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Jean-Claude Bradley presents "Accelerating Discovery by Sharing: a case for Open Notebook Science" at the National Breast Cancer Coalition Annual Advocacy Conference in Arlington, VA on May 1, 2011.
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Accelerating Discovery by Sharing: a case for Open
Notebook Science
Jean-Claude Bradley
May 1, 2011
National Breast Cancer Coalition Annual Advocacy Conference
Associate Professor of ChemistryDrexel University
Outline
1. Trends in sharing for drug discovery
2. ONS for malaria research3. Crowdsourcing solubility with
ONS4. Leveraging the educational
system to contribute new science
5. Open modeling and web services
6. Discovering connections7. Moving forward: tools and
practices
Industry is Sharing More
Opportunities for Competitive Collaboration
Some Initiatives Promoting More Openness in Drug Discovery
Motivation: Faster Science, Better Science
There are NO FACTS, only measurements embedded
within assumptions
Open Notebook Science maintains the integrity of data
provenance by making assumptions explicit
TRUST
PROOF
First record then abstract structure
In order to be discoverable use Google friendly formats (simple HTML, no
login) In order to be replicable use free hosted tools (Wikispaces, Google
Spreadsheets)
Strategy for an Open Notebook:
UsefulChem Project:UsefulChem Project: Open Primary Open Primary Research in Drug Design using Web2.0 Research in Drug Design using Web2.0
toolstools
Docking
Synthesis
Testing
Rajarshi GuhaIndiana U
JC BradleyDrexel U
Phil RosenthalUCSF
(malaria)
Dan ZaharevitzNCI
(tumors)
Tsu-Soo TanNanyang Inst.
Malaria Target: falcipain-2 involved in hemoglobin metabolism
Dana.org
The Ugi Reaction
Outcome of Guha-Bradley-Outcome of Guha-Bradley-Rosenthal collaborationRosenthal collaboration
References to papers, blog posts, lab notebook pages, raw
data
The Ugi reaction: can we predict precipitation?
Can we predict solubility in organic solvents?
Crowdsourcing Solubility Data
ONS Challenge Judges
ONS Challenge Award Winners
Solubilities collected in a Google Spreadsheet
Rajarshi Guha’s Live Web Query using Google Viz API
Data provenance: From Wikipedia to…
…the lab notebook and raw data
Interactive NMR spectra using JSpecView and JCAMP-DX
(Andy Lang, Tony Williams)
Open Data JCAMP spectra for education
(Andy Lang, Tony Williams, Robert Lancashire)
Raw Data As Images
Splatter?
Some liquid
YouTube for demonstrating experimental YouTube for demonstrating experimental set-upset-up
The importance of raw data availability
Missed in a prior publication on
solubility for this compound
Case study: Chemical Information
Retrieval course at Drexel (Fall 2009/2010)
Leveraging the educational system to contribute new science
The Chemical Information Validation Sheet
567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course
The Chemical Information Validation Explorer
(Andrew Lang)
Discovering outliers for melting points (stdev/average)
Investigating the m.p. inconsistencies of EGCG
Investigating the m.p. inconsistencies of cyclohexanone
Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting
points
Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling
points
Sigma-Aldrich, Acros and Wolfram Alpha apparently
DO NOT use the same sources for flash points
Most popular data sources
Alfa Aesar donates melting points to the public
Open Melting Point Explorer
Outliers
MDPI dataset
EPI (via ChemSpider)
Outliers
Alfa Aesar
Inconsistencies and SMILES problems within MDPI dataset
MDPI Dataset labeled with High Trust Level
Open Melting Point Datasets
Open Random Forest modeling of Open Melting Point data using CDK descriptors
(Andrew Lang)
R2 = 0.78, TPSA and nHdon most important
Melting point prediction service
Other Web Services…
(Andrew Lang)
General Transparent Solubility Prediction
Convenient web services for solubility measurement and
prediction
(Andrew Lang)
Integration of Multiple Web Services to Recommend Solvents
for Reactions
(Andrew Lang)
Using melting point for temperature dependent solubility prediction
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 Prediction (Andy Lang uses Abraham Model)
Reaction Attempts Book
Reaction Attempts Book: Reactants listed Alphabetically
Dynamic links to private tagged Mendeley collections
(Andrew Lang)
All ONS web services
For all Formats of ONS Projects
ONS Challenge Solubility Book cited for nanotechnology
application
Visualizing molecule-researcher connection maps reveals link between 2 Open Notebooks (Todd
and Bradley)
(Don Pellegrino)
The Intersection of Open Notebooks (Bradley/Todd) and IP implications
Open Notebook could have blocked patent
if done earlier
Decanoic acid
WaterNaCl
Phrase searching for useful solubility applications
Search for applications of solubility for breast cancer research
Solubility prediction for Taxol using Abraham descriptors
Pred Exp
Predicted temperature dependent solubility of Taxol in water (M)
Current research questions for Taxol solubility
1. Does Taxol have a meaningful solubility in methanol or does it decompose too quickly?
2. Why is methanol reported to decompose Taxol but not ethanol?
3. Can the solubility of Taxol in solvent mixtures be predicted, especially for approved excipients?
4. Can the solubility of Taxol analogs be used to create reliable models for the solubility of this class of compounds?
Moving Forward: Tools and Practices
Use free hosted web tools and open data formats
1. Google Spreadsheets (numerical data)2. Wikispaces (human readable format)3. YouTube, SlideShare, LuLu, Nature Precedings,
etc. (multiple data formats)4. JCAMP-DX for spectral data
Practices1. Report all findings immediately – even if tentative2. Participate in social media to share progress and
find collaborators3. Abstract experiments and findings to machine
readable formats and make these easily discoverable