| Welcome to the URI Bioinformatics Research
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Dr. Joan Peckham, Professor, Computer Science
Dr. Jean-Yves Hervé, Associate Professor, Computer Science
Dr. Lutz Hamel, Assistant Professor, Computer Science
Dr. Liliana Gonzalez, Assistant Professor, Statistics
Dr. Lenore Martin, Associate Professor, Cell and Molecular Biology
Dr. Clinton Chichester, Professor, Biomedical Sciences
|In modern biological science research, a critical issue to success is
handling and processing large amounts of data. Bioinformatics emerged in
response to this requirement. The new field uses information technology
to organize, visual analyze large set of biological information such as
DNA sequences and expression from DNA microarrays, structure-function relationships
of proteins, etc. Hopefully, with bioinformatics tools, researchers can
get answers to a variety of biological questions in much less time than
it would take using traditional analysis techniques. In realizing the big
value of bioinformatics, we propose a bioinformatics core to serve the University
of Rhode Island BRIN project. The goals of the bioinformatics core are as
Protein Fluorescense and Structure Toolkit (PFAST), Spring 2005|
Dr. Yana Reshetnyak, Dr. Joan Peckham, Chi Shen, Nidhi Bansal, Neelima Gudura, Rajiv Menon, Stephen Jaegle
In this Bioinformatics course project, students implemented a web interface to some protein analysis tool written by Dr. Reshetnyak. Also, a new and unique protein fluorescence database was designed and implemented as well.
Cryo-TEM, Spring 2005
Dr. Lenore Martin, Lewis Collier
For this Bioinformatics course project, Lewis investigates the shape of certain lipids by applying computer vision techniques for image analysis. He has successfully implemented prototype software for matching lipids in a cryogenic TEM image against the hypothesized disc shape.
MolMod, Spring 2005
Dr. Lenore Martin, Stanley Lan, Nathan Mockler
In this course project, the students attempt to create a universal format for specifying the force fields parameters used in molecular modeling. They have implemented a prototype program for converting between the popular force fields AMBER and GROMOS.
Universal Research Interchange Format (URI), Spring 2004
Dr. Joan Peckham, Dr. Lenore Martin, Mike Carroll, Catalina Price, Anita Panse, Keeley Wray, Jing Zhang
For this course project, the students designed a new format to improve on the PDB format for storing protein structure information. In addition, they also have implemented a PDB to XML converter.