Category: Blog

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Replication of UsefulChem Exp098 in the Southampton blog notebook

In a previous post I said I would try to replicate an experiment from the UsefulChem open Wiki notebook within our blog system to see how it might look. This post is to record what I am doing as I do it. Thus this is the lab book I am using to record the process and decisions I have taken in using a lab book. The pages in the notebook can be found at;

http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/15/

I have chosen to use Exp098 as this involved several different stages and modifications to the wiki page over many weeks. My aim is to try and record this in the way we would. This will involve some changes to the text and the process but I will try to re-use the original text as far as is possible. In the spirit of open notebook science I will make this visible as I go but as this may take me a while (days to a week or two) to finish this page is likely to be unstable and you may wish to come back to it. Ironically I am therefore using this notebook more in the way that Jean-Claude’s group use the Wiki than the way we use the blog.

  1. 13/09 16:58 UTC I have added two initial posts. In the first I have created a product from the previous notional reaction. Exp098 is a study on the stability of a previously generated compound, utilising a specific instance of that compound described in a previous experiment (Exp064). The second post is the initial description of the protocol. This is cut and pasted from the very first version of Exp098 and represents the experimental plan that I would put into the blog before going into the lab.
  2. In Exp098 the process is split into two phases, first a series of reagents are mixed and the reaction is monitored by NMR. After completion the reaction was neutralised and then extracted into organic solvent and dried before further analysis. Because analysis has been carried out on two different ‘samples’ I am therefore going to split the post up in what might appear to be a slightly odd way to an organic chemist. The first stage will generate one product, which will then be subject to analyses (further procedures). The first product will then be subjected to a second procedure (neutralization and drying) to generate a further product (the ‘real’ product) which will be subjected to further analysis.
  3. 13/09 17:20 UTC I have added the first procedure and product post. I now need to make a decision about whether I set up one post with all the NMR analysis from the time course in it or multiple analyses, one for each time point (I can do this with a template) with the data for each in that. Or I could set it up with one procedure post containing all the NMR descriptors but a separate product for each that contains the actual spectrum. I think the latter may be the best. This provides a way of scraping metadata for each of the spectra. It also means that the data can be added slightly later without directly editing the procedure post. I will create a new section for ‘Analysis’ to distinguish it from procedure.
  4. 17/09 13:06 UTC: I have now added all the NMR data for the time course. This was a laborious process obviously but it does meant that it is reasonably clear what goes where. For the separate HOMODEC experiment I didn’t bother putting the data in separately as this is obvious which goes with which. I haven’t as yet put in the NMR data for the starting material 064C which ought really to have been there first.
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The ‘inpenetrable’ OMII-UK workshop

Following on from the post yesterday I actually went along to the workshop with the title I didn’t understand. There was much I didn’t understand and a lot of technical terminology that went straight over my head. Terminology is an issue here, particularly where there is a desire to bring in new people. There is an argument that if I’m coming to this meeting it is incumbent on me to figure out the technical terms but if one of the themes of this meeting is expanding the reach of e-science to the ‘general science public’ then using terminology that could be simplified but still maintain a precise (enough) meaning then that is helpful.

It turns out that OMII-UK stands for Open Middleware Infrastructure Institute and that they are involved in sorting out and integrating software tools that are available or should be available and providing a central body that can look after people using these systems. Some of these are of potential use to interlink with our e-lab notebook, particularly Taverna and myExperiment, and I will be aiming to talk to the people involved about connecting these things up over the course of the meeting.

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UK E-Science all hands meeting – initial thoughts

If it hasn’t been obvious from what has gone previously I am fairly new to the whole E-science world. I am definitely not in any form a computer scientists. I’m not a computer-phobe either but my skills are pretty limited. It’s therefore a little daunting to be going for the first time to an e-science meeting. This is the usual story of not really knowing the people from this community and not necessarily having a clear idea of what people within the field or community think the priorities are.

The programme is available online and my first response on looking at it in detail was that I don’t even understand what most of the session titles mean. “OMII-UK” is a fairly inpenetrable workshop title for which the first talk is “Portalization Process for the Access Grid”. Now to be fair these are somewhat more specialised workshops and many of the plenary session names make more sense. This is normal when you go to an out-of-your-field conference but it will be interesting to see how much of the programme makes sense.

One of the issues with e-science programmes is the process of bringing the ‘outside’ scientist into the fold. Systems such as our lab e-notebook require an extra effort to use, certainly at the beginning, and during the development process there are often very few tangible benefits. Researchers are always time poor people so they want to see benefits. In theory we are here to demonstrate and promote our e-notebook system but I suspect this may be a case of preaching to the converted. It will be interesting to see a) whether we get much interest b) whether the comments we get are more on the technical implementation or the practical side of actually using it to record experiments.

One of the great things about starting this blog has been the way it has facilitated discussion with others interested in open notebook science and open science in general. I am less sure it has brought scientists who are interested in the details of the work in our notebook. My feeling is that this meeting may be a bit similar. On the other hand it may get us some good ideas on solving some of the problems of visualising the notebook that I want to discuss in a future post.

So if you are at the meeting and want to see the notebook please drop by to the BBSRC booth on Wednesday afternoon and do say hello if you see a shortish balding bearded guy who is looking lost or confused.

p.s. Thanks to whoever was running a meeting upstairs today. I didn’t realise I was stealing your lunch!

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When is open notebook science not?

Well when it’s not open obviously.

There are many ways to provide all the information imagineable while still keeping things hidden. Or at least difficult to figure out or to find. The slogan ‘No insider information’ is useful because it provides a good benchmark to work towards. It is perhaps an ideal to attain rather than a practical target but thinking about what we know but is not clear from the blog notebook has a number of useful results. Clearly it helps us to see how open we are being but also it is helpful in identifying what it is that the notebook is not successfully capturing.

I have put up a series of posts recently in the ‘Sortase Cloning‘ blog notebook. The experiments I did on 29th August worked reasonably well. However this is not clear from the blog. Indeed I suspect our hypothetical ‘outsider’ would have a hard time figuring out what the point of the experiment is. Certainly the what is reasonably obvious, although it may be hidden in the detail, but the why is not. So the question is how to capture this effectively. We need a way of noting that an experiment works and that the results are interesting. In this case we have used Sortase to do two things that I don’t believe have yet been reported, fluorescently label a protein, and ligate a protein to a piece of DNA. This therefore represents the first report of this type of ligation using Sortase.

Perhaps more importantly, how do we then provide the keys that let interested people find the notebook? UsefulChem does this by providing InChi and smiles codes that identify specific molecules. Searching on the code by Google will usually bring UsefulChem up in the top few searches if the compound has been used. Searching on ‘Sortase’ the enzyme we are doing our conjugation with brings up our blog at number 14 or so. So not bad but not near the top and on the second page not the first. For other proteins with a wider community actively interested the blog would probably be much further down. Good tags and visibility on appropriate search engines (whatever they may turn out to be) is fairly critical to making this work.

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How to get critical mass? Scifoo Lives on Session on Medicine and Web 2.0

I attended the session held on Nature Island as part of the Scifoo Lives On series being organised by Jean-Claude Bradley and Bertalan Mesko and wanted to record some of my impressions. The mechanics of the meeting itself were interesting. My initial reaction to the idea of meetings in Second Life was pretty sceptical. My natural inclination would have been to setup some sort of video cast or conference call. However there are advantages to the sense of actually having people milling around (and I apologise to all the people I bumped into or whose slides I inadvertantly changed). It was good to ‘meet’ Jean-Claude if not in the flesh then in the fur and the sense of actually seeing a person or at least a representation makes this somethow seem more natural.

The disadvantage was that as the dialogue is typed and at least on my connection was coming through quite slow it is difficult to have a real conversation. Several times I would start typing a question or comment and by the time I’d got through to the end the conversation seemed to have moved on. Audio would be better and this can be enabled but it would probably have its own problems with people talking over each other. Maybe we would need to learn to put our hands up? The advantage of SL is that it is a single package which once you’ve got working, gives you the slides, the talk, and the questions all in one package. I use video conferencing quite regularly for meetings but there are real issues with ensuring that participants are compatible with the package you are using – in practise it is almost entirely used either for internal (multi-site) meetings or one-to-one meetings via Skype or something similar.

The Scifoo Lives on session itself has been covered by Jean-Claude who also provides a transcript. An issue that came up with several of the posters is how big the community that supports them is or needs to be and how you go about growing that community. Sites that provide a ‘Wikipedia for Medical Information’ or a ‘digg for the bioscience literature’ are laudable efforts. Their succes, like that of other sites featured depends on a large enough community actively contributing to the site and providing added value. Wikipedia ‘works’ (not wishing to get into the argument about accuracy here) because an enormous number of people provide their time freely to add value. Arguably a number of other Wiki sites aimed at smaller communities have not achieved as much as hoped because the community support isn’t enough to provide critical mass. Its a tough world out there and competing sites will rise and fall but there is some critical mass required before they attract a big enough audience that the site builds itself.

This is also true of open research more generally. We are a long way from the critical mass that makes it worthwhile for people to put in a little bit of effort on a regular basis because they get a lot back. They key question to my view is what are the best steps to take that will put us on the right path as fast as is sensible. And where can we find some sociologists to help us on this? An argument for using the term ‘Open Research’ may be that we need the help of the social sciences community to figure out how best to proceed.