Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Genomics:GTL Program Projects
Sandia National Laboratories
25
BiLab – A New Tool that Combines the Ease-of-Use of MatLab and the Power of Multiple Computational Biology Libraries
Al Geist* (gst@ornl.gov) and David Jung
Oak Ridge National Laboratory, Oak Ridge, TN
As part of the Genomics:GTL Synechococcus: From Molecular Machines to Hierarchical Modeling project, we are developing a new tool called BiLab that we hope will revolutionize computational biology the way the MatLab revolutionized numerical linear algebra. MatLab is widely used to do analysis, to develop new algorithms, and to teach students. MatLab is easy enough for new users and powerful enough for sophisticated users. Yet under the covers it is just a scripting language that provides easy access to the robust linear algebra functions in the LAPACK library. BiLab takes a similar approach except instead of only understanding matrices and doing linear algebra, BiLab understands biological objects such as DNA, proteins, and molecules and is able to manipulate them through any of the functions in a half-dozen standard computational biology libraries. And BiLab is able to display results in biologically relevant form, for example, a protein may be displayed as a molecule, a sequence alignment as stacked sequences.
We developed the BiLab scripting language to cater to different level of expertise in the user, from biologists who just want a quick way to use existing functions to bioinformatics programmers who want to write sophisticated programs in the BiLab scripting language. We have developed the tool to allow the easy addition of new biological objects and functions. Today BiLab provides access to all the functions in bioJava, bioPython, the text based NCBI tools, Jmol, JalView, and CDK. Developers can extend the scripting language to understand new biology. Thus the tool is designed to evolve with the Genomics: GTL program.
Like MatLab, data can be typed in manually or read in from files. BiLab understands the concept of remote biological databases and is able to dynamically load data from SwissProt, GenBank, FASTA, Protein Data Bank, EMBL, and other databases for analysis and study.
This presentation will describe how BiLab is built, how it can be extended, and hands-on demonstrations of the capabilities of the BiLab prototype.
Acknowledgement: This project is supported by the U.S.Department of Energy’s Genomics:GTL Program under project “Carbon Sequestration in Synechococcus sp: From Molecular Machines to Hierarchical Modeling” (http://www.genomes-to-life.org)
* Presenting author
