Tuesday, September 25, 2007

ONS Case Studies

We had about a dozen participants at the Open Notebook Science Case Studies SciFoo Lives On session yesterday.

I talked about using a free and hosted blog (Blogger), wiki (Wikispaces), referral tracker (Sitemeter), mailing list (Google Groups), molecule database (ChemSpider) and raw data visualization (JSpecView) for managing UsefulChem.

Cameron Neylon described the use of blogs to track research in his group. In his approach each post is an object with a unique ID. His system will probably be more amenable to being read by automated agents and ultimately I would like to see something similar with the UsefulChem wiki experiment pages, although for the time being, we'll stick to freeform lab page entry that is easy to be read by humans. Cameron is now in the process of representing our experiment pages with his system and it will be interesting to see how it comes out. At the very least we are both learning from the exercise about how science is done and recorded in different fields by different researchers.

Jeremiah Faith also presented his system based on LaTeX. Jeremiah first used it privately to keep track of his research and then recently made it public. His lab notebook is now 400 pages. His advisor had no problem with letting him open his notebook to the world. It made me wonder if it would be worthwhile keeping a list of "Open Science Friendly" faculty on the SFLO wiki for students now looking for postdocs. I think there are probably several researchers who are not interested in actively pursuing some form of Open Science but would not have an objection to members of their group indulging in the practice.

Here is the transcript of the session.

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At 4:41 PM, Blogger J said...

Thanks again for the speaking invitation. Although I was initially skeptical of the utility of giving a "virtual talk". I was really impressed to find more debate and discussion in the virtual world conference than in a real world one. Typing is a drag for the talk itself though...

I think an Open Science Friendly faculty list would be hard to generate (what would you do, send around an email?). Though an anonymous survey might be useful (e.g. 100 professors in 3-5 different fields) to at least get a feel for what prevents open notebook science (i.e. extra effort required, reluctant professors, reluctant students, or just never considered the idea). Such a survey might even make an interesting open science editorial publication.

Is there at least a list somewhere of all of the current open science notebooks? I think having a dedicated page for such a list would be useful. Perhaps in a year or two the page could even include a plot of # of open notebooks -vs- year.

At 2:51 PM, Anonymous Anonymous said...

Thanks for organising the session. I think that an Open Science faculty list would be a great idea. I can see it might be difficult to implement but a combination of adding people as they can be asked and letting people add themselves might be effective.

I think it should also distinguish between different levels. This might vary from 'happy to allow ONS (some specific projects excluded)' through to 'requires ONS for group members'.

In this case I think a Wiki is definitely the best place to put such a list! Could go on the existing nodalpoint pages or OpenWetWare or another WikiSpaces Wiki.

I also like the idea of a list of current open science notebooks. There is a cute tool being developed at MIT called timelines (http://simile.mit.edu/timeline) which someone might be able to configure to automatically generate the plot Jeremiah suggests. This might provide a nice demo of the potential of having stuff open.

At 12:21 PM, Blogger J said...

I think both the faculty list and the open notebook list would work well as individual wiki pages. That way folks could add their names as they find the page.

I've use that timeline tool to organize my personal photo album. It won't really let you plot the number of open science notebooks as a function of time. But it is a pretty cool way to make a timeline of the history of open notebook science. I don't think we need that plot now anyways, since I think we can count the number of open science notebooks on one hand.

At 4:20 PM, Blogger Jean-Claude Bradley said...

J - I have listed all of the systems that are close enough to Open Notebooks on the front page of our wiki - let me know if you come across any others.

At 9:01 AM, Anonymous Anonymous said...

Jeremiah, there's a new version of timelines called timeplot (simile.mit.edu/timeplot) that does do exactly that - if we congregated around an appropriate tag it might actually be do-able at some point


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