Tuesday, November 04, 2008

Drexel iSchool Open Notebook Science Talk

I'll be speaking on November 11, 2008 at 12:30 in Rush-014 at the Drexel iSchool. Based on the audience I'll focus more on the technology aspects of UsefulChem and go light on the chemistry. Thanks to Bob Allen for the invitation.

Open Notebook Science: a stepping stone toward automation of the scientific process

The communication of research in a transparent manner in as close to real time as possible has been termed "Open Notebook Science" (see Wikipedia entry for more details). The basic philosophy is that researchers keep to a minimum the amount of private information. By making available all relevant raw data and making the analysis transparent, the scientific process can migrate from validation heavily based on trust to one dependent upon proof. A case will be made that such an approach, coupled with zero read/write costs on the open web is ideal for further automation of the scientific method using distributed intelligence. As an example the UsefulChem project, an ONS initiative mainly focussed on the synthesis of anti-malarial compounds, will be described. The project makes use of free hosted tools as much as possible so that the infrastructure can be easily replicated by other research groups. For example, CDD is used to store assay results, ChemSpider is used to store characterization information and enable chemical database queries, Wikispaces is used to record the laboratory notebook, Blogger is used to summarize research progress and GoogleDocs are used to store tabular data. Such an open architecture is conducive to productive collaboration between groups of complementary competency. For example, the design, synthesis and testing of novel anti-malarial agents, bringing together groups from Indiana University, Drexel University and UCSF, will be detailed.

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