BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment.
BACKGROUND
Graphs and networks are common analysis representations for biological systems. Many traditional graph algorithms such as k-clique, k-coloring, and subgraph matching have great potential as analysis techniques for newly available data in biology. Yet, as the amount of genomic and bionetwork information rapidly grows, scientists need advanced new computational strategies and tools for dealing with the complexities of the bionetwork analysis and the volume of the data.


RESULTS
We introduce a computational framework for graph analysis called the Biological Graph Environment (BioGraphE), which provides a general, scalable integration platform for connecting graph problems in biology to optimized computational solvers and high-performance systems. This framework enables biology researchers and computational scientists to identify and deploy network analysis applications and to easily connect them to efficient and powerful computational software and hardware that are specifically designed and tuned to solve complex graph problems. In our particular application of BioGraphE to support network analysis in genome biology, we investigate the use of a Boolean satisfiability solver known as Survey Propagation as a core computational solver executing on standard high-performance parallel systems, as well as multi-threaded architectures.


CONCLUSIONS
In our application of BioGraphE to conduct bionetwork analysis of homology networks, we found that BioGraphE and a custom, parallel implementation of the Survey Propagation SAT solver were capable of solving very large bionetwork problems at high rates of execution on different high-performance computing platforms.
Chin
George
G
High Performance Computing Group, Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, Washington, USA. george.chin@pnl.gov
Chavarria
Daniel G
DG
Nakamura
Grant C
GC
Sofia
Heidi J
HJ
D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
D020543:Proteome