O'Reilly Bioinformatics Conference 2003

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Session
The SLRITools Project: Providing a Platform for Bioinformatics Research
Michel Dumontier, SLRI / University of Toronto

Track: Bioinformatics.Org
Date: Wednesday, February 05
Time: 4:45pm - 5:30pm
Location: Plaza
Dumontier discusses the Samuel Lunenfeld Research Institute Toolkit (SLRITools), a mainly C-based cross-platform toolkit for dealing with biological information, especially protein structure/function (sourceforge.net/projects/slritools). This toolkit extends the freely available NCBI C Toolkit and forms the basis for a number of powerful applications:

The Biomolecular Interaction Network Database (BIND) is designed to store full descriptions of interactions, molecular complexes, and pathways. The BIND data model includes virtually all components of molecular mechanisms including interactions between any two molecules composed of proteins, nucleic acids, and small molecules. These are abstracted in such a way that graph theory methods may be applied for effortless data mining.
SeqHound is a sequence and structure database management system that provides locally-hosted and daily-updated contents of the NCBI’s Entrez sequence databases, in addition to 3-D structural data and multiple links to sequence neighbors, taxonomy, functional annotation, and literature. SeqHound is accessible via a Web interface as well as through a C, C++, and PERL application programming interface (API) for access to a local installation or over a network from a client workstation.
NBLAST is a cluster-computing solution to generate and store BLAST sequence alignments and pre-computed neighbors.
Kangaroo is a pattern search program using regular expression searching that enables searching through annotated coding regions.

Taken together, these tools provide a platform for research in a Bioinformatics group setting.

Adds Dumontier, “Bioinformatics is necessarily an integrative part of hypothesis-driven investigative science for the modern Life Science laboratory. Successful life scientists will use bioinformatics to drive and support hypotheses as well as feedback into laboratory experiments. However, with the massive explosion in biological information, more practical systems will have to be developed to manage and present relevant information.

“My presentation focuses on the technology and open-source tools that have been developed in our lab to build a solid infrastructure for investigative science. These tools provide the means by which both the computational biologist and the life scientists can further investigate scientific questions using sequence, structure and biomolecular interaction information. My goal is for attendees to learn how our open-source bioinformatics infrastructure can be setup within their own organization so as to enhance their abilities to make discovery.”

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