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=== IBB-CEB === | === IBB-CEB === | ||
− | '''[http://www.ibb.pt/ IBB - Institute for Biotechnology and Bioengineering]''' | + | '''[http://www.ibb.pt/ IBB - Institute for Biotechnology and Bioengineering]''' |
− | '''[http://ceb.uminho.pt/ Centre of Biological Engineering]''' | + | '''[http://ceb.uminho.pt/ Centre of Biological Engineering]''' |
− | [[Image:Logo_ibb.png]] | + | [[Image:Logo_ibb.png]] |
=== CCTC === | === CCTC === | ||
− | '''[http://cctc.di.uminho.pt CCTC - Computer Science and Technology Center]''' | + | '''[http://cctc.di.uminho.pt CCTC - Computer Science and Technology Center]''' |
− | [[Image:Logo_cctc.png]] | + | [[Image:Logo_cctc.png]] |
Revision as of 00:02, 11 February 2009
Introduction
The OptGene application includes a number of tools to support in silico metabolic engineering. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the wild type and mutants (original strain with a set of selected gene deletions).
The simulation of these strains will be conducted using a number of approaches (e.g. Flux-Balance Analysis or Minimization of Metabolic Adjustment) that allow the set of fluxes in the organism's metabolism to be determined, given a set of environmental constraints. The software also includes a number of optimization methods (e.g. Evolutionary Algorithms or Simulated Annealing) to reach the best set of gene deletions given an objective function, typically related with a given industrial goal. It also integrates visualization tools from the BioVisualizer application.
A more complete description can be found in the manual, linked bellow. The OptGene application is being developed taking as a basis the AIBench framework. This is an environment for the development of Data Mining/ Bioinformatics tools, using the Java programming language. The details of this project, a collaboration between the universities of Minho (Portugal) and Vigo (Spain), as well as updated documentation can be found at the web site.
Institutions
University of Minho
University of Minho
IBB-CEB
IBB - Institute for Biotechnology and Bioengineering
Centre of Biological Engineering
CCTC
CCTC - Computer Science and Technology Center