heinz
Heinz 1.0 is an outdated version. For the most recent version, see https://github.com/ls-cwi/heinz
The planet LiSA library is now hosted in
"Amsterdam"
heinz ("heavy induced subgraphs") computes exact solutions to the maximum-weight connected subgraph problem. The tool is a result of a cooperation with researchers from the Biozentrum, University of Würzburg, where we use it to identify significantly differentially expressed functional modules in protein-protein interaction data.
The data we used in our paper "Identifying Functional Modules in Protein-Protein Interaction Networks: An Integrated Exact Approach" can also be found on this page.
heinz works together with the
BioNet R package.

Please note that you need a CPLEX license to run the current version of our software (more precisely, the dhea code needs the license). If you do not have CPLEX, you can also compute heuristic modules using only
BioNet.
See also Ivana Ljubic's
page on dhea and the corresponding paper
An algorithmic framework for the exact solution of the prize-collecting Steiner tree problem. Mathematical Programming, Series B, 105(2-3):427-449, 2006, by I. Ljubic, R. Weiskircher, U. Pferschy, G. Klau, P. Mutzel, and M. Fischetti.
Quick Start
All the tasks are performed by the main python script
heinz.py
.
Typing
$./heinz.py -h
will yield the following output:
Usage: heinz.py [options]
Options:
-h, --help show this help message and exit
-n FILE, --nodefile=FILE
WUE file with node information
-e FILE, --edgefile=FILE
WUE file with edge information
-s NO_SUBOPT, --no_subopt=NO_SUBOPT
number of suboptimal solutions
-d SUBOPT_DIFF, --subopt_diff=SUBOPT_DIFF
difference between sol (Ham. dist in % or -1)
-t TOLERANCE, --tolerance=TOLERANCE
solutions may be this percentage off optimum (default:
0)
-H HEINZTMP, --heinztmp=HEINZTMP
heinz tmp dir
-r RUN_HEINZ, --run=RUN_HEINZ
run PCST code on transformed instances
-c COLLECT_SOLUTIONS, --collect=COLLECT_SOLUTIONS
collect solutions and write heinz outputfile
-a ADDITIONAL_DHEA_OPTIONS, --additional=ADDITIONAL_DHEA_OPTIONS
additional options for dhea
-v, --verbose verbose output
-N CONSIDER_NODE_WEIGHTS, --consider_node_weights=CONSIDER_NODE_WEIGHTS
consider node weights
-E CONSIDER_EDGE_WEIGHTS, --consider_edge_weights=CONSIDER_EDGE_WEIGHTS
consider edge weights
-D, --DIMACS convert to DIMACS format
Installation
If you have trouble with the installation, please contact
G. Klau.
Download
version |
date |
link |
description |
1.0 |
Jan 08 |
heinz 1.0 |
version (64 bit Linux) used for computations in our paper submitted to ISMB 2008 |
|
Apr 08 |
Edges.txt |
edges of the network used in the ISMB 2008 paper |
|
Apr 08 |
Score0001.txt |
nodes of the network used in the ISMB 2008 paper with weights according to a FDR of .0001 |
1.63 |
Mar 10 |
heinz package |
version (64 bit Linux) that works in combination with BioNet |
1.67 |
16 Jul 2012 |
heinz package |
works with CPLEX 12.4 |