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+ | <center> | ||
+ | [[Image:Optflux splash 20141020.png]] | ||
+ | </center> | ||
+ | |||
__NOTOC__ | __NOTOC__ | ||
− | [[Image:1258649492 label new red.png]] | + | |
− | '''OptFlux | + | {| |
− | Check the [ | + | |- |
+ | |[[Image:1258649492 label new red.png]] | ||
+ | || | ||
+ | *'''New Optflux3 available! Download it here -> [http://sourceforge.net/projects/optflux/files/latest/download (Multi-platform)] <br> | ||
+ | A major new release of OptFlux is now available, with several important improvements and new features.<br> | ||
+ | Please visit also the new OptFlux website at [http://www.optflux.org www.optflux.org].<br> | ||
+ | '''A new tutorial is available in the section [[BeginnersTutorial]].''' | ||
+ | |} | ||
+ | |||
+ | '''SOURCEFORGE NOW AVAILABLE:''' - All the code is now available at sourceforge. | ||
+ | |||
+ | * Go to the [http://sourceforge.net/projects/optflux/ OptFlux Sourceforge Project]. | ||
+ | * You can also subscribe the [http://sourceforge.net/export/rss2_keepsake.php?group_id=327485 RSS Feed] to keep track of all the changes, releases and news ! | ||
+ | |||
+ | |||
+ | '''OptFlux is published, Please cite using:''' | ||
+ | |||
+ | *Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira and Miguel Rocha. | ||
+ | [http://www.biomedcentral.com/1752-0509/4/45 OptFlux: an open-source software platform for in silico metabolic engineering]. | ||
+ | ''BMC Systems Biology'' 2010, '''4''':45 | ||
+ | |||
+ | *Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha. | ||
+ | [http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains]. | ||
+ | ''BMC Bioinformatics'' 2008, '''9''':499 | ||
+ | |||
+ | *Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen. | ||
+ | [http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering]. | ||
+ | ''BMC Bioinformatics'' 2005, '''6''':308 | ||
+ | |||
+ | {| | ||
+ | |- | ||
+ | || | ||
+ | '''Older versions: | ||
+ | *'''OptFlux 2.4 with Add Reactions plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br> | ||
+ | *'''OptFlux 2.3 with Over and Under Expression plug-in ''' Check the [[Plugins|plugins section]] for the download link and the documentation. <br> | ||
+ | *'''Regulatory Tool''' Check the [[Downloads|downloads section]] and the [[Plugins|plugins documentation]]. | ||
+ | |} | ||
+ | |||
+ | Problems with SBML? Validate your sbml model [http://sbml.org/Facilities/Validator here]! | ||
== Introduction == | == Introduction == | ||
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'''The OptFlux application includes a number of tools to support <font color="#FF7800">''in silico'' metabolic engineering</font>. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the <font color="#FF7800">wild type and mutants</font> (original strain with a set of selected gene deletions).''' | '''The OptFlux application includes a number of tools to support <font color="#FF7800">''in silico'' metabolic engineering</font>. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the <font color="#FF7800">wild type and mutants</font> (original strain with a set of selected gene deletions).''' | ||
− | + | ||
− | |||
− | |||
'''The simulation of these strains will be conducted using a number of approaches (e.g. <font color="#FF7800">Flux-Balance Analysis, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes</font>) 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. <font color="#FF7800">Evolutionary Algorithms or Simulated Annealing</font>) 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.''' | '''The simulation of these strains will be conducted using a number of approaches (e.g. <font color="#FF7800">Flux-Balance Analysis, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes</font>) 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. <font color="#FF7800">Evolutionary Algorithms or Simulated Annealing</font>) 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.''' | ||
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[[Image:Uminho.gif]] | [[Image:Uminho.gif]] | ||
− | === | + | === CEB === |
− | |||
− | |||
'''[http://ceb.uminho.pt/ Centre of Biological Engineering]''' | '''[http://ceb.uminho.pt/ Centre of Biological Engineering]''' | ||
− | [[Image: | + | [[Image:Logoceb.png]] |
− | === | + | === SilicoLife === |
− | '''[http:// | + | '''[http://www.silicolife.com SilicoLife]''' |
− | [[Image: | + | [[Image:Silicolife_logo_w.png]] |
− | |||
− | |||
− | |||
== Powered By == | == Powered By == | ||
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== License == | == License == | ||
− | <br><font color="#FF7800"><b>Copyright 2009<br> | + | <br><font color="#FF7800"><b>Copyright 2009-2014<br> |
− | [http:// | + | [http://www.ceb.uminho.pt/ CEB - Centre of Biological Engineering]<br> |
− | [http://www | + | [http://www.uminho.pt/ University of Minho]<br> |
− | [http://www. | + | [http://www.silicolife.com/ SilicoLife Lda.] |
<br> | <br> | ||
<br>This is free software: you can redistribute it and/or modify | <br>This is free software: you can redistribute it and/or modify | ||
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<br><font color="#FF7800">Created inside the SysBio Research Group [http://sysbio.di.uminho.pt/ (http://sysbio.di.uminho.pt)] | <br><font color="#FF7800">Created inside the SysBio Research Group [http://sysbio.di.uminho.pt/ (http://sysbio.di.uminho.pt)] | ||
</font> | </font> | ||
− | + | <br><font color="#FF7800">Supported by SilicoLife Lda. [http://www.silicolife.com/ (http://www.silicolife.com)] | |
+ | </font> | ||
[[Image:Gpl.png]] | [[Image:Gpl.png]] | ||
[http://www.gnu.org/licenses/gpl-3.0.html http://www.gnu.org/licenses/gpl-3.0.html] | [http://www.gnu.org/licenses/gpl-3.0.html http://www.gnu.org/licenses/gpl-3.0.html] |
Latest revision as of 14:31, 21 October 2014
![]() |
A major new release of OptFlux is now available, with several important improvements and new features. |
SOURCEFORGE NOW AVAILABLE: - All the code is now available at sourceforge.
- Go to the OptFlux Sourceforge Project.
- You can also subscribe the RSS Feed to keep track of all the changes, releases and news !
OptFlux is published, Please cite using:
- Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira and Miguel Rocha.
OptFlux: an open-source software platform for in silico metabolic engineering. BMC Systems Biology 2010, 4:45
- Miguel Rocha , Paulo Maia , Rui Mendes , José P Pinto , Eugénio C Ferreira , Jens Nielsen , Kiran Raosaheb Patil and Isabel Rocha.
Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics 2008, 9:499
- Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster and Jens Nielsen.
Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005, 6:308
Older versions:
|
Problems with SBML? Validate your sbml model here!
Introduction
The OptFlux 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, Minimization of Metabolic Adjustment or Regulatory On/Off Minimization of metabolic fluxes) 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.
The OptFlux 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![]()
CEB
Centre of Biological Engineering![]()
SilicoLife
SilicoLife![]()
Powered By
License
Copyright 2009-2014
CEB - Centre of Biological Engineering
University of Minho
SilicoLife Lda.
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)
Supported by SilicoLife Lda. (http://www.silicolife.com)