mhs-calculator: a minimal hitting sets calculator
mhs-calculator is a free, command line tool for the computation of minimal hitting sets (mhs) in hypergraphs. mhs-calculator provides two different algorithmic implementations: a modified Berge algorithm and an integer program formulation (see below for references). The latter requires an external linear programming solver. MHScalculator provides interfaces to
- GLPK (open source)
- Gurobi (commerical, but free academic license)
- CPLEX (commerical, but free academic license)
If you use this software for your publications, please read and cite
- Christian Jungreuthmayer, Govind Nair, Steffen Klamt, and Jürgen Zanghellini. Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics 14:318 (2013). DOI:10.1186/1471-2105-14-318
- Christian Jungreuthmayer, Marie Beurton-Aimar, and Jürgen Zanghellini. Fast Computation of Minimal Cut Sets in Metabolic Networks with a Berge Algorithm that Utilizes Binary Bit Pattern Trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10:1 (2013). DOI:10.1109/TCBB.2013.116
Current version
MHScalculator version 1.0 (November 14, 2013)
License
MHScalculator can be redistributed and used in source form, with or without modification, provided agreeing to the Simplified BSD License.
Supported platforms
We developed, tested, and used MHScalculator on MAC OS X and Linux Debian systems. MHScalculator will certainly also run on other Linux distributions. Note that Windows computers are not supported by MHScalculator.
Download and installation
- Download and unzip and untar MHScalculator, e.g. tar -xzf 20131114_mhsCalculator_v1.1.<wbr></wbr>tar.gz
- Change to the newly created MHScalculator directory
- Read the provided README file
Compilation
The MHScalculator requires an installed posix thread library libpthread (including header file glpk.h). In order to use MHScalculator's linear programming algorithm - at least - one of the following solvers must be installed (library and header files):
- GLPK
- GUROBI
- CPLEX
If they cannot be found by make, the executables for the linear programming algorithms are not built! However, the Berge algorithm does not require any 'exotic' library and can be built anyway. In order to compile the executables, do the following:
- Execute ./configure
- Use ./configure's CFLAGS and LDFLAGS to tell make where to find the required header and library files
- Execute make
For details and examples how to use CFLAGS and LDFLAGS see the provided README file.
Usage
The package contains several examples including start scripts to run these examples. Read the README file and have a look at the directory example for further details.
Contact
Send comments, suggestions, feed back, and bug reports to:
Jürgen Zanghellini, juergen(dot)zanghellini(at)acib(dot)at *
* Please replace '(dot)' with '.' and '(at)' with '@'
Austrian Centre for Industrial Biotechnology (acib)
Web: http://www.acib.at