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

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

Very large problem: 300-500 million cases per year with one million deaths

Not a lucrative market: IP control less important

Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN

Where is Science headed? WE ARE HERE

The Robot Scientist

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 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

How can machines know what is important? Ask the humans

UsefulChem Blog

What chemists think is important in 2005

Find-A-Drug

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

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

usefulchem.blogspot.com The blog as an integrative tool

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

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

Processing Molecules on ChemSpider

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

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

UsefulChem and Open Science in Second Life scifooliveson.wikispaces.com