab – but the visual product is a clear description of the experiment that is immediately accessible to an outsider as to how to repeat the experiment and what the data and conclusions were. The point is,within the wiki framework, there is no need to worry about editing the page because the history is all still there. This means that it can be taken from the record as it goes – which is still kept – right through to ‘finished’ in a form that can go straight into a thesis or paper. I’m still not entirely comfortable with this, but I’m not entirely sure that this is particularly logical.

In any case in the end I think it will depend on what you want and why you want to go down the ONS route. There’s still a lot of work to be done.

Limits to openness

There was a discussion on where the boundaries should lie as to what can be open or not. I will handle this in another post because I think this is something I want to think about quite hard.

Postscript

On my way into work on Thursday last week I bumped into one of my RAL colleagues who, among other things, works on our communications and public relations. He thought that the ‘talk’ in SL made a nice little story and went to our central STFC comms people to see whether he might place it somewhere (website, newsletter, etc). Apparently the answer came back that they wouldn’t issue a press release (which would have been rather over the top in any case) because we didn’t have an institutional policy on Open Access.

Postscript 2

Jean-Claude has also reviewed the session at the UsefulChem Blog.