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NIST Dec08 Open Notebook Science Talk

NIST Dec08 Open Notebook Science Talk



Jean-Claude Bradley presented on Open Notebook Science at the NIST Social Media Day on December 11, 2008. The talks starts with an overview of ONS and how it is being used to assess solubility ...

Jean-Claude Bradley presented on Open Notebook Science at the NIST Social Media Day on December 11, 2008. The talks starts with an overview of ONS and how it is being used to assess solubility measurements being crowdsourced in the ONS Challenge and Submeta Awards. The use of wikis, blogs, Google Spreadsheets, YouTube, Flickr, ChemSpider and other free hosted Web2.0 tools is highlighted. The UsefulChem project, involving the synthesis of anti-malarial agents, is then briefly covered. Finally, a very recent application of using Google Spreadsheets to automatically call web services to calculate volumes and weights of chemicals needed in reactions is demonstrated (code by Rajarshi Guha).



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    NIST Dec08 Open Notebook Science Talk NIST Dec08 Open Notebook Science Talk Presentation Transcript

    • Open Notebook Science Jean-Claude Bradley Dec 11, 2008 NIST 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    • Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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
    • 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
    • ONS Challenge Students
    • ONS Challenge Judges
    • Solubility Experiments
    • Solubilities collected in a 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!
    • Exploring Solubility in Second Life (Andy Lang)
    • Collaborative Drug Discovery (CDD) Database
    • Outcome of Guha-Bradley-Rosenthal collboration
    • Google Spreadsheet linked to Open Web Services = Chemistry Dashboard
    • Potential Trends for the Future of Chemistry Fast, Fuzzy, Open, Automated, Green, Crowdsourced, Simple (e.g. mix and filter)
    • 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.)