Monday, August 02, 2010

Berkeley Open Science Summit 2010 Notes

I just returned from the Open Science Summit held at Berkeley July 29-31, 2010.

There certainly was an impressive list of presenters as well as attendees. Many of the talks were quite good, although several on the last day were more about closed collaborations than Open Science. During these presentations the assumption that patents are required to exploit discoveries in health care was repeated. This was in sharp contrast to the second day's session on gene patents, where IP protection was shown to stifle innovation and the exploitation of discoveries.

A refreshing exception to this pattern on the last day was Andrew Hessel's presentation on the Pink Army Cooperative. Andrew's strategy to cure cancer is based on the idea of customizing drugs for each individual affected by the disease. Since each drug is only applicable to one individual, the approach of expensive clinical trials doesn't apply. Since he is not interested in generating a profit from selling the drugs, IP protection also doesn't apply and allows him to make every part of the drug design process, including genetic analysis, publicly available. It wasn't clear if such an approach would be legal in the US but he did mention going to another country if necessary. Although he didn't currently have cancer, he did indicate that he might have need of this technology one day by pulling out a pack of cigarettes in the middle of his talk.

Unfortunately my panel on Open Data was canceled at the last minute due to time management problems (see FF discussion on how it happened). However, I did have a chance to generally catch up with old friends (Carmen Drahl, Joanna Scott, Cameron Neylon, Jack Park).

I also discussed some promising collaborations with several people:

1) CoLab. I spoke at length with DJ Sprouse and Casey Stark about their system for scientific collaboration. We will try to represent one solubility experiment from the ONS Challenge notebook and one organic synthesis experiment from the UsefulChem notebook to see how the information can be represented within CoLab. There may be some opportunities to visualize raw data in new ways - perhaps using non-Java tools to interact with JCAMP-DX spectra.

2) IPzero Principles. I continued a conversation with Lisa Green started with John Wilbanks and Thinh Nguyen at Creative Commons about coming up with a series of simple recommendations for ensuring that an Open Notebook can effectively prevent the patenting of inventions within an area of interest to the Open Science community.

3) Open Chemistry Reactions. I had the chance to discuss our Reaction Attempts database with Peter Murray-Rust over breakfast on Saturday. He also showed me how he is using Oscar to extract chemical reaction information from various documents. Peter suggested that we pool together our data for a demonstration in September at the London Science Online Conference. Reaction Attempts will cover the reactions done in the UsefulChem and the Todd group's Open Notebooks. Peter will extract information from both patents and Acta Crystallographica.

4) ChemTaverna. I was pleased to learn from Carole Goble that Taverna is extending its coverage to cheminformatics applications with the ChemTaverna project. I had just mentioned that we would be interested in revisiting Taverna for creating virtual libraries of organic compounds and filtering them based on predicted solubilities in various solvents. This would allow us to contribute cheminformatics workflows to MyExperiment. Carole put me in touch with the project leader Peter Li at the University of Manchester.

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