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Educational Activities in Cheminformatics at IU Gary Wiggins

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Presentation on theme: "Educational Activities in Cheminformatics at IU Gary Wiggins"— Presentation transcript:

1 Educational Activities in Cheminformatics at IU Gary Wiggins

2 Overview Enrollment data Newer educational activities Formal courses Degree programs

3 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 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

4 Breakdown by Courses Enrollment by Courses, (August 2005 – present, across both campuses) I/C3719 I/C37214 I5336 I57144 I57212 I5735 I5902 I6474 TOTAL96

5 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

6 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

7 Cheminformatics Resources Web Guide 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

8 Training Modules for Chemical Informatics Instruction Mesa Analytics Cheminformatics Virtual Classroom BCCE (Biennial Conference on Chemical Education) workshop on cheminformatics, July 30, 2006

9 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.

10 DDD keeps track of data o Features o Entry of reagents in the database o Generation of combinatorial products o Entry of synthesized products information o 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)

11 Database Built on: oPostgreSQL oJava and HTML user interfaces oTomcat Server and JDBC driver oChemaxon oMarvin Sketch oMarvin View oJChem Reactor ohttp://cheminfo.informatics.indiana.edu:8080/ ddd/first.htmlhttp://cheminfo.informatics.indiana.edu:8080/ ddd/first.html

12 Entity-Relationship Diagram

13 Student Participation in DDD o The synthetic laboratory experimental work is done in these locations around the world: o Indianapolis o Barcelona o Moscow o Lublin. o IUPUI C444 Organic Chemistry Laboratory o Summer 2006: 33 students o Fall 2006: 20? students

14 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

15 Cheminformatics Seminar I533 Seminar in Chemical Informatics Spring 2006 Topic: Molecular Informatics, the Data Grid, and an Introduction to eScience Six students enrolled

16 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 4 students enrolled

17 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

18 Unique MS Program at IUPUI Laboratory Informatics at IUPUI Instrumentation and data interfacing Laboratory notebooks Laboratory Information Management Systems (LIMS)

19 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.

20 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

21 END

22 Software/DBs Used in the Program Company Products and/or (Target Area) ArrgusLab(Molecular modeling) Digital Chemistry (formerly, BCI)Toolkit (Clustering) Cambridge Cryst Data CenterCambridge Structrual DB & GOLD CambridgeSoftChemDraw Ultra Chemical Abstracts ServiceSciFinder Scholar ChemaxonMarvin (and other software) Daylight Chemical Info SystemToolkit FIZ KarlsruheInorganic Crystal Structure DB IO-InformaticsSentient MDLCrossFire Beilstein and Gmelin OpenEyeToolkit (and other software) Sage InformaticsChemTK Serena SoftwarePCmodel SpotfireDecisionSite STN InternationalSTN Express with Discover (Anal Ed) WavefunctionSpartan

23 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)

24 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.)

25 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)

26 Introducing Graduate Students to Cheminformatics Research I571, I572, and seminar projects Research rotations of PhD students RA assignments


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