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Software for Organization Computation

OrgTools consists of several applications that integrate into the Systems Biology Workbench framework (SBW). In order for the integration of the applications to work properly, SBW needs to be installed (download here).
A manual and detailed installation instructions can be found in the downloads. If you use Linux you can choose, depending on your system, either the 32 bit or 64 bit version with precompiled libraries. They have been compiled under OpenSuSE 10.3. If they don't work properly on your system you might try to compile the libraries yourself and download the uncompiled distribution. For windows only a 32 bit version is available. If you have a 64 bit system, most functionality of the software will still work since only the heuristic and the constructive algorithms for organization computation rely on external libraries.

Required 3rd Party software

Systems Biology Workbench > 2.5
Java Runtime Environment >=1.5 for the precompiled distribution
Java SE Development Kit >=1.5 for the uncompiled distribution

Software distributions


Linux uncompiled
Linux 32 bit precompiled
Linux 64 bit precompiled


Only a 32 bit version is currently available.
Windows precompiled

Mac OS

No dedicated version for Mac OS is available yet. However, since the flux-based algorithm for organization computation does not necessitate the external libraries most functionality from the Linux uncompiled distribution should work without problems.

Bugs and Problems

If you encounter any bugs and problems please do not hesitate to email me: Christoph Kaleta