Educational Activities in Cheminformatics at IU

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Educational Activities in Cheminformatics at IU

• Gary Wiggins
• wiggins_at_indiana.edu

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Overview

• Recent developments
• Formal courses
• Degree programs
• Graduate certificate program
• Guide to web resources
• Collaborative work on educational modules

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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
• I533 Chemical Informatics Seminar
• I647/I657 Advanced Chemical Informatics Seminar
  I-II

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Recent Developments - 1

• Enrollment data in the period of the NIH grant
• 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 I571
• 1 DE student in I573

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Recent Developments - 2

• Enrollment by Courses,
• (August 2005 present, across both campuses)

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Recent Developments - 3

• BCCE workshop on cheminformatics, July 30
• Ongoing work with Mesa Analytics on the
  Cheminformatics Virtual Classroom
• Graduate Certificate in Chemical Informatics

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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

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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
  

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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
• IUB Bioinformatics, Chemical Informatics,
  Human-Computer Interaction
• IUPUI also New Media, Health Informatics,
  Laboratory Informatics
• Includes a 6-hour capstone/research project

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Unique MS Program at IUPUI

• Laboratory Informatics at IUPUI
• Instrumentation and data interfacing
• Laboratory notebooks
• Laboratory Information Management Systems (LIMS)

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Degree Programs 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 Rotation (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.

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Concentration Areas for the PhD in Informatics

• Tracks
• bioinformatics chemical informatics health
  informatics human-computer interaction design
  social and organizational informatics
• Under development
• complex systems, networks, modeling and
  simulation cybersecurity discovery and
  application of information logical and
  mathematical foundations music informatics

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Other Educational Activities

• Experiments with teleconferencing as a distance
  education tool
• I571 as CIC CourseShare offering
• Distributed Drug Discovery database for organic
  chemistry laboratory course at IUPUI
• Graduate Certificate in Chemical Informatics

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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

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General Cheminformatics Resources

• 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

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Training Modules for Chemical Informatics
Instruction

• Mesa Analytics Cheminformatics Virtual Classroom
• http//www.chemvc.com/

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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

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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)

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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.)

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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 IUs School of Library
  and Information Science (SLIS)

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Introducing Graduate Students to Cheminformatics
Research

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