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Educational Activities in Cheminformatics at IU

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

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Educational Activities in Cheminformatics at IU

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  1. Educational Activities in Cheminformatics at IU Gary Wiggins wiggins@indiana.edu

  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 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

  4. Breakdown by Courses • Enrollment by Courses, (August 2005 – present, across both campuses)

  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 • 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

  8. 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

  9. Creating a Distributed Drug Discovery Database • 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.

  10. DDD keeps track of data • Features • Entry of reagents in the database • Generation of combinatorial products • Entry of synthesized products information • Release: • Web application to enable data entry/searching of DDD database • Workflow environment to support pipelining of tasks involving DDD database • Web services to facilitate integration with other resources (e.g., PubChem)

  11. Database Built on: • PostgreSQL • Java and HTML user interfaces • Tomcat Server and JDBC driver • Chemaxon • Marvin Sketch • Marvin View • JChem Reactor • http://cheminfo.informatics.indiana.edu:8080/ddd/first.html

  12. Entity-Relationship Diagram

  13. Student Participation in DDD • The synthetic laboratory experimental work is done in these locations around the world: • Indianapolis • Barcelona • Moscow • Lublin. • IUPUI C444 Organic Chemistry Laboratory • Summer 2006: 33 students • 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 • http://www.indiana.edu/~cheminfo/I533/533home.html • 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 • http://www.indiana.edu/~cheminfo/I647/647home.html • 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 CompanyProducts 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

  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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