Bit Research and Software

  • is a comprehensive desktop bioinformatics system integrating many of the commonly-used bioinformatics programs
  • is a framework of tools, files, and documentation for organizing and managing a bioinformatics core facility
  • can be customized by seamlessly merging 3rd party applications into BIRCH
BioLegato is best thought of as a program that runs other programs. bioLegato is the primary graphic interface for launching programs in BIRCH. For each program, bioLegato provides a menu that lets you set program parameters, launch the program, and view the output. bioLegato takes care of all of the background details, such as translating files from one format into another. In many cases, output also goes to a new bioLegato window, making it possible to do ad hoc pipelining. This is one of the most powerful aspects of bioLegato, because it means that you can usually run additional programs using the output of one program as the input of the next. In contrast, most browser-based applications display output in a human-readable form that allows no further analysis by other programs.
Turtleshell - Turtleshell is a subset of the bash shell, written in Java. The big question is, why?
  • run existing shell scripts on any platform
  • cross-platform wrappers and scripts

Turtleshell is currently a partly-working prototype. Our immediate goal is to implement enough bash-like functionality to make it possible for BIRCH to run on MS-Windows. However, Turtleshell quite generic, and could potentially be used for almost any software development project, we

Ph.D. student Abiel Roche (Computer Science) is investigating the application of a class of Finite State Automata, called Transducers, to the comparison of biological networks between different species, or between members of the same species in different experimental conditions. The goal is to develop metrics for quantifying the differences between congruent pathways, and for identifying subnetworks that are congruent between larger networks.

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