Open Notebook Science for Collaborative Drug Development Jean-Claude Bradley Sept 5, 2008 University of Manchester E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University

Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING

Motivations for ONS Faster Science Better Science

A recent example in Southampton Sept 3, 2008 usefulchem.wikispaces.com/exp207

Investigating solubilities in organic solvents Boc-glycine vanillinglucoseNaCl

The lab notebook page

The Log: No Insider Information

The Results in a GoogleDoc reliable unreliable

Representation in the Neylon notebook

Open Notebook Science Grand Challenge design procedures to determine the solubility of compounds in organic solvents teams or individuals welcome Open Notebooks will be validated by experts “mystery prizes” for creativity, productivity, reproducibility and other metrics of scientific quality details coming soon….. Round one

UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.

BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE

Where’s the Beef?

Link to Lab Notebook Page in Wiki

Link to Molecules

Link to Docking Procedure (Rajarshi Guha)

Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)

Link to Raw Data with JSpecView (data in JCAMP-DX format) (by Robert Lancashire)

Using ChemSpider to archive compound characterization

Conclusion is Fully Supported

Table of Contents

Indexing the Experiments in Google

Searching with Google Custom Search

How are people finding our experiments? NMR in TFA Phenylacetaldehyde c4h6o2 nmr methylene chloride/methanol h'nmr of benzophenone sulfuric acid pka tertbutylamine tosyl isocyanide amino furan dichloromethane polar? Reaction between Benzaldehyde and NaBH4 phosphoric acid pka veratraldehyde wiki kinetics boc deprotection Rf value in polar solvent why glycerol is immiscible with ether side reaction of imines 5.8 ppm nmr nmr cdcl3 chloroform side reaction diasterotopic wiki adding anhydrous MgSO4 to the dichlormethane ether extraction hnmr doublet of doublet Boc-protected NMR chromatotron recipe triplet cdcl3 "13c nmr" Specific CompoundsExperimental Conditions

How are people finding UsefulChem? free downloading chemistry video organic chemistry project + high school how to make poster in second life organic chem. quiz 3d periodic tables animation protein docking docking animation why are acid-base reactions exothermic? lysosomal targets protease and malaria cheminformatics project proposal automated reactions malaria review project synthesis CHEMISTRY WEB 2.0 projects on QSAR & drug design chemistry experiment results database EducationalBig Picture

How Should Open Notebook Science be Used?

How did this experiment evolve? Third party timestamp

Comparing wiki page versions

Comparing Experiments Ugi Master Table

YouTube for demonstrating experimental set-up

Older Males Prefer Organic Chemistry!

Mailing List Facilitates inter-group collaboration

Outcome of Guha-Bradley-Rosenthal collboration

Collaborative Drug Discovery (CDD) Database

Interacting with NMR spectra (JCAMP-DX) in Second Life

Talk to the spectrum: zoom (Andy Lang)

3D molecules in Second Life

Imine Formation Mechanism: talk to the molecules!

Gus Rosania’s Notebook

Cameron Neylon’s Notebook

Results in Machine-Friendly Format

Mettler-Toledo MiniMapper

Mettler-Toledo MiniBlock System

GoogleDoc to program and report

XML reports from MiniMapper robot

Writing Code in the Murray-Rust House

Experiments in Chemical Markup Language

Paper written on Wiki

References to papers, blog posts, lab notebook pages, raw data

Pre-print on Nature Precedings

Methanol 0.4M xs of imine best

Paper on Journal of Visualized Experiments (JoVE)

Where is Science headed? WE ARE HERE

Conclusion Communicate first Communicate first Standardize second Standardize second In a Science2.0 world redundancy is king In a Science2.0 world redundancy is king