UsefulChem project: Open source chemical research with blogs and wikis

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Presentation transcript:

UsefulChem project: Open source chemical research with blogs and wikis Jean-Claude.Bradley@drexel.edu September 14, 2006 American Chemical Society National meeting in San Francisco

Where is Science headed? WE ARE HERE

The Robot Scientist

How will this happen? Self-organizing reduntant processes Agents can participate with zero or near-zero cost (free hosted services) Fully Open Access (Read and Write) Publication of all aspects of the scientific process: Open Source Science

How can machines know what is important? Ask the humans

UsefulChem Blog

What chemists think is important in 2005

Find-A-Drug

Diketopiperazine Library First iteration: Solid Support Synthesis Evolves to: on pot Ugi reaction/cyclization

The Molecules Blog

The Experiments Blog

Comments from peers

The UsefulChem Wiki

Telling the story of the failures

Experiments moved to wiki

Experiment History

Experiment Edits

Third Party Time-Stamp on Experiment Versions

Monitoring experimental progress

How are people finding our experiments?

Molecules found by InChI

Automation in UsefulChem

CMLRSS feed on Bioclipse

CMLRSS feed on Bloglines

The value of peer review in finding information Before Internet -> “pre-validation” saves time when searching is laborious Fewer publications to keep track of After Internet -> online availability is more valuable when searching is fast and easy Many new publications - who are the peers?

The value of peer review in academia These are two separate problems: Communicating science Justifying the value of scholarship

Open science connectivity More info on open source science here http://usefulchem.wikispaces.com

Extending the interaction outside of science

Next Steps Incorporate our molecules into Emolecules to enable substructure searching Custom CMLRSS feeds (e.g. only new commercial sources found) Get spectra in JCAMP format Extend our collaboration with other chemists (e.g. docking data) Get our anti-malarials made and tested

Acknowledgments Khalid Mirza (grad student) James Giammarco (undergrad) Lin Chen (undergrad) Dave Strumfels (cheminformatics) Bloggers (Egon Willighagen, Peter Murray-Rust, etc.)