#solo2010: Green Chain Reaction – update and more volunteers!

Dictated into Arcturus

A brief update of the Green Chain Reaction.

Viewed in the light of normal projects with Gantt charts, milestones, etc. the GCR project is completely mad. There is very little formal support other than the excellent wikis provided by the conference organizers. It relies almost completely on volunteer contributions over which we have no moral or other control. People promise what they can when they can, but often they find that they can't deliver. There's no shame in that whatever. We all have day jobs, including myself. It's just that it's such a wonderful opportunity to do something new and exciting.

What is fantastic it is that we have had already a number of really valuable offers and I have no doubt that we will continue to get more.

I could reasonably count on Jean-Claude Bradley and Mat Todd and today I shall be exploring how they manage reactions and seeing if we can come up with a common representation. This will also be closely coupled to our own work on the JISC funded AMI project. But the other offers have been unexpected and delightful.

Heather Piwowar, who is very well known for her work on the value of Scientific Data, has offered significant help. She has been a tireless campaigner for making scientific content openly available. She's also approved the pragmatic and utilitarian value of doing so. This is not the place to do justice to her work, but he is a recent blog post (https://researchremix.wordpress.com/2010/07/05/studying-reuse-of-geo-datasets-in-the-published-literature/ )

The real value-add of data archiving, though, is in the potential for more efficient and effective scientific progress through data reuse. There have been many calls to quantify the extent and impact… to do a cost/benefit analysis. An estimate of value of reuse would help to make a business case for repository funding, an ethical case for compelling investigators to bear the personal cost of sharing data, and clarify that sharing even esoteric data is useful — as the Nature Neuroscience editorial Got Data? puts it, "After all, no one ever knocked on your door asking to buy those figurines collecting dust in your cabinet before you listed them on eBay."

The GCR project is looking at re-use and Heather's contribution will be invaluable.

We've also had two amazing offers of computing support. I have already mentioned Dan Hagon, but yesterday we also got an offer from Mark W:

Mark W says:

August 10, 2010 at 10:05 pm  (Edit)

I'm no chemistry expert (more bioinformatics) but can contribute Java coding and/or computing power. Please get in touch if I can help with either!

This is brilliant. I have put Dan and Mark in touch and pointed them at the first batch of data and code to see if they can get this working. They both have experience with high throughput computing and these will be magnificent for the project.

We've also had three contributions about the greenness of the project. I have already mentioned Rob Hanson and the tools that he has built.

Please keep the contributions coming. Today I shall concentrate on making sure that the next batch of code is likely to work, and also that we have a good formal representation for the chemical reactions.

I'm confident that we will get many more volunteers and that between us we will be able to show not only that there is significant value in the published literature but also that A rapidly convened group of committed people can make enormous progress.

Why do I believe this? Because of a wonderful project over 10 years ago that produced the SAX specification for XML. In only one month (see http://www.saxproject.org/sax1-history.html ) a group of people on the xml-dev mailing list had created and tested a de facto standard which now runs on every computer on the planet. There is no reason why the same dynamics should not apply to this project.

A month is a long time in an enthusiastic group of collaborators.


This entry was posted in Uncategorized. Bookmark the permalink.

3 Responses to #solo2010: Green Chain Reaction – update and more volunteers!

  1. Pingback: Twitter Trackbacks for Unilever Centre for Molecular Informatics, Cambridge - #solo2010: Green Chain Reaction – update and more volunteers! « petermr’s blog [cam.ac.uk] on Topsy.com

  2. Peter, as I always I'd love to contribute to open initiatives... but the coming few weeks I just do not have time :(

    If there is a really targeted question regarding Bioclipse or CDK let me know though...

    • pm286 says:

      Thanks. The main thing we may face is mapping reactants and products though I don't think we shall need to. So it will be a specific questions

Leave a Reply

Your email address will not be published. Required fields are marked *

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>