Science Commons Open Notebook Science Talk

Using Free Hosted Web2.0 Tools for Open Notebook Science Jean-Claude Bradley February 20, 2010 Science Commons Symposium Associate Professor of Chemistry Drexel University

The case for Open Notebook Science
Is our current system working?
Is ONS difficult or expensive to implement?
Does ONS prevent peer-reviewed publication?
Can ONS data be easily discoverable?
Can ONS information be easily archived and cited?
Is ONS compatible with IP protection?

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

The Scandal of Bell’s Lab Notebook

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

Solubility Prediction (Andy Lang’s Model)

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)

Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING Where do Libraries fit in the communication of science and education in the Open/Closed Continuum?

The Missing Pieces of the Puzzle
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

Where We Are Now

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)

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

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 )

More about the ONSarchive project:

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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Science Commons Open Notebook Science Talk

by Jean-Claude Bradley on Feb 20, 2010

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Science Commons Open Notebook Science Talk — Presentation Transcript