Algorithms for Strain Optimization

This page contains libraries developed in the Java programming language intended to support in silico metabolic engineering tasks.


Instructions


Dependencies:

The use of Java JRE 1.6.x is mandatory. The user must also install the GLPK package and have the executable glpsol in the PATH or in the directory where the application (executable.jar) is executed (both windows and linux).

Running:

  1. download the archive example.tar.gz from the link bellow
  2. extract the files therein contained to a directory of your choice
  3. inside the user will find 6 files:
    executable.jar - this is the software itself packed in a java archive
    exampleEA.conf - configuration file to perform optimization using the Evolutionary Algorithm (instructions inside the file)
    exampleSA.conf - configuration file to perform optimization using the Simulated Annealing Algorithm (instruction inside the file)
    EcoliSimp.fluxes - flux bound information for the E. coli metabolic model (Reed et al, 2003)
    EcoliSimp.matrix - stoichiometric coefficients for the E. coli metabolic model (Reed et al, 2003)
    EcoliSimp.crit - some of the critical fluxes identified
  4. to start a process use the command:

    java -jar executable.jar example[EA/SA].conf



  5. to modify or tune a given process the user must redefine the properties of the configuration file. The properties and their options are explained inside those files

Downloads:

Software binary and examples (platform independent) - example.tar.gz
Libraries source code - source.tar.gz


License:




Copyright 2008
CCTC - Computer Science and Technology Center
IBB-CEB - Institute for Biotechnology and Bioengineering - Centre of Biological Engineering
University of Minho


This is free software: you can redistribute it and/or modify
it under the terms of the GNU Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This code is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Public License for more details.

You should have received a copy of the GNU Public License
along with this code. If not, see http://www.gnu.org/licenses/>

Created inside the SysBio Research Group (http://sysbio.di.uminho.pt)