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IGERT Drexel Open Notebook Science Talk
 

IGERT Drexel Open Notebook Science Talk

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Jean-Claude Bradley presents "Open Notebook Science as an efficient means for transparency in science" on April 15, 2011 at the Drexel Nanotechnology Institute IGERT Meeting.

Jean-Claude Bradley presents "Open Notebook Science as an efficient means for transparency in science" on April 15, 2011 at the Drexel Nanotechnology Institute IGERT Meeting.

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    IGERT Drexel Open Notebook Science Talk IGERT Drexel Open Notebook Science Talk Presentation Transcript

    • Open Notebook Science as an efficient means for transparency in science
      IGERT Drexel Meeting
      Jean-Claude Bradley
      Department of Chemistry
      Drexel University
      April 15, 2011
    • The current state of transparency in scientific communication
      Case study of melting point data
    • The Chemical Information Validation Sheet
      567 curated and referenced measurements from
      Fall 2010 Chemical Information Retrieval course
    • The Chemical Information Validation Explorer
      (Andrew Lang)
    • Discovering outliers for melting points (stdev/average)
    • Investigating the m.p. inconsistencies of EGCG
    • Investigating the m.p. inconsistencies of cyclohexanone
    • Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting points
    • Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling points
    • Sigma-Aldrich, Acros and Wolfram Alpha apparently
      DO NOT use the same sources for flash points
    • Most popular data sources
    • Alfa Aesar donates melting points to the public
    • Open Melting Point Explorer
    • Outliers
      MDPI
      dataset
      EPI (via ChemSpider)
    • Outliers
      Alfa Aesar
    • Inconsistencies and SMILES problems within MDPI dataset
    • MDPI Dataset labeled with High Trust Level
    • Open Melting Point Datasets
    • Open Random Forest modeling of Open Melting Point data using CDK descriptors
      (Andrew Lang)
      R2 = 0.78, TPSA and nHdon most important
    • Melting point prediction service
    • Using melting point for temperature dependent solubility prediction
    • Motivation: Faster Science,Better Science
    • There are NO FACTS,
      only measurements embedded within assumptions
      Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
    • TRUST
      PROOF
    • Strategy for an Open Notebook:
      First record then abstract structure
      In order to be discoverable use Google friendly formats (simple HTML, no login)
      In order to be replicable use free hosted tools (Wikispaces, Google Spreadsheets)
    • Crowdsourcing Solubility Data
    • Data provenance:
      From Wikipedia to…
    • …the lab notebook and raw data
    • Calculations Made Public on
      Google Spreadsheets
    • Interactive NMR spectra using JSpecView and JCAMP-DX
    • Raw Data As Images
      Splatter?
      Some liquid
    • YouTube for demonstrating experimental set-up
    • The importance of raw data availability
      Missed in a prior publication on solubility for this compound
    • Solubilities collected in a Google Spreadsheet
    • Rajarshi Guha’s Live Web Query using Google Viz API
    • Web services for summary data
      (Andrew Lang)
    • Web service calls from within a Google Spreadsheet for solubility measurement and prediction
      (Andrew Lang)
    • Integration of Multiple Web Services to Recommend Solvents for Reactions
      (Andrew Lang)
    • Reaction Attempts Book
    • Reaction Attempts Book: Reactants listed Alphabetically
    • ONS Challenge Solubility Book cited for nanotechnology application
    • Lulu.com Data Disks
    • Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd and Bradley)
      (Don Pellegrino)
    • All ONS web services
    • For all Formats of ONS Projects
    • Conclusions
      • Our current system of publication is not as transparent as it could be
      • Open Notebook Science offers an efficient way to make research transparent and discoverable