BIRCH
is
- 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
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| 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. |
 |
A
collaboration with Abiel Roche (Univ. of Puerto
Rico) 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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