Open Source/Open Notebook Science: Doing science with blogs and wikis Jan 20, 2007 Drexel University Chemistry Department
Agenda This session will cover the dissemination of primary scientific information via blogs, wikis and other non-traditional vehicles This session will cover the dissemination of primary scientific information via blogs, wikis and other non-traditional vehicles 1. Types of information raw experimental data (Open Notebook Science) raw experimental data (Open Notebook Science) analyzed data analyzed data hypotheses hypotheses “failed” experiments “failed” experiments generalized protocols generalized protocols traditional article format traditional article format
2. Issues Intellectual Property Intellectual Property Referencing and claims to priority Referencing and claims to priority Academic Validation Academic Validation Peer Review – mandatory and elective Peer Review – mandatory and elective
3. Opportunities Increasing productivity in terms of universally usable knowledge units Increasing productivity in terms of universally usable knowledge units Making explicit the nature and quantity of work in collaborations Making explicit the nature and quantity of work in collaborations Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity? Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity?
Where is Science headed? WE ARE HERE
The Robot Scientist
How will this happen? Self-organizing reduntant processes Self-organizing reduntant processes Agents can participate with zero or near- zero cost (free hosted services) Agents can participate with zero or near- zero cost (free hosted services) Fully Open Access (Read and Write) Fully Open Access (Read and Write) Publication of all aspects of the scientific process: Open Source Science / Open Notebook Science Publication of all aspects of the scientific process: Open Source Science / Open Notebook Science
How can machines know what is important? Ask the humans
UsefulChem Blog
What chemists think is important in 2005
Find-A-Drug
Diketopiperazine Library Evolves to: on pot Ugi reaction/cyclization First iteration: Solid Support Synthesis
The Molecules Blog
The Experiments Blog
Comments from peers
The UsefulChem Wiki
Telling the story of the failures
Experiments moved to wiki
Experiment History
Experiment Edits
Third Party Time-Stamp on Experiment Versions
Monitoring experimental progress
How are people finding our experiments?
Molecules found by InChI
Automation in UsefulChem
CMLRSS feed on Bioclipse
CMLRSS feed on Bloglines
Open science connectivity More info on open source science here
Extending the interaction outside of science
usefulchem.blogspot.com The blog as an integrative tool
usefulchem.wikispaces.com/Exp049 The wiki as the laboratory notebook
usefulchem.wikispaces.com/Exp049 (2 min) Graphical Mining of Data with JSpecView
neurodatabase.org Raw Experimental Data
Selected Experiments (some failed) Orgprepdaily.wordpress.com
Orgprepdaily.wordpress.com Vendor Reliability
Generalized Protocols Openwetware.org
Lab Notebook for intra-group communication Openwetware.org
Discussing Hypotheses RRResearch.blogspot.com
Writing Code for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust