open notebook science and malaria
DESCRIPTION
My presentation to Chemists Without Borders on September 6, 2007. I introduce the basics of the UsefulChem project and Open Notebook Science and why malaria is a particularly good target for Open Science. This includes the CombiUgi project and our collaborations with ChemSpider, Rajarshi Guha, Phil Rosenthal, Dan Zaharevitz and Tsu-Soo Tan. The final slide shows the presentation of our work on Second Life at a SciFoo Lives On session.TRANSCRIPT
Open Notebook Science and Malaria
Jean-Claude Bradley
Drexel University
September 6, 2007
Chemists Without Borders
Malaria is a Logical Application Malaria is a Logical Application of Open Scienceof Open Science
•Very large problem: 300-500 million cases per year with one million deaths
•Not a lucrative market: IP control less important
Open and Closed ScienceOpen and Closed Science
TraditionalLab Notebook(unpublished)
TraditionalJournal Article
Open Access Journal Article
Open Notebook Science (full transparency)
CLOSED
OPEN
Where is Science headed?Where is Science headed?
WE ARE HEREWE ARE HERE
The Robot ScientistThe Robot Scientist
How will this happen?How will this happen?
Self-organizing redundant processesSelf-organizing redundant processes Agents can participate with zero or Agents can participate with zero or
near-zero cost (free hosted services – near-zero cost (free hosted services – e.g. Google)e.g. Google)
Fully Open Access (Read and Write)Fully Open Access (Read and Write) Publication of all aspects of the Publication of all aspects of the
scientific process: Open Source scientific process: Open Source Science / Science / Open Notebook ScienceOpen Notebook Science
How can machines know what How can machines know what is important?is important?
Ask the humansAsk the humans
UsefulChem BlogUsefulChem Blog
What chemists think is What chemists think is important in 2005important in 2005
Find-A-DrugFind-A-Drug
Diketopiperazine LibraryDiketopiperazine LibraryEvolves to: on pot Evolves to: on pot
Ugi Ugi reaction/cyclizationreaction/cyclization
First iteration: First iteration: Solid Support Solid Support
SynthesisSynthesis
The Molecules BlogThe Molecules Blog
The Experiments BlogThe Experiments Blog
Comments from peersComments from peers
The UsefulChem WikiThe UsefulChem Wiki
Telling the story of the failuresTelling the story of the failures
Experiments moved to wikiExperiments moved to wiki
Experiment HistoryExperiment History
Experiment EditsExperiment Edits
Third Party Time-Stamp on Third Party Time-Stamp on Experiment VersionsExperiment Versions
Monitoring experimental Monitoring experimental progressprogress
How are people finding our How are people finding our experiments?experiments?
Molecules found by InChIMolecules found by InChI
usefulchem.blogspot.comusefulchem.blogspot.com
The blog as an integrative The blog as an integrative tooltool
usefulchem.wikispaces.com/Exp049usefulchem.wikispaces.com/Exp049
The wiki as the laboratory The wiki as the laboratory notebooknotebook
Graphical Mining of Data with Graphical Mining of Data with JSpecViewJSpecView
usefulchem.wikispaces.com/Exp070 (48h 7 min)usefulchem.wikispaces.com/Exp070 (48h 7 min)
Processing Molecules on Processing Molecules on ChemSpiderChemSpider
The CombiUgi ProjectThe CombiUgi Project
Focus on cheap starting materials and a product that precipitate easily from solution
Open Primary Research in Drug Design Open Primary Research in Drug Design using Web2.0 toolsusing Web2.0 tools
(blogs, wikis, Second Life, mailing (blogs, wikis, Second Life, mailing lists)lists)
Docking
Synthesis
Testing
Rajarshi GuhaIndiana U
JC BradleyDrexel U
Phil RosenthalUCSF
(malaria)
Dan ZaharevitzNCI
(tumors)
Tsu-Soo TanNanyang Inst.
UsefulChem and Open UsefulChem and Open Science in Second LifeScience in Second Life
scifooliveson.wikispaces.com