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The implications of
Open Notebook Science
and other new forms of scientific
communication for Nanoinformatics
Jean-Claude Bradley
November 3, 2010
Nanoinformatics 2010
Associate Professor of Chemistry
Drexel University
LIMS CENS
Single
Instrument
Automation
Laboratory
Information
Management
Systems
Collaborative
Electronic
Notebook
Systems
Human
/Autonomous
Agent Hybrid
Systems
Human Managed
Fully Autonomous
Scientific
Research
Systems
TODAY
SMIRP bridge
The Evolution of Automation in Scientific Research
Standard
Modular
Integrated
Research
Protocols
Capturing semantic structure in research
at the point of data entry
Nanoinformatics 2010 SMIRP-ONS Talk
Human
Agent
Autonomous
Agent
SMIRP
(Bot)
Browser
Excel
The SMIRP model for a hybrid Human/Autonomous Agent System
Anthropomimetic
Design
Approaches to Collaborative Electronic Notebooks
rigid
SMIRP
compromise:
Rigid information representation
Flexible linking of modules
flexible
•Structured
•Generally
domain
specific
•Adaptable
•Unstructured
http://smirp.drexel.edu
Fundamental Information
Representation in SMIRP
Module 1 Module 2
Parameter 1
Parameter 2
Parameter 4
Parameter 5
instance
Record 1
instance
Record 2
(People)
(Name)
(Employee of)
(Company)
(Name)
Parameter 3(email)
(Address)
Bill Gates Microsoft
Two approaches to the development of databases
Communicate
anticipated
need
Design
database
structure
Let database structure
evolve
through useSMIRP
Case-study:
Evolution of SMIRP structure in a nanoscience laboratory
Location Drexel University
Department of Chemistry
Users faculty, undergraduate students, graduate
students, librarians and other university
personnel
Period Feb 1999 – April 2001, with a detailed focus
on
last 7 months (Sept 2000-April 2001)
Total accounts (last 7 months) 78
Active Accounts (added records) 50
Administrators (changed
database structure)
9
Human
Resource
Management
13%
Maintenance
1%
Knowledge
Processing
72%
Most Active Module Categories (9/00 – 4/01)
Labwork
14%
118 modules 1/3 account for
98% of activity
Activity Analysis by Category over Time
2000-10-3
2000-10-17
2000-10-30
2000-11-12
2000-11-25
2000-12-8
2000-12-21
2001-1-3
2001-1-16
2001-1-30
2001-2-12
2001-2-25
2001-3-10
2001-3-23
2001-4-5
2001-4-18
Maintenance
Human Resource Management
Laboratory Work
Knowledge Processing
0
1000
2000
3000
4000
5000
6000
7000
8000
Recruitment
events 2%
Project
Manager
5%Errors
5%
Productivity
Tracking
14%
People 28%
Workstudy
hours reporting
46%
Most Active Human Resource Management Modules
Most Active Maintenance Modules
SMIRP
Problems
22%
Orders
19%
Invoice (TEM/SEM and
other instrument charges)
19%
Laboratory
materials
16%
Vendor
15%
Order
forms
9%
Most Active Knowledge Processing Modules
Journal 9%
Knowledge
Filter 3%
Reformat
Reference
requests
20%
Find
Reference
66%
Publisher
Document Production
Reference Processing
Parameter Correlation
Data source files
Experimental Conclusion Generation
Knowledge consolidation
Seamless Integration of Human and
Autonomous Agents in Workflows
Real-Time Workflow Designs
Automated
Human
(default)
State A State B
Workflow for Extraction of Article information and URL
Queries Web and
extracts information
Most Active Laboratory Modules
Preparation of Silver rods for SCBE
TEM Micrographs Of Pd on C
SCBE on membranes
Hydrogenation of Crotonaldehyde using Pd Catalysts
Reduction of Methylene blue by Pd
Metal Particles in a Field
Electrodeposition of
Pd on Graphite
29%
Protocol Prototyping
25%
Pd onto Carbon
Nanofibers
17%
Electroless plating
on Membranes
9%
Synthesis of Pd catalysts
by Bipolar electrochemistry
5%
TEM Micrographs
Of Pd on C
3%
Pd particle size
analysis using TEM
3%
Keyword Search Results: example “nanotube”
From Keyword to Orders
From Keyword to Article
From Keyword to Knowledge Filter
From Keyword to
Protocol
Prototyping
Sharing results semi-automatically:
SMIRP Knowledge Product
•Single Experiment
•Full Context
•Supporting Data
•Not suitable for traditional peer-
reviewed publications
Non-traditional publication options in
2003
(Elsevier)
Nanoinformatics 2010 SMIRP-ONS Talk
Nanoinformatics 2010 SMIRP-ONS Talk
Nanoinformatics 2010 SMIRP-ONS Talk
Nanoinformatics 2010 SMIRP-ONS Talk
Nanoinformatics 2010 SMIRP-ONS Talk
Nanoinformatics 2010 SMIRP-ONS Talk
To Cite or Not to Cite?
Nanoinformatics 2010 SMIRP-ONS Talk
“I would never consider a
claim made in a patent as
blocking an author's claim of
novelty.” Langmuir Editor
What is a Scientific Precedent in Academia?
What is a Scientific Precedent in Patent Law?
What is Scholarship?
*also indexed in Chemical Abstracts!
The UsefulChem Project (2005)
What would happen if a chemistry
project was completely transparent in
real time?
Motivation: Faster Science, Better Science
TRUST
PROOF
First record then abstract structure
In order to be discoverable use Google
friendly formats (simple HTML, no login)
In order to be replicable use free hosted
tools (Wikispaces, Google Spreadsheets)
Strategy for an Open Notebook:
UsefulChem Project: Open Primary
Research in Drug Design using Web2.0
tools
Docking
Synthesis
Testing
Rajarshi Guha
Indiana U
JC Bradley
Drexel U
Phil Rosenthal
UCSF
(malaria)
Dan Zaharevitz
NCI
(tumors)
Tsu-Soo Tan
Nanyang Inst.
Malaria Target: falcipain-2
involved in hemoglobin metabolism
Dana.or
Outcome of Guha-Bradley-Rosenthal
collaboration
The Ugi reaction: can we predict
precipitation?
Can we predict solubility in organic solvents?
Crowdsourcing Solubility Data
ONS Challenge Judges
ONS Submeta Award Winners
Data provenance:
From Wikipedia to…
…the lab notebook and raw data
•Concentration (0.4, 0.2, 0.07 M)
•Solvent (methanol, ethanol, acetonitrile, THF)
•Excess of some reagents (1.2 eq.)
How does Open Notebook Science fit with
traditional publication?
Paper written on Wiki
References to papers, blog posts,
lab notebook pages, raw data
Paper on Journal of Visualized
Experiments (JoVE)
Pre-print on Nature Precedings
ONSArchive: Semi-Automated Snapshot of
the Entire Scientific Record
Automated
Download of
Spreadsheets
and Parsing of
Web Pages
Manual
Backup of
Spectral
Data Files
Manual
Export of
Wikispaces
Lulu.com Data Disks
Interactive NMR spectra using JSpecView
and JCAMP-DX
Raw Data As Images
Splatter?
Some liquid
YouTube for demonstrating experimental set-up
The importance of raw data availability
Missed in a prior
publication on solubility
for this compound
The Intersection of Open Notebooks
(Bradley/Todd) and IP implications
Open Notebook could
have blocked patent if
done earlier
Convenient web services for solubility
measurement and prediction
(Andrew Lang)
Other Web Services…
(Andrew Lang)
General Transparent Solubility Prediction
Semi-Automated Measurement of
solubility via web service analysis
of JCAMP-DX files
(Andy Lang)
Integration of Multiple Web Services to
Recommend Solvents for Reactions
(Andrew Lang)
Nanoinformatics 2010 SMIRP-ONS Talk
Nanoinformatics 2010 SMIRP-ONS Talk
Reaction Attempts Book
Reaction Attempts Book: Reactants
listed Alphabetically
For all Formats of ONS Projects
Dynamic links to private tagged
Mendeley collections
(Andrew Lang)
Conclusions
•Open Notebook Science can provide an additional
channel to communicate useful scientific information
•Recording first for human consumption followed by
abstracting the semantics later works but the format
will be field specific
•As long as proof is valued over trust there is no limit
to what useful forms of scientific communication will
emerge.

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