crowdsourcing solubility using open notebook science
DESCRIPTION
Jean-Claude Bradley presents at the American Chemical Society on August 16, 2009. The talk starts with highlighting how Open Notebook Science has been used to shed light on the recent report of using sodium hydride (NaH) as an oxidant. Next the Open Notebook Science Challenge is described, where ONS coupled to crowdsourcing is used to measure and share non-aqueous solubility data. Recent developments in using bots to contribute to the scientific process and applications to the Ugi reaction are mentioned.TRANSCRIPT
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
The NaH oxidation controversy
Information spreads quickly through the blogosphere
15% NMR yield
Khalid Mirza and Marshall Moritz
Top results on a Google search
Motivation: Faster Science, Better Science
Open Notebook Science Logos (Andy Lang, Shirley Wu)
Sharing: how much and when
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 YouTube for demonstrating experimental set-upset-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
Linking to Molecules in Chemistry Databases
Experimental Spectra and User-Deposited Data on ChemSpider
(Andy Lang, Tony Williams)
Open Data JCAMP spectra for education
(Andy Lang, Tony Williams, Robert Lancashire)
Crowdsourcing Solubility Data
ONS Submeta Award Winners
ONS Challenge Judges
Teaching Lab: Brent Friesen (Dominican University)
Solubility Experiment List
Solubilities collected in a Google Spreadsheet
Rajarshi Guha’s Live Web Query using Google Viz API
Rajarshi Guha and Andy Lang: Chemical Space Explorer
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)
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
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
Crowdsourcing Reaction Requests: DoUgi sheet
Understanding in addition to empirical modeling
Missed in a prior publication on
solubility for this compound
Data provenance: From Wikipedia to…
…the lab notebook and raw data
Including links to the literature
Pierre Lindenbaum’s Solubility Data as RDF Triples
•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?
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
Paper on Journal of Visualized Experiments (JoVE)
Pre-print on Nature Precedings
ChemSpider Automated Mark-up of Chemical Names
Cameron Neylon’s NotebooksCameron Neylon’s Notebooks
Other Open NotebooksOther Open Notebooks
Anthony Salvagno’s Notebook Anthony Salvagno’s Notebook (Steve Koch group)(Steve Koch group)
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.)