The Redirector framework is a set of methods based on a steady state model of bacterial metabolism (Flux Balance Analysis FBA) for finding metabolic engineering target to optimize microbial factories, or a desired flux phenotype. The core concept of the Redirector approach is to model the impact of alterations to the organisms genetic / enzyme level components on the flux of metabolites through its metabolic network by reconstructing the metabolic objective.

This software package has only just been opened to general usage so please be aware that it has not been thoroughly tested by public users. I will be working to make it less buggy, better commented and easier to use. Constructive feedback and suggestions are appreciated but development time is limited, thanks for your patience.

• See the Redirctor GIT Wiki: 'http://github.com/bionomicron/Redirector/wiki'
• Also try auto documentation from in line python documentation

• PuLP-or: http://code.google.com/p/pulp-or/
• Installing PuLP-or: http://code.google.com/p/pulp-or/wiki/InstallingPulpatHome

• ModelFactory: Factory object for parsing and generating LinearModel objects from flat files
• LinearModel: Main data file for flux balance analysis and objective construction models
• OptimizationControlRedirector: Analysis object which performs progressive target discovery

• Default config file is 'Redirector.config'
• Format: standard python config setup
• Changing '''Redirector Model''' configuration in this file will change the setting for all other configurations
• Setting up different Config Tags will allow for easy development and tracking of all framework features related to a particular optimization.

• Command line help information

  $ python Redirector.py -h

• Most used command line inputs information

  $ python Redirector.py -c <config file> -n <configuration tag>\
			---model_config <model config file> -m <model name>\
			-b <biological objective> -s <production objective>\
			 --iter <number of iterations> --sn <search neighborhood>\
			--section <subsection of loaded model to use>\
			--control <flat,binary,sense>\
			--simocontrol <number of simulatanious metabolic alterations to a target>\
			--report

• Pre-made configuration

  $ python Redirector.py --n <configuration tag>

• Example configuration using very simple model (included in repository) ''' $ python Redirector.py -n "Test Simple Model" '''

• Example command line of iAF1260 model test configuration

$ python Redirector.py -n "Test iAF1260"