C571 Chemical Information Technology Projects

Updated: 6 October 2003

The names of the students have been added to the projects they have chosen. Please check to be sure that I have your name at the appropriate place.

Students who wish to work on projects other than those listed below must first clear them with Dr. Milosevich or Dr. Wiggins. Likewise, if you want to substitute a research paper for the project, you should clear the topic with one of the instructors before beginning the research.

Efforts on 3D Cell Modeling: Jianmiao Fan (IUB)

Metadata, XML, CML: Spencer Lerch (IUPUI), Xiang Zhou (IUB), Jianyong Zhu (IUB)
Using a well-known format for images, EXIF 2.2-compliant JPEG, how can we enhance the information associated with a molecular image so that it is not only viewable, but searchable by appropriate applications?

Protein Folding (review article) David Shaw (IUPUI), Jain Manojkumardhoka (IUPUI), Mandi Zins (IUPUI), Joey Strausburg (IUPUI), Abdulkadir Genel (IUB), Robert Hollo (IUB), Kent Krieg (IUB), Paul Myrda (IUB)
What is the current state of the art in protein folding? (Broad or deep coverage, but not both)

Molecular Dynamics
Given motion pictures of molecular dynamics trajectories, how is the data behind the visual image mined? Most do not treat the trajectory file as a database, but as frames in a movie.

De novo Drug Design (review article): Allyson Novotny (IUPUI), JoAnna Hernandez (IUPUI), Ryan Denton (IUPUI), Tulay Ercanli (IUPUI)
What specific progress can we claim with de novo drug design at this point in time?

Daylight Chemical Information System Software
Learn to use the software and give a classroom presentation on its main features.

Bioinformatics Software and Databases from Commercial Companies
What aspects of commercial software (i.e., not free and publicly available on the Web) offer significant enhancements to the features that can be had from the free options?

Other Potential Projects/Review Articles:

In addition to the options above, it might be acceptable to write a paper on one of the following topics (these are larger topics used at the University of Sheffield in conjunction with their MS program):

These topics must be cleared with the instructors before you begin the work.

Copyright 2003
Gary Wiggins