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.)