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Open Notebook Science Jean-Claude Bradley Nov 11, 2008 Drexel iSchool 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Open and Closed Science  Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook  Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures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
Motivation:  Faster Science,   Better Science
Where is Science headed? WE ARE HERE
There are NO FACTS,  only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
TRUST PROOF
The solubility of 4-chlorobenzaldehyde
The Log makes Assumptions Explicit
The Rationale of Findings Explicit
Raw Data Made Public Splatter? Some liquid
YouTube for demonstrating experimental set-up
Calculations Made Public on  Google Spreadsheets
Revision History on  Google Spreadsheets
Wiki Page History
Comparing Wiki Page Versions
Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
Indexing Molecules on Google
Linking to Molecules in Chemistry Databases
Experimental Spectra and User-Deposited Data on ChemSpider
Crowdsourcing Solubility Data
Solubility Experiments
“ Validated” Solubilities in Google Spreadsheet
Rajarshi Guha’s Live Web Query using Google Viz API
Pierre Lindenbaum’s Solubility Data as RDF Triples
Results and Workflows in Machine-Friendly Format
UsefulChem Workflows in myExperiment
Experiments in Chemical Markup Language
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.
Malaria Target: falcipain-2  involved in hemoglobin metabolism Dana.org
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 Docking Procedure  (Rajarshi Guha)
Link to Docking Results:  Lists of SMILES in GoogleDocs  (Rajarshi Guha)
Comparing Experiments Ugi Master Table
Concentration (0.4, 0.2, 0.07 M) Solvent (methanol, ethanol, acetonitrile, THF) Excess of some reagents (1.2 eq.) Reaction to Optimize
Mettler-Toledo MiniMapper
Mettler-Toledo MiniBlock System
XML reports from MiniMapper robot
GoogleDoc to program and report
Paper written on Wiki
References to papers, blog posts, lab notebook pages, raw data
ChemSpider Automated Mark-up of Chemical Names
Paper on Journal of Visualized Experiments (JoVE)
Pre-print on Nature Precedings
Reaction Optimization Visualization in Second Life
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!
 
Collaborative Drug Discovery (CDD) Database
Outcome of Guha-Bradley-Rosenthal collboration
Gus Rosania’s Notebook
Cameron Neylon’s Notebook
Acknowledgements Khalid Mirza (Drexel) Kevin Owens (Drexel) Tim Bohinsky (Drexel) James Giammarco (Drexel) Tom Osborne (Mettler-Toledo) Antony Williams (ChemSpider) Andrew Lang (Oral Roberts U.) Cameron Neylon (Southampton U.)

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