Having just posted that there didn’t seem to be too much of this we have a talk in the Social Sciences parallel session that covers exactly this. Continue reading “Web2.0 tools for Social Sciences at AHM2007”
Distributed data
Some responses to John Wood’s talk on e-science infrastructure at AHM2007. Continue reading “Distributed data”
Themes at the All Hands Meeting
Some themes seem to emerge to me from the talks I have been to. Continue reading “Themes at the All Hands Meeting”
AHM2007 Medical E-science session
Brief notes on this parallel session from E-science all hands meeting on Tuesday morning. Continue reading “AHM2007 Medical E-science session”
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.
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!
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.
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.
Through a PRISM darkly
I don’t really want to add anything more to what has been said in many places (and has been rounded up well by Bora Zivkovic on Blog Around the Clock, see also Peter Suber for the definitive critique, also updates here and here). However there is a public relations issue here for the open science movement in general that I think hasn’t come up yet.
PRISM is an organisation with a specific message designed by PR people which is essentially that ‘Mandating Open Access for government funded science undermines the traditional model of peer review’. We know this is demonstrably false in respect of both Open Access scientific journals and more generally of making papers from other journals available after a certain delay. It is however conceivable, for someone with a particularly twisted mindset, to construe the actions of some members of the ‘Open Science Community’ as being intended to undermine peer review. We think of providing raw data online or using blogs, Wikis, pre-print archives or whatever other means to discuss science as an exciting way to supplement the peer reviewed literature. PRISM, and other like-minded groups, will attempt to link Open Access and Open Science together so as to represent an attempt by ‘those people’ to undermine peer review.
What is important is control of the language. PRISM has focussed on the term ‘Open Access’. We must draw a sharp distinction between Open Access and ‘Open Science’ (or ‘Open Research‘ which may be a better term). The key is that while those of us who believe in Open Research are largely in favour of Open Access literature, publishing in the Open Access literature does not imply any commitment to Open Research. Indeed it doesn’t even imply a commitment to providing the raw data that supports a publication. It is purely and simple a commitment to provide specific peer reviewed research literature in a freely accessible form which can be freely re-used and re-mixed.
We need some simple messages of our own. Here are some suggested ideas;
‘Open Access literature provides public access to publicly funded research’
‘Publically supported research should be reported in publically accessible literature’
‘How many times should a citizen have to pay to see a report on research supported by their tax dollars?’
‘Open Access literature improves the quality of peer review’
Emphasis here is on ‘public’ and ‘literature’ rather than ‘government’ and ‘results’ or ‘science’
I think there is also a need for some definitions that the ‘Open Research Community’ feels able to sign up to. Jean-Claude Bradley and Bertalan Mesko are running a session in Second Life on Nature Island next Tuesday (1600 UTC) which will include a discussion of definitions (see here for details and again the link to Bill Hooker’s good discussion of terminology). I probably won’t be able to attend but would encourage people to participate in whatever form possible so as to take this forward.
Southampton blog notebook at UK All Hands E-science meeting
Just a short note to say we will be doing a demonstration of the blog notebook at the UK E-science All Hands meeting being held in Nottingham in a few weeks time. We will be on the BBSRC stall at 13:40 on Wednesday 12th September assuming everyone else runs to schedule. If you are at the meeting do drop in and say hello.