Transcript Open Notebook Science and Cheminformatics Indiana University Cheminformatics Class Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University March 25, 2008

Open Notebook Science and
Cheminformatics
Indiana University Cheminformatics Class
Jean-Claude Bradley
E-Learning Coordinator
College of Arts and Sciences
Associate Professor of Chemistry
Drexel University
March 25, 2008
Open and Closed Science
Traditional
Lab Notebook
(unpublished)
Traditional
Journal
Article
Open Access
Journal Article
Open Notebook
Science (full
transparency)
RESEARCH
OPEN
CLOSED
TEACHING
Traditional
Paper
Textbook
F2F lectures
Lectures
Notes
public
Assigned
problems
public
Archived
Lectures
Public and
free online
textbooks
What is the role of blogging in
scientific research transparency?
UsefulChem
BLOG
Mailing List
WIKI
GoogleDocs
Discussing Funding
Supporting Funding Initiatives
Highlight Popular Media Coverage
Highlight Peer-Reviewed Coverage
Announce Collaborator:
Gus Rosania
Announce Collaborator:
Matthias Zeller
Announce Collaborator:
Phil Rosenthal
Discuss Presentations in Real Life
Discuss Presentations in Second Life
Showcase Science in New Media
Showcase Teaching in New Media
Hiro Sheridan’s Molecule Rezzer takes SMILES, InChI or InChIKeys
Alerts to Broader Impact
Opportunities
Science Philosophy
Where’s the Beef?
Link to Lab Notebook Page in Wiki
Link to Molecules
Link to Experimental Plan
Link to Docking Procedure
(Rajarshi Guha)
Link to Docking Results
(Rajarshi Guha)
Procedure Section
Link to Raw Data with JSpecView
(data in JCAMP-DX format)
Conclusion is Fully Supported
Indexing the Experiments in Google
Comparing Experiments
The Most Important Section!
Results in Machine-Friendly Format
Comparing Results in a Table
Table of Contents
Recent Changes in Wiki
Tracking Versions of Wiki Pages
Comparing Versions of Wiki Pages
How are people finding our
experiments?
Telling the story of the failures
Mailing List Facilitates inter-group
collaboration
Open Primary Research in Drug Design
using Web2.0 tools
(blogs, wikis, Second Life, mailing lists)
Rajarshi Guha
Indiana U
JC Bradley
Drexel U
Phil Rosenthal
UCSF
(malaria)
Docking
Tsu-Soo Tan
Nanyang Inst.
Synthesis
Testing
Dan Zaharevitz
NCI
(tumors)
Gus Rosania’s Notebook
Cameron Neylon’s Notebook
Automation in UsefulChem
CMLRSS feed on Bioclipse
Graphical Mining of Data with
JSpecView
usefulchem.wikispaces.com/Exp070 (48h 7 min)
Using ExcelVBA to automate
kinetics analysis
Specify NMR regions and internal
standard
NMR spectra of monitoring
samples calculated
Reaction profile plotted
automatically
Next Step: Reading JCAMP-DX
files in Second Life
Where is Science headed?
WE ARE HERE