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News

Aug 2013
yoshiko version 2.0

We have released yoshiko version 2.0, a mature version of our cluster editing algorithm. It has been implemented mostly by Emanuel Laude and contains a lot of helpful redcution rules from fixed parameter algorithmics and a powerful heuristic for large data sets.

24 Aug 2011
natalie version 2.0

We have released natalie version 2.0, a mature version of our network alignment algorithm.

27 Jun 2011
side chain placement

scp is a package that contains our code for exact side chain placement as used in a recent paper in Optimization Letters.

5 Mar 2010
heinz and BioNet

heinz now works together with the BioNet package.

17 Dec 2008
yoshiko/charles

The yoshiko/charles code is now online. The tool solves the cluster editing problem as well as its directed "cousin", the transitivity editing problem, to provable optimality.

1 Sep 2008
planet lisa moves to Amsterdam

The planet lisa project is now based at the Centre for Mathematics and Computer Science (CWI) in Amsterdam, The Netherlands.

20 Jul 2008
ISMB 2008

Our paper Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach has won the oustanding paper award at ISMB 2008 in Toronto, Canada. See the heinz section for more information on our software to discover optimal subnetworks with respect to our signal-based scoring scheme of p-values.

Jul 2008
ISMB 2008

We will give a presentation at ISMB 2008 on Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach. Our software is available as the heinz package.

Oct 07
Algorithmic Operations Research

Our theoretical lara paper has been accepted for publication in Algorithmic Operations Research.

27 Jul 07
BMC Bioinformatics

The paper describing the lara program has been accepted for publication in BMC Bioinformatics.

28 Jun 07
4SALE support for lara

lara has been integrated into the RNA alignment and editing framework 4SALE. Get the latest lara version that is compatible with 4SALE.

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Heinz 1.0 is an outdated version.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.

warning 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
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