Open Notebook Science:Research in Real Time

Jean-Claude Bradley

E-Learning Coordinator College of Arts and Sciences

Associate Professor of ChemistryDrexel University

Nov 27, 2007

Sigma XiSwarthmore College Chapter

Open and Closed Science Open and Closed Science

TraditionalLab Notebook(unpublished)

TraditionalJournal Article

Open Access Journal Article

Open Notebook Science (full transparency)

CLOSED OPEN

TraditionalPaper TextbookF2F lectures

Lectures Notes public

Assigned problems public

Archived Lectures Public and free online textbooks

RESEARCH

TEACHING

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

Fully Open Access (Read and Write)Fully Open Access (Read and Write)

Publication of all aspects of the scientific Publication of all aspects of the scientific process: Open Source Science / process: Open Source Science / Open Open Notebook ScienceNotebook Science

Using semantically rich formats and Using semantically rich formats and automation at zero publication cost – is this automation at zero publication cost – is this the way to the technological singularity?the way to the technological singularity?

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

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

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

Table of Contents ViewTable of Contents View

usefulchem.blogspot.comusefulchem.blogspot.com

The blog as an integrative The blog as an integrative tooltool

How are people finding our How are people finding our experiments?experiments?

Molecules found by InChIMolecules found by InChI

Processing Molecules on Processing Molecules on ChemSpiderChemSpider

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)

Student assignments on a Student assignments on a wikiwiki

Student assignment on NMR using live research data and JSpecView

Using ExcelVBA to automate Using ExcelVBA to automate kinetics analysiskinetics analysis

Specify NMR regions and Specify NMR regions and internal standardinternal standard

NMR spectra of monitoring NMR spectra of monitoring samples calculatedsamples calculated

Reaction profile plotted Reaction profile plotted automaticallyautomatically

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.

Mailing List Facilitates inter-Mailing List Facilitates inter-group collaborationgroup collaboration

Open science connectivityOpen science connectivity

More info on open source science here

http://usefulchem.wikispaces.com

CombiUgi Virtual LibrariesCombiUgi Virtual Libraries

Falcipain-2 inhibitor?Falcipain-2 inhibitor?

http://usefulchem.wikispaces.com/Exp148Khalid Mirza

More Flexible Scientific More Flexible Scientific PublicationPublication

neurodatabase.orgneurodatabase.org

Raw Experimental DataRaw Experimental Data

Selected Experiments (some Selected Experiments (some failed)failed)

Orgprepdaily.wordpress.comOrgprepdaily.wordpress.com

Generalized ProtocolsGeneralized Protocols

Openwetware.orgOpenwetware.org

Orgprepdaily.wordpress.comOrgprepdaily.wordpress.com

Vendor ReliabilityVendor Reliability

Lab Notebook for intra-group Lab Notebook for intra-group communicationcommunication

Openwetware.orgOpenwetware.org

Discussing HypothesesDiscussing Hypotheses

RRResearch.blogspot.comRRResearch.blogspot.com

Cameron Neylon’s NotebookCameron Neylon’s Notebook

UsefulChem and Open UsefulChem and Open Science in Second LifeScience in Second Life

scifooliveson.wikispaces.com

Merging Research and Teaching in Second Life

QuestionQuestion: Is it really a good thing to let anyone who thinks : Is it really a good thing to let anyone who thinks they have a scientific breakthrough have access to free, they have a scientific breakthrough have access to free, open, public, Googleable media? open, public, Googleable media?

YESYES QuestionQuestion: What if I make a mistake in my data, never fix it, : What if I make a mistake in my data, never fix it,

no one catches it, and then someone dies because a no one catches it, and then someone dies because a medical decision was based on my "findings"? Isn't this medical decision was based on my "findings"? Isn't this exactly why we have formal peer review in formal exactly why we have formal peer review in formal publications? publications?

Peer review is not designed to catch errors from the Peer review is not designed to catch errors from the analysis of raw dataanalysis of raw data

Open Notebook Science is more difficult where Open Notebook Science is more difficult where human subjects are involvedhuman subjects are involved

QuestionQuestion: Who is the audience for science blogs and wikis : Who is the audience for science blogs and wikis anyway? Scientists or laypeople? anyway? Scientists or laypeople?

For UsefulChem, wiki is for chemists, blog for wider For UsefulChem, wiki is for chemists, blog for wider audienceaudience

QuestionQuestion: Can you get published if you've already posted : Can you get published if you've already posted your results to your blog/wiki? your results to your blog/wiki?

We’ll find out….We’ll find out…. QuestionQuestion: Can scientists establish their : Can scientists establish their

credibility/reputation by writing blogs and wikis? credibility/reputation by writing blogs and wikis? Certainly we’ve found collaborators this wayCertainly we’ve found collaborators this way