Schedule of Classes
C571 Chemical Information Technology
(CHEM 696 at IUPUI)


Updated: 3 October 2004

[Structure Systems] [Database Systems] [Bioinformatics]

 Description
Overview of chemical informatics techniques, including chemical information and data systems, chemical structure and data representation and search systems, and bioinformatics techniques.

Class Meeting Times are Tuesdays and Thursdays 11:15 AM - 12:30PM.

Meeting Places:
IUB:    Chemistry A400
IUPUI: ES2101


  Grading and Requirements
Grades will be based on 5 exercises and a paper or project. Each exercise counts 10 percent of the grade, and the paper or project counts 50 percent.

Some of the exercises will give the students hands-on experience with the major coding concepts and databases used in chemical information systems today.

 Introduction to Chemical Informatics
Instructor:  Dr. Sam A.F. Milosevich
Thursday, 8/21 and Thursday, 8/28: IUPUI ONLY [No class on Tuesday, 8/26]

Information Anxiety, Knowledge Value Revolution. (PowerPoint)

 Laboratory Information Management Systems and Electronic Notebooks
Instructor: Dr. Doug Perry
Tuesday, 9/2   Laboratory Information Management Systems (PowerPoint)
Thursday, 9/4   Electronic Laboratory Notebooks (PowerPoint)

 Chemical Nomenclature
Instructor:  Dr. Charles H. Davis
Tuesday, 9/9   "Nomenclature Lite:" A Guide to Naming and Indexing Chemical Compounds

  Introduction to Chemical Informatics
Instructor: Dr. Gary Wiggins
Thursday, 9/11
Chemoinformatics, cheminformatics, chemical informatics: What is it? (PowerPoint by Gary Wiggins)

Chemoinformatics: Where it has come from, where it is now, where it is going. (PowerPoint by Peter Willett)

 Guest Lecturer
Instructor: Dr. David Wild
Tuesday, 9/16 Hot topics in chemoinformatics in the pharmaceutical industry

  Chemical Information and Database Systems
Instructor: Dr. Gary Wiggins
Thursday, 9/18 Commercial Vendors (STN, Questel-ORBIT, etc.)
Tuesday, 9/23 Personal Database Software

 Chemical Patent Databases
Instructor:  Gary Wiggins
Thursday, 9/25 Patent Information (PowerPoint by Ron Kaminecki)
Patent Information (PowerPoint by Ms. Adele Hoskin, IU SLIS)
         Patent Sources
         Patent Information 2 (PowerPoint by Ms. Adele Hoskin, IU SLIS)
         Patent Transcript

  Spectral Databases
Instructor:  Dr. John C. Huffman
Tuesday, 9/30   NIST and Other Spectral Databases (PowerPoint)


 Chemical Reaction Databases
Instructor: Dr. Sam Milosevich
Thursday, 10/2 and Tuesday, 10/7     Reactions: Databases and Data Management (PowerPoint by Dr. Guenter Grethe, MDL Information Systems)

 Molecular Modeling and Computational Chemistry
Instructor: Dr. Mu-Hyun (Mookie) Baik
Thursday, 10/9 Molecular Modeling and Computational Chemistry I
Tuesday, 10/14 Molecular Modeling and Computational Chemistry II

Introduction to Molecular Visualization and Modeling Software by Dr. Xinfeng (Frank) Gao

 Guest Lecturer
Instructor: Dr. Marc Nicklaus (NIH NCI Laboratory of Medicinal Chemistry)
Thursday, 10/16 Chemical Databases, Identifiers, Tool Kits and Web Services (PowerPoint by Dr. Marc Nicklaus)

 Molecular Modeling and Computational Chemistry
Instructor: Dr. Mu-Hyun (Mookie) Baik
Tuesday, 10/21 Molecular Modeling and Computational Chemistry III

  Bioinformatics: Overview of Techniques
Instructor:   Dr. Sun Kim
Thursday, 10/23 Bioinformatics: A Project-Oriented View (PDF File)

  Chemical Structure Representation and Search Systems
Instructor:  Dr. John Barnard

Tuesday, 10/28
   Structure Representation and Computers
. (PowerPoint)
structure diagrams
nomenclature
line notations(emphasizing SMILES)
connection tables(emphasizing Molfile)
Instructor:   Dr. John M. Barnard

Thursday, 10/30
   Structure Representation Problem Areas (PowerPoint)
  
aromaticity
tautomerism
stereochemistry
markush structures
Tuesday, 11/4
   More Graph Theory (PowerPoint)
   Structure Analysis and Processing
ring perception
functional group identification
structure fingerprints and fragments
canonicalisation and symmetry perception
  Crystallographic Databases
Instructor:  Dr. John C. Huffman
Thursday, 11/6   Crystallography Databases (PowerPoint)


  Chemical Structure Representation and Search Systems
Tuesday, 11/11 and Thursday 11/13
   Structure Searching I (PowerPoint)
   Reaction Searching; 3D Substructure Search; Searching Markush Structures in Patents (PowerPoint)
  Structure Searching
full structure search
substructure search
SMARTS
  Screening and Fingerprints
  Markush searching
  Reaction searching
  MCS
Tuesday, 11/18 and Thursday, 11/20
   Similarity Searching; Chemical Diversity and Its Measurement (PowerPoint)
   Clustering; Topological Indexes; Property Prediction; The Drug Discovery Process (PowerPoint)
  Topological indexes
  Property prediction
  3D Substructure Search
  Crystallographic Databases
Instructor:  Dr. John C. Huffman
Tuesday, 11/25   Cambridge Structural Database  (CSD)

 Thanksgiving
Thursday, 11/27 No class

 Presentations of Student Projects or Papers
Tuesday, 12/2 IUPUI Students
Thursday, 12/4 IUB and IUPUI Students
Tuesday, 12/9 IUB Students Only
Thursday, 12/11 IUB Students Only