Equilibrium & Solubility: The Solubility Product Constant, Ksp
Crowdsourcing Solubility using Open Notebook Science
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Transcript of Crowdsourcing Solubility using Open Notebook Science
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Crowdsourcing non-aqueous solubility and synthesis using
Open Notebook Science
Jean-Claude Bradley
August 16, 2009
American Chemical Society meeting
Associate Professor of ChemistryDrexel University
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The NaH oxidation controversy
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Information spreads quickly through the blogosphere
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15% NMR yield
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Khalid Mirza and Marshall Moritz
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Top results on a Google search
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Motivation: Faster Science, Better Science
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Open Notebook Science Logos (Andy Lang, Shirley Wu)
Sharing: how much and when
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There are NO FACTS, only measurements embedded
within assumptions
Open Notebook Science maintains the integrity of data
provenance by making assumptions explicit
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TRUST
PROOF
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The solubility of 4-chlorobenzaldehyde
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The Log makes Assumptions Explicit
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The Rationale of Findings Explicit
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Raw Data Made Public
Splatter?
Some liquid
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YouTube for demonstrating experimental YouTube for demonstrating experimental set-upset-up
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Calculations Made Public on Google Spreadsheets
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Revision History on Google Spreadsheets
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Wiki Page History
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Comparing Wiki Page Versions
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Proof of Purity with interactive NMR spectrum using JSpecView and
JCAMP-DX
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Linking to Molecules in Chemistry Databases
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Experimental Spectra and User-Deposited Data on ChemSpider
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(Andy Lang, Tony Williams)
Open Data JCAMP spectra for education
(Andy Lang, Tony Williams, Robert Lancashire)
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Crowdsourcing Solubility Data
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ONS Submeta Award Winners
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ONS Challenge Judges
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Teaching Lab: Brent Friesen (Dominican University)
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Solubility Experiment List
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Solubilities collected in a Google Spreadsheet
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Rajarshi Guha’s Live Web Query using Google Viz API
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Rajarshi Guha and Andy Lang: Chemical Space Explorer
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Semi-Automated Semi-Automated Measurement of solubility via Measurement of solubility via
web service analysis of web service analysis of JCAMP-DX files JCAMP-DX files
(Andy Lang)(Andy Lang)
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Solubility Measurement Requests: DoSol sheet
•Outlier Bot: flags measurements with high standard deviation to mean ratios•Google Analytics queries – new solvent/solute searches•Solubility request form – researcher in Israel requesting pyrene in acetonitrile solubility for environmental soil contamination study•Application based models – high priority Ugi reactants
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Solvent mixture and temperature: multidimensional solubility data
Actual Data (4-nitrobenzaldehyde)
From quadratic regression of 5D space
Feeds DoSol Sheet the next points to measure to best cover the space
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Crowdsourcing Reaction Requests: DoUgi sheet
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Understanding in addition to empirical modeling
Missed in a prior publication on
solubility for this compound
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Data provenance: From Wikipedia to…
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…the lab notebook and raw data
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Including links to the literature
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Pierre Lindenbaum’s Solubility Data as RDF Triples
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•Concentration (0.4, 0.2, 0.07 M)•Solvent (methanol, ethanol, acetonitrile, THF)•Excess of some reagents (1.2 eq.)
How does Open Notebook Science fit with traditional publication?
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Mettler-Toledo MiniMapper
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Mettler-Toledo MiniBlock System
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XML reports from MiniMapper robot
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GoogleDoc to program and report
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Paper written on Wiki
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References to papers, blog posts, lab notebook pages, raw
data
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Paper on Journal of Visualized Experiments (JoVE)
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Pre-print on Nature Precedings
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ChemSpider Automated Mark-up of Chemical Names
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Cameron Neylon’s NotebooksCameron Neylon’s Notebooks
Other Open NotebooksOther Open Notebooks
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Anthony Salvagno’s Notebook Anthony Salvagno’s Notebook (Steve Koch group)(Steve Koch group)
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AcknowledgementsAcknowledgements Khalid Mirza (Drexel)Khalid Mirza (Drexel) Jenny Hale (Southampton U.)Jenny Hale (Southampton U.) David Bulger (Oral Roberts U.)David Bulger (Oral Roberts U.) Tim Bohinsky (Drexel)Tim Bohinsky (Drexel) Kevin Owens (Drexel)Kevin Owens (Drexel) Tom Osborne (Mettler-Toledo)Tom Osborne (Mettler-Toledo) Antony Williams (ChemSpider)Antony Williams (ChemSpider) Andrew Lang (Oral Roberts U.)Andrew Lang (Oral Roberts U.) Rajarshi Guha (Indiana U.)Rajarshi Guha (Indiana U.) Cameron Neylon (Southampton U.)Cameron Neylon (Southampton U.)