Open Notebook Science and Malaria

Slide 1: Open Notebook Science and Malaria Chemists Without Borders Jean-Claude Bradley Drexel University September 6, 2007

Slide 2: Malaria is a Logical Application of Open Science •Very large problem: 300-500 million cases per year with one million deaths •Not a lucrative market: IP control less important

Slide 4: Open and Closed Science Open Notebook Science (full transparency) Open Access Journal Article Traditional OPEN Journal Article Traditional Lab Notebook (unpublished) CLOSED

Slide 5: Where is Science headed? WE ARE HERE

Slide 6: The Robot Scientist

Slide 7: How will this happen? Self-organizing redundant processes  Agents can participate with zero or near-  zero cost (free hosted services – e.g. Google) Fully Open Access (Read and Write)  Publication of all aspects of the scientific  process: Open Source Science / Open Notebook Science

Slide 8: How can machines know what is important? Ask the humans

Slide 9: UsefulChem Blog

Slide 10: What chemists think is important in 2005

Slide 11: Find-A-Drug

Slide 12: Diketopiperazine Library First iteration: Solid Evolves to: on pot Ugi Support Synthesis reaction/cyclization

Slide 13: The Molecules Blog

Slide 14: The Experiments Blog

Slide 15: Comments from peers

Slide 16: The UsefulChem Wiki

Slide 17: Telling the story of the failures

Slide 18: Experiments moved to wiki

Slide 19: Experiment History

Slide 20: Experiment Edits

Slide 21: Third Party Time-Stamp on Experiment Versions

Slide 22: Monitoring experimental progress

Slide 23: How are people finding our experiments?

Slide 24: Molecules found by InChI

Slide 25: The blog as an integrative tool usefulchem.blogspot.com

Slide 26: The wiki as the laboratory notebook usefulchem.wikispaces.com/Exp049

Slide 27: Graphical Mining of Data with JSpecView usefulchem.wikispaces.com/Exp070 (48h 7 min)

Slide 28: Processing Molecules on ChemSpider

Slide 29: The CombiUgi Project Focus on cheap starting materials and a product that precipitate easily from solution

Slide 30: Open Primary Research in Drug Design using Web2.0 tools (blogs, wikis, Second Life, mailing lists) Rajarshi Guha Tsu-Soo Tan Docking Indiana U Nanyang Inst. JC Bradley Synthesis Drexel U Phil Rosenthal Dan Zaharevitz Testing UCSF NCI (malaria) (tumors)

Slide 31: UsefulChem and Open Science in Second Life scifooliveson.wikispaces.com