UPennONS

Open Notebook Science and other Science2.0 Approaches to Communicate Research Jean-Claude Bradley January 21, 2010 University of Pennsylvania Associate Professor of Chemistry Drexel 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

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 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

Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)

Link to Docking Procedure (Rajarshi Guha)

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

NMR game in Second Life (Andy Lang)

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

Rajarshi Guha and Andy Lang: Chemical Space Explorer

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

The Robot Scientist

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)

Solubility prediction can generate requests for additional measurements

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

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

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)

Educational “Open Notebooks”

Crowdsourcing ChemInfo Resource Collection

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

The ONS backup spreadsheet and ONSPreserver (Andy Lang)

Publishing Google Spreadsheets as XLS

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....

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 )

Possible role for libraries: citation to objective third party archives of digital scholarship

More about the ONSarchive project:

UPennONS

by Jean-Claude Bradley

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UPennONS

by Jean-Claude Bradley

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Categories

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UPennONS Presentation Transcript

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