Difference between revisions of "Main Page"

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'''MediaWiki has been successfully installed.'''
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_NOTOC__
  
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Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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{|
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|-
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|[[Image:1258649492 label new red.png]]
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||
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*'''OptFlux 2.4 with Add Reactions plug-in ''' is now available! Check the [[Plugins|plugins section]] for the download link and the documentation. <br>
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*'''OptFlux 2.3RC1 with Over and Under Expression plug-in ''' is now available! Check the [[Plugins|plugins section]] for the download link and the documentation. <br>
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*'''NOTE:''' This is a release candidate version, it does not include most of the plug-ins included in the previous release. OptFlux 3 will be released soon.
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|}
  
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== Getting started ==
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'''SOURCEFORGE NOW AVAILABLE:''' - All the code is now available at sourceforge.
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* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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* Go to the [http://sourceforge.net/projects/optflux/ OptFlux Sourceforge Project].
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* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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* 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 !
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'''OptFlux is now published'''. Please cite using:
 +
 
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*Isabel Rocha , Paulo Maia , Pedro Evangelista , Paulo Vilaça , Simão Soares , José P Pinto , Jens Nielsen , Kiran R Patil , Eugénio C Ferreira  and Miguel Rocha.
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[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.
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[http://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains].
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''BMC Bioinformatics'' 2008, '''9''':499
 +
 
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*Kiran Raosaheb Patil , Isabel Rocha , Jochen Förster  and Jens Nielsen.
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[http://www.biomedcentral.com/1471-2105/6/308/ Evolutionary programming as a platform for in silico metabolic engineering].
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''BMC Bioinformatics'' 2005, '''6''':308
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{|
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|-
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|[[Image:1258649492 label new red.png]]
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||
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*'''OptFlux 2.2''' is now available! Check the [[Downloads|downloads section]] and the [[HowTos|new documentation]]. <br>
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*'''Regulatory Tool''' is now available! Check the [[Downloads|downloads section]] and the [[Plugins|plugins documentation]].
 +
|}
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Problems with SBML? Validate your sbml model [http://sbml.org/Facilities/Validator here]!
 +
 
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== Introduction ==
 +
 
 +
'''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).'''
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<center>
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[[Image:Logo.png]]
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</center>
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'''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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'''The OptFlux application is being developed taking as a basis the <font color="#FF7800">AIBench framework</font>. 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.'''
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== Institutions ==
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=== University of Minho ===
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'''[http://www.uminho.pt University of Minho]'''
 +
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[[Image:Uminho.gif]]
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=== IBB-CEB ===
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'''[http://www.ibb.pt/ IBB - Institute for Biotechnology and Bioengineering]'''
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'''[http://ceb.uminho.pt/ Centre of Biological Engineering]'''
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[[Image:Logo_ibb.png]]
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=== CCTC ===
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'''[http://cctc.di.uminho.pt  CCTC - Computer Science and Technology Center]'''
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[[Image:Logo_cctc.png]]
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== Powered By ==
 +
 
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[[Image:Aibenchlogo.png]] [http://www.aibench.org  www.aibench.org]
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[[Image:Sbml.jpg]] [http://www.sbml.org www.sbml.org]
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== License ==
 +
 
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<br><font color="#FF7800"><b>Copyright 2009<br>
 +
[http://cctc.uminho.pt CCTC - Computer Science and Technology Center]<br>
 +
[http://www.ceb.uminho.pt/ IBB-CEB - Institute for Biotechnology and  Bioengineering - Centre of Biological Engineering]<br>
 +
[http://www.uminho.pt/ University of Minho]
 +
<br>
 +
<br>This is free software: you can redistribute it and/or modify
 +
<br>it under the terms of the GNU Public License as published by
 +
<br>the Free Software Foundation, either version 3 of the License, or
 +
<br>(at your option) any later version.
 +
<br>
 +
<br>This code is distributed in the hope that it will be useful,
 +
<br>but WITHOUT ANY WARRANTY; without even the implied warranty of
 +
<br>MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 +
<br>GNU Public License for more details.
 +
<br>
 +
<br>You should have received a copy of the GNU Public License
 +
<br>along with this code.  If not, see [http://www.gnu.org/licenses/ http://www.gnu.org/licenses/]
 +
<br>
 +
<br><font color="#FF7800">Created inside the SysBio Research Group [http://sysbio.di.uminho.pt/ (http://sysbio.di.uminho.pt)]
 +
</font>
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 +
 
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 +
[[Image:Gpl.png]]
 +
[http://www.gnu.org/licenses/gpl-3.0.html http://www.gnu.org/licenses/gpl-3.0.html]

Revision as of 11:16, 26 March 2012

_NOTOC__

1258649492 label new red.png
  • OptFlux 2.4 with Add Reactions plug-in is now available! Check the plugins section for the download link and the documentation.
  • OptFlux 2.3RC1 with Over and Under Expression plug-in is now available! Check the plugins section for the download link and the documentation.
  • NOTE: This is a release candidate version, it does not include most of the plug-ins included in the previous release. OptFlux 3 will be released soon.

SOURCEFORGE NOW AVAILABLE: - All the code is now available at sourceforge.


OptFlux is now 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

1258649492 label new red.png

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).

File:Logo.png

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

Uminho.gif

IBB-CEB

IBB - Institute for Biotechnology and Bioengineering

Centre of Biological Engineering

Logo ibb.png

CCTC

CCTC - Computer Science and Technology Center

Logo cctc.png



Powered By

Aibenchlogo.png www.aibench.org

File:Sbml.jpg www.sbml.org



License


Copyright 2009
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)


Gpl.png http://www.gnu.org/licenses/gpl-3.0.html

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