An Extensible Knowledge-Base and Visual Programming Environment for the Community Annotation of Multiple Genomes

Virginia Commonwealth University, Richmond VA

Investigators

Abstract

Virginia Commonwealth University is awarded a grant to develop a graphical programming environment based on the textual language BioLingua, that biologists with no computer experience beyond word processors can use effectively; by developing representation tools that will enable biologists to consider raw data in a meaningful way, so that they may see novel patterns that computers are incapable of recognizing without human guidance; and by integrating these tools with the community-based annotation resource, the SEED, so that programming becomes a natural extension of annotation. The annotation of all available cyanobacterial genomes by the community of cyanobacteriologists will serve as the test case. There is little doubt that many biologists will welcome the availability of a powerful new tool for the analysis of genomic information... but recoil at the thought that they might be called upon to program. An essential part of this project is therefore a vigorous educational program that introduces biologists to programming through collaborative research. A traveling post-doc who will coordinate efforts to annotate specific systems will also visit labs for extended stays, collaborating on annotation efforts and simultaneously showing the host lab how simple programming can radically transform its research landscape. At the same time, undergraduate bioinformatics students will pair with participating labs on research projects where the student brings knowledge of BioLingua to the association. The major objective is to alter the relationship of a broad international community of researchers towards bioinformatics so that it becomes part of the way they think. This community, interconnected through the knowledge base, may serve as a model for others that follow. At the same time, the project will focus on the next generation, using collaborative research and mentoring, based on BioLingua, to introduce programming and bioinformatics to high school and undergraduate students.