Bioinformatics: Genetics at Barnard and GARP
Assistant Professor of Biology Brian Morton has continued to upgrade and enhance the website that he and his students developed for use in his Genetics class: http://barnard.edu/biology/gab. The website has proven to be a boon for students enrolled in his class.
During the current reporting period, students have been working with Assistant Professor Brian Morton on a Bioinformatics Project. They have completed the initial development of a software package called GARP (Genome Analysis and Research Program). The two primary goals of the project are (1) to introduce students to techniques in computer programming with biological applications and (2) to develop a research tool for other Barnard students and for the wider scientific community. To accomplish these goals they are developing a software package that has many applications in bioinformatics and that can be expanded indefinitely by future students. The software package reads DNA sequence data files from GenBank, the international database that holds all published sequence information, including the data from genome sequence projects. Once the file is read, all of the information is presented in a simple format that allows the user to view and manipulate the data easily. It allows the user to work with any number of GenBank files simultaneously, to update information about genetic sequence data present in the file, and to launch analytical applications on any selected set of genes or sequence regions read from the GenBank files. By taking this route in developing GARP Professor Morton can accomplish the two goals: his students are introduced to the application side end of bioinformatics (i.e., the use of GARP to analyze genetic data) as well as bioinformation programming. Both of these areas will become increasingly important as the amount of sequence data increases in the coming years.
During the past year, three Barnard seniors have worked on the GARP package. Regina Schmitt worked as an HSPP Research Intern during the summer of 2001 and then through the 2001-2002 academic year. She wrote the core Java classes of the package, which are responsible for reading and parsing a GenBank file and then displaying the information in the file within a Java window. The user can then edit the data and use the menu system to launch applications. Rebecca Machalow wrote a series of applications to graph compositional properties along the length of the sequence in the GenBank file. She then used her application to analyze the structure and evolution of plastid genomes for her senior research project. Bhavanna Nancherla wrote an application class for GARP that plots comparisons for homologous genes contained in any two GenBank files.
With the basis of GARP now written, future students can supplement it very easily by writing new Java classes and allowing GARP to launch that class from a menu item. In this way Professor Morton and his students can continually update GARP to introduce novel analytical techniques. In addition, students can use GARP to analyze GenBank files in their own research. The main applications in the near future will be in the area of organelle genome evolution - particularly analyses of structural features centered on the origin of replication - and analyses of codon usage bias.
GARP is still under development and not yet ready for its public debut. We anticipate providing access to the program in next year's annual report, either on a CD or through the Genetics at Barnard website.