Open Notebook Science using Blogs and Wikis Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Drexel University March 27, 2007 American.

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Presentation transcript:

Open Notebook Science using Blogs and Wikis Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Drexel University March 27, 2007 American Chemical Society Symposium on Communicating Chemistry

Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN

Where is Science headed? WE ARE HERE

The Robot Scientist

How will this happen? Self-organizing redundant processes Self-organizing redundant processes Agents can participate with zero or near-zero cost (free hosted services – e.g. Google) Agents can participate with zero or near-zero cost (free hosted services – e.g. Google) 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 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?

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

usefulchem.blogspot.com The blog as an integrative tool

usefulchem.wikispaces.com/Exp049 The wiki as the laboratory notebook

Open science connectivity More info on open source science here

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

UsefulChem in Second Life

Display blog post as poster

Click on Images for Descriptions

Click on the Blue Obelisk for a Chemistry Quiz Thanks Beth and Eloise!

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

Feedback for the Automation Component Also – Rich Apodaca, Christoph Steinbeck, Peter Murray-Rust