FastMEDUSA: a parallelized tool to infer gene regulatory networks.
BACKGROUND
In order to construct gene regulatory networks of higher organisms from gene expression and promoter sequence data efficiently, we developed FastMEDUSA. In this parallelized version of the regulatory network-modeling tool MEDUSA, expression and sequence data are shared among a user-defined number of processors on a single multi-core machine or cluster. Our results show that FastMEDUSA allows a more efficient utilization of computational resources. While the determination of a regulatory network of brain tumor in Homo sapiens takes 12 days with MEDUSA, FastMEDUSA obtained the same results in 6 h by utilizing 100 processors.


BACKGROUND
Source code and documentation of FastMEDUSA are available at https://wiki.nci.nih.gov/display/NOBbioinf/FastMEDUSA
Bozdag
Serdar
S
Neuro-Oncology Branch, National Cancer Institute, National Institute of Neurological Diseases and Stroke, Bethesda, MD 20892, USA.
Li
Aiguo
A
Wuchty
Stefan
S
Fine
Howard A
HA
D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software