OpenSciNY Open Notebook Science

Open Notebook Science Jean-Claude Bradley May 14, 2010 OpenSciNY Associate Professor of Chemistry Drexel University

What is a Scientific Precedent? What is a Scientific Publication? What is Peer Review? What is Scholarship?

Asked to Review an Article…

“ I would never consider a claim made in a patent as blocking an author's claim of novelty.” Langmuir Editor What is a Scientific Precedent in Academia? What is a Scientific Precedent in Patent Law?

Chemistry Preprint Archive (Elsevier)

What is Scholarship?

What is Peer Review?

The Scandal of Bell’s Lab Notebook

How bad is our current system? Try to find the solubility EGCG?

=2.3 g/L WTF?!

The End of the Chain of Provenance

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 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

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)

Database Curation via Game Playing

Over 100,000 spectrum views so far - worldwide

Link Spectral Game to Open Educational Content

The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?

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

WE ARE HERE How can the scientific process become more automated?

Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (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

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

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?

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

BUT… Open Access: the Choice that Keeps Giving.. and Giving…

Beware of your addiction to metrics: redundancy will reduce them

Cameron Neylon’s Notebooks Other Open Notebooks

Anthony Salvagno’s Notebook (Steve Koch group)

Archiving and Libraries
Automatic Backup of Science 2.0 Data
Archiving of Open Notebooks
Science 2.0 Community Needed Resources - Preservation, Cataloging, Archiving, Cite-ability

Librarians and Science 2.0 "The Internet Archive is a 501(c)(3) non-profit that was founded to build an Internet library, with the purpose of offering permanent access for researchers, historians, and scholars to historical collections that exist in digital format." The internet Archive is not practical for practitioners of Open Notebook Science or Science 2.0

Good concept but.....

Most pages look like this....

Where We Began: The ONS backup spreadsheet and ONSPreserver

Publishing Google Spreadsheets as XLS

ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record

Snapshot is Self-Contained and Live on the Internet

Lulu.com Data Disks

DSpace – Handle (hdl)

Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL:http://spreadsheets.google.com/pub?key=plwwufp30hfq0udnEmRD1aQ&output=xls. Accessed: 2009-12-11. (Archived by WebCite® at http://www.webcitation.org/5lx5ry3BV )

Lulu.com - ISBN Google Spreadsheets Google Documents Web Services ChemSpider & Indiana Real Time Linear Regression, Unit Conversions, Style Sheet, etc Data Book

Solubility Prediction (Andy Lang uses Abraham Model)

Reaction Attempts Book

Reaction Attempts Book: Reactants listed Alphabetically

For all Formats of ONS Projects

Conclusions
Is our current system working? NO
Is ONS difficult or expensive to implement? NO
Does ONS prevent peer-reviewed publication? NO – but depends of publisher
Can ONS data be easily discoverable? YES
Can ONS information be easily archived and cited? YES
Is ONS compatible with IP protection? Maybe to a limited extent

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OpenSciNY Open Notebook Science

by Jean-Claude Bradley on May 14, 2010

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OpenSciNY Open Notebook Science — Presentation Transcript