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Open Notebook Science for Collaborative Drug Development University of Manchester Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University Sept 5, 2008 Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) RESEARCH OPEN CLOSED TEACHING Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks 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 vanillin glucose NaCl 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 Round one •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….. UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Docking Tsu-Soo Tan Nanyang Inst. Synthesis Testing Dan Zaharevitz NCI (tumors) Architecture: Distributed, Interlinked and Redundant BLOG CDD WIKI Nature Precedings FriendFeed JoVE ChemSpider GoogleDocs Mailing List 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? Specific Compounds 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 Experimental Conditions 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" How are people finding UsefulChem? Educational 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? Big Picture 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 How Should Open Notebook Science be Used? How did this experiment evolve? Third party timestamp http://usefulchem.wikispaces.com/page/diff/Exp037/1577428 Comparing wiki page versions http://usefulchem.wikispaces.com/SO+Research+Report 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 2.1-2.3 (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 Standardize second In a Science2.0 world redundancy is king