Heuristics for simulated annealing search of active sub-networks in bio-molecular interaction network

Software and Case Studies

Heuristics for simulated annealing search of active sub-networks in bio-molecular interaction network
Kiran Raosaheb Patil, Simão Soares, Isabel Rocha

Software Download
Binary - Linux/Unix 64bit (with dynamic library)
Binary - SunOS/Sparc

Case studies
A - Yeast / GDH1
B - Yeast / SDH3
C - Human / T2DM

How to quickly run Sub-network discovery algorithm

./Subnetwork -r 1 -b 0 -q 0 -p <int> -s 1 -a <node association file> -d <p-values file> <network file> <output file>

Initalization heuristics defined using -p <int value>
-p 1    Random
-p 2    P0
-p 3    P1
-p 4    P0P1
-p 5    Algorithmic lower bound

For more information use --help option.

Contacts:
krp @ bio.dtu.dk
simao.soares @ deb.uminho.pt