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
Linux uncompiled
Linux 32 bit precompiled
Linux 64 bit precompiled
Windows
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 at
ckaleta@minet.uni-jena.de