Transcript Educational Activities in Cheminformatics at IU

Educational Activities in
Cheminformatics at IU
Gary Wiggins
[email protected]
Overview
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Enrollment data
Newer educational activities
Formal courses
Degree programs
Enrollment Data in the Period
of the NIH Grant
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Currently have 4 PhD students, 2 MS, 1 BS
96 students have taken at least one
cheminformatics course since August 2005
29 of them (30 percent) accessed the
courses through distance education means
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17 DE students in I571
9 CIC CourseShare students in I571
2 DE students in I572
1 DE student in I573
Breakdown by Courses
Enrollment by Courses,
(August 2005 – present,
across both campuses)
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I/C371
I/C372
I533
I571
I572
I573
I590
I647
TOTAL
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14
6
44
12
5
2
4
96
Newer Educational Activities
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Graduate Certificate in Chemical Informatics
Cheminformatics Resources Web Guide
Ongoing Work with Mesa Analytics on the
Cheminformatics Virtual Classroom
Drug Discovery Database at IUPUI
Development of Formal Courses
Graduate Certificate in Chemical
Informatics
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Requirements: 4 courses; each 3 cr. hours
 I571 Chemical Information Technology
 I572 Computational Chemistry and
Molecular Modeling
 I573 Programming for Science Informatics
 I553 Independent Study in Chemical
Informatics
Available to on-site IUB/IUPUI and Distance
Education students
Cheminformatics Resources
Web Guide
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http://www.chembiogrid.org/related/index.html
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Academic Programs
Chemistry Databases on the Web
Professional Societies and Groups
Companies and Independent Institutions
Publications and Conferences
Data Standards and Standards Groups
Molecular Visualization Tools and Sites
Web Services Technology Resources
Other Guides to Cheminformatics Resources
Training Modules for Chemical
Informatics Instruction
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Mesa Analytics Cheminformatics Virtual
Classroom
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http://www.chemvc.com/
BCCE (Biennial Conference on Chemical
Education) workshop on cheminformatics, July
30, 2006
Creating a Distributed Drug
Discovery Database
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Enumeration software is used to create large sets of
potential product molecules.
A list of potential drug lead candidates is split into small
batches for synthesis in academic laboratories
throughout the world.
The pooled molecular products are tested by a
distributed screening effort.
The sum of these efforts becomes a powerful globally
distributed drug lead process and solution.
DDD keeps track of data
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Features
o Entry of reagents in the database
o Generation of combinatorial products
o Entry of synthesized products information
Release:
o Web application to enable data entry/searching of
DDD database
o Workflow environment to support pipelining of tasks
involving DDD database
o Web services to facilitate integration with other
resources (e.g., PubChem)
Database Built on:
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PostgreSQL
Java and HTML user interfaces
Tomcat Server and JDBC driver
Chemaxon
o Marvin Sketch
o Marvin View
o JChem Reactor
o http://cheminfo.informatics.indiana.edu:8080/
ddd/first.html
Entity-Relationship Diagram
Student Participation in DDD
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The synthetic laboratory experimental work is
done in these locations around the world:
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Indianapolis
Barcelona
Moscow
Lublin.
IUPUI C444 Organic Chemistry Laboratory
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Summer 2006: 33 students
Fall 2006: 20? students
Formal Courses
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Undergraduate courses
 I371 Chemical Informatics (1 cr. hour)
 I372 Molecular Modeling (2 cr. hours)
Introductory graduate courses
 I571 Chemical Information Technology
 I572 Computational Chemistry and Molecular Modeling
 I573 Programming for Science Informatics
 I617 Informatics in Life Sciences and Chemistry (core PhD
course for non-majors)
Seminars, etc.
 I590 Information Retrieval from Chemistry and Life Sciences
Databases (Topics Course)
 I533 Chemical Informatics Seminar
 I647/I657 Advanced Chemical Informatics Seminar I-II
Cheminformatics Seminar
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I533 Seminar in Chemical Informatics
Spring 2006 Topic: Molecular Informatics, the
Data Grid, and an Introduction to eScience
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http://www.indiana.edu/~cheminfo/I533/533home.html
Six students enrolled
I647 & I657 Advanced Chemical
Informatics Seminars I-II
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Topics vary yearly and include:
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representation of chemical compounds
representation of chemical reactions
chemical data, databases and data sources
searching chemical structures
calculation of physical and chemical data (molecular mechanics
and quantum mechanics)
calculation of structure descriptors
methods for chemical data analysis
integration of cheminformatics and bioinformatics
Fall 2006 topic: Bridging Bioinformatics and Chemical
Informatics
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http://www.indiana.edu/~cheminfo/I647/647home.html
4 students enrolled
Degree Programs: BS and MS
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BS degree
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34 credit hours of Informatics courses
Cognate area, usually a minor in areas such as chemistry,
biology, computer science, fine arts, business, etc.
MS degree: 36 semester hours
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Includes a 6-hour capstone/research project
IUB: Bioinformatics, Chemical Informatics, HumanComputer Interaction
IUPUI: also, New Media, Health Informatics, Laboratory
Informatics
Unique MS Program at IUPUI
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Laboratory Informatics at IUPUI
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Instrumentation and data interfacing
Laboratory notebooks
Laboratory Information Management Systems
(LIMS)
Degree Program: PhD in
Informatics
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Began in August 2005
The 90 hours of credit for the PhD in Informatics
(cheminformatics track) consist of:
27 hours of required informatics courses
 I501 Introduction to Informatics (3 cr.)
 Core informatics courses (9 cr.)
 Seminars in the cheminformatics track (6 cr.)
 Professionalism/Pedagogy course (3 cr.)
 Research Rotations (6 cr.)
12 hours in theory or methodology courses (or credits from an
MS degree)
21 hours of electives (or credits from an MS degree)
30 hours of dissertation research.
Concentration Areas for the
PhD in Informatics
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Tracks:
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Bioinformatics
Chemical informatics
Health informatics
Human-computer interaction
Social and organizational informatics
Under development:
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Complex systems, networks, modeling and simulation
Security
Music informatics
New media
END
Software/DBs Used in the
Program
Company
Products and/or (Target Area)
ArrgusLab
(Molecular modeling)
Digital Chemistry (formerly, BCI) Toolkit (Clustering)
Cambridge Cryst Data Center
Cambridge Structrual DB & GOLD
CambridgeSoft
ChemDraw Ultra
Chemical Abstracts Service
SciFinder Scholar
Chemaxon
Marvin (and other software)
Daylight Chemical Info System Toolkit
FIZ Karlsruhe
Inorganic Crystal Structure DB
IO-Informatics
Sentient
MDLCrossFire
Beilstein and Gmelin
OpenEye
Toolkit (and other software)
Sage Informatics
ChemTK
Serena Software
PCmodel
Spotfire
DecisionSite
STN International
STN Express with Discover (Anal Ed)
Wavefunction
Spartan
Core and Affiliated Faculty
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MU-HYUN BAIK
KELSEY FORSYTHE
GEOFFREY C. FOX
SANTIAGO SCHNELL
DAVID J. WILD
DIMITRIS AGRAFIOTIS (adjunct)
JOHN M. BARNARD (adjunct)
DONALD B. BOYD (affiliated)
ROBERT D. CLARK (adjunct)
DAVID E. CLEMMER (adjunct)
CHARLES H. DAVIS (affiliated)
THOMPSON N. DOMAN (adjunct)
KEVIN E. GILBERT (affiliated)
GARY M. HIEFTJE (adjunct)
JOHN C. HUFFMAN (adjunct)
PETER J. ORTOLEVA (adjunct)
GARY D. WIGGINS (adjunct)
FAMING ZHANG (affiliated)
Outreach Activities
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Research relationships with
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IU School of Medicine
IUB/IUPUI bioinformatics and proteomics
research programs
Commercial firms through internships
(LeadScope, Rosetta Inpharmatics, Lilly, etc.)
Why IU for Chemical Informatics?
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Outstanding Faculty
Excellent computer facilities and infrastructure
Close proximity to major pharmaceutical companies
(Lilly, Abbott, Pfizer) and to chemical informatics
companies (Tripos, LeadScope, Chemical Abstracts
Service)
History of innovative, IT-based chemical information
services (QCPE, MSC)
Complementary programs in IU’s School of Library
and Information Science (SLIS)
Introducing Graduate Students
to Cheminformatics Research
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I571, I572, and seminar projects
Research rotations of PhD students
RA assignments