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<br>
 
<br>
 
http://sites.google.com/site/optfluxhowtos/howtos/1/newProjectWizard.png
 
http://sites.google.com/site/optfluxhowtos/howtos/1/newProjectWizard.png
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<br><br>
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<br>
 
<b>1st step</b><br>
 
<b>1st step</b><br>
 
In the 1st step of the wizard you have to enter a name to the project and choose SBML as the model source input.<br>
 
In the 1st step of the wizard you have to enter a name to the project and choose SBML as the model source input.<br>
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<b>
 
<div style="display: block; text-align: left;">
 
<div style="display: block; text-align: left;">
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http://sites.google.com/site/optfluxhowtos/howtos/1/Step1NewProjectSBML.png</div><br>
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http://sites.google.com/site/optfluxhowtos/howtos/1/Step1NewProjectSBML.png</div>
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<b>2nd step</b><br>
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</b><br>
 
OptFlux
 
OptFlux
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allows you to load Standard SBML files and also CellDesigner SBML files.<br>
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allows you to load pure SBML files and also CellDesigner SBML files.<br>
 
In
 
In
 
the 2nd step, you have to define the type of the file, and also choose
 
the 2nd step, you have to define the type of the file, and also choose
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<b>
 
<b>
 
[[Image:Step2 sbml.png]]
 
[[Image:Step2 sbml.png]]
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</b><br><br>
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</b><br>
 
<b>3th step</b><br>
 
<b>3th step</b><br>
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To allow OptFlux to determine the external metabolites you can choose to use "Use compartments heuristics" or "Use regular expressions".
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For each external metabolite, OptFlux will automatically assign a drain reaction for its uptake or secretion. In the 4th step, you can change add/or validate the information regarding external metabolites / drains detected by OptFlux adding or removing elements to the original list.<br>
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<br>
 
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The first detects external metabolites based on the definitions of the compartments contained in the SBML file.
 
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Using the regular expressions option you can easily set up an expression to detect external metabolites from patterns in their names using the options: "starting with" / "ending with" / "contains" / "match regexp".<br>
 
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You can also load the most commonly used regular expressions using the option "Load common regexps".
 
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<br>
 
<br>
 
[[Image:Step3 sbml.png]]
 
[[Image:Step3 sbml.png]]

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