This is an archive project page.

Welcome to the URI Bioinformatics Research Group home page! We're pleased you're visiting us and hope you enjoy our site. Please contact us with any questions you may have and enjoy your stay!
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

About Us
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 follows:
  1. Support end-user access to biological information resources and bioinformatics tools with a focus on visualization, data mining, and data exchange issues;
  2. Provide consultation and education in using biomedical database and bioinformatics tools; and
  3. Enhance communication and data sharing among Rhode Island biological researchers.

Past Projects
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.