Software Developed by T. M. Murali's Research Group
We have released all software on this page under version 3 of the
GNU General Public
. Many of these individual packages are available as
part of the Biorithm software suite
packages that are part of Biorithm, the links below take you to
the documentation for each package.
T. M. Murali
(murali at cs dot vt dot edu)
Last modified: Mon Oct 5 11:41:25 EDT 2015
- Network and Pathway Analysis
- GraphSpace, a
website for uploading, sharing, and collaborating with
a path-based algorithm to reconstruct
interactions in signaling pathways.
halp, a library of algorithms for directed and undirected hypergraphs.
- XTalk, a path-based approach for detecting crosstalk
between signaling pathways.
- Data-Driven Systems Biology
- Concise, Functional
Enrichment of Ranked Gene Lists, a method to compute a
small set of non-redundant functions that annotated a ranked
list of genes.
- NetworkLego, find
networks of molecular interactions activated in a cell state
or in response to a particular perturbation or stimulus and
compare and contrast these active networks to
construct network legos, building blocks of the
molecular interaction network.
enrichment, different methods for computing which sets of
pre-defined genes (e.g., biological pathways) are
over-represented in another set of genes, e.g.,
differentially-expressed genes in a treatment-control study.
a method for finding conserved protein interaction
networks. This software is not part of Biorithm.
- Predicting Gene Function
GAIN, a system for whole-genome
prediction of gene functions
- Gene Expression Analysis
- xMotif, an algorithm for computing
biclusters in gene expression data and (optionally) building
nearest-neighbour sample classifiers based on these biclusters.
- BiVoC, a system for automatic
layout and visualisation of biclusters
- Data Mining
- Bicluster mining in
binary matrices, our implementation of a level-wise
algorithm to find closed biclusters in binary matrices. This
algorithm is similar to Apriori (it incrementally adds rows
rather than columns), except that whenever it finds a new
bicluster it immediately adds all possible rows that make the
bicluster closed. The software outputs both the rows and columns
of the biclusters it finds.
mining, a method to find truth tables in binary and