educational activities in cheminformatics at iu gary wiggins wiggins@indiana.edu

Educational Activities in Cheminformatics at IU

Gary Wiggins

wiggins@indiana.edu

Overview

Enrollment data Newer educational activities Formal courses Degree programs

Enrollment Data in the Period of the NIH Grant

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 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)

I/C371 9

I/C372 14

I533 6

I571 44

I572 12

I573 5

I590 2

I647 4

TOTAL 96

Newer Educational Activities

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

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

http://www.chembiogrid.org/related/index.html 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

Mesa Analytics Cheminformatics Virtual Classroom http://www.chemvc.com/ BCCE (Biennial Conference on Chemical

Education) workshop on cheminformatics, July 30, 2006

Creating a Distributed Drug Discovery Database

o Enumeration software is used to create large sets of potential product molecules.

o A list of potential drug lead candidates is split into small batches for synthesis in academic laboratories throughout the world.

o The pooled molecular products are tested by a distributed screening effort.

o The sum of these efforts becomes a powerful globally distributed drug lead process and solution.

DDD keeps track of datao Features

o Entry of reagents in the databaseo Generation of combinatorial productso Entry of synthesized products information

o Release:o Web application to enable data entry/searching of

DDD databaseo 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:

o PostgreSQLo Java and HTML user interfaceso Tomcat Server and JDBC drivero Chemaxon

o Marvin Sketcho Marvin Viewo JChem Reactor

o http://cheminfo.informatics.indiana.edu:8080/ddd/first.html

Entity-Relationship Diagram

Student Participation in DDD

o The synthetic laboratory experimental work is done in these locations around the world:o Indianapoliso Barcelonao Moscowo Lublin.

o IUPUI C444 Organic Chemistry Laboratoryo Summer 2006: 33 studentso Fall 2006: 20? students

Formal Courses 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

I533 Seminar in Chemical Informatics Spring 2006 Topic: Molecular Informatics, the

Data Grid, and an Introduction to eScience http://www.indiana.edu/~cheminfo/I533/533home.html Six students enrolled

I647 & I657 Advanced Chemical Informatics Seminars I-II

Topics vary yearly and include: 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 http://www.indiana.edu/~cheminfo/I647/647home.html 4 students enrolled

Degree Programs: BS and MS

BS degree 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 Includes a 6-hour capstone/research project IUB: Bioinformatics, Chemical Informatics, Human-

Computer Interaction IUPUI: also, New Media, Health Informatics, Laboratory

Informatics

Unique MS Program at IUPUI

Laboratory Informatics at IUPUI Instrumentation and data interfacing Laboratory notebooks Laboratory Information Management Systems

(LIMS)

Degree Program: PhD in Informatics

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

Tracks: Bioinformatics Chemical informatics Health informatics Human-computer interaction Social and organizational informatics

Under development: 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 & GOLDCambridgeSoft ChemDraw UltraChemical Abstracts Service SciFinder ScholarChemaxon Marvin (and other software)Daylight Chemical Info System ToolkitFIZ Karlsruhe Inorganic Crystal Structure DBIO-Informatics SentientMDLCrossFire Beilstein and GmelinOpenEye Toolkit (and other software)Sage Informatics ChemTKSerena Software PCmodelSpotfire DecisionSiteSTN International STN Express with Discover (Anal Ed)Wavefunction Spartan

Core and Affiliated Faculty 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

Research relationships with 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?

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

I571, I572, and seminar projects Research rotations of PhD students RA assignments