Open Notebook Science: Research in Real Time Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University Nov 27, 2007 Sigma Xi Swarthmore College Chapter

Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING

Where is Science headed? WE ARE HERE

The Robot Scientist

How will this happen? Self-organizing redundant processes Self-organizing redundant processes 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

Malaria is a Logical Application of Open Science Very large problem: million cases per year with one million deaths Not a lucrative market: IP control less important

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

Table of Contents View

usefulchem.blogspot.com The blog as an integrative tool

How are people finding our experiments?

Molecules found by InChI

Processing Molecules on ChemSpider

Graphical Mining of Data with JSpecView usefulchem.wikispaces.com/Exp070 (48h 7 min)

Student assignments on a wiki

Student assignment on NMR using live research data and JSpecView

Using ExcelVBA to automate kinetics analysis

Specify NMR regions and internal standard

NMR spectra of monitoring samples calculated

Reaction profile plotted automatically

Open Primary Research in Drug Design using Web2.0 tools (blogs, wikis, Second Life, mailing lists) Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.

Mailing List Facilitates inter-group collaboration

Open science connectivity More info on open source science here

CombiUgi Virtual Libraries

Falcipain-2 inhibitor? Mirza

More Flexible Scientific Publication

neurodatabase.org Raw Experimental Data

Selected Experiments (some failed) Orgprepdaily.wordpress.com

Generalized Protocols Openwetware.org

Orgprepdaily.wordpress.com Vendor Reliability

Lab Notebook for intra-group communication Openwetware.org

Discussing Hypotheses RRResearch.blogspot.com

Cameron Neylon’s Notebook

UsefulChem and Open Science in Second Life scifooliveson.wikispaces.com

Merging Research and Teaching in Second Life

Question: Is it really a good thing to let anyone who thinks they have a scientific breakthrough have access to free, open, public, Googleable media? Question: Is it really a good thing to let anyone who thinks they have a scientific breakthrough have access to free, open, public, Googleable media? YES YES Question: What if I make a mistake in my data, never fix it, no one catches it, and then someone dies because a medical decision was based on my "findings"? Isn't this exactly why we have formal peer review in formal publications? Question: What if I make a mistake in my data, never fix it, no one catches it, and then someone dies because a medical decision was based on my "findings"? Isn't this exactly why we have formal peer review in formal publications? Peer review is not designed to catch errors from the analysis of raw data Peer review is not designed to catch errors from the analysis of raw data Open Notebook Science is more difficult where human subjects are involved Open Notebook Science is more difficult where human subjects are involved Question: Who is the audience for science blogs and wikis anyway? Scientists or laypeople? Question: Who is the audience for science blogs and wikis anyway? Scientists or laypeople? For UsefulChem, wiki is for chemists, blog for wider audience For UsefulChem, wiki is for chemists, blog for wider audience Question: Can you get published if you've already posted your results to your blog/wiki? Question: Can you get published if you've already posted your results to your blog/wiki? We’ll find out…. We’ll find out…. Question: Can scientists establish their credibility/reputation by writing blogs and wikis? Question: Can scientists establish their credibility/reputation by writing blogs and wikis? Certainly we’ve found collaborators this way Certainly we’ve found collaborators this way