Editing How to create a new model/project from SBML

<b>
How to create a new model/project from SBML</b><br>
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In OptFlux, metabolic models are the basis for all the work. The concept of Project gathers all data generated for a given model. Therefore, projects can be created providing a model. In this How To, we show how to create a model, given an SBML file with the required information. To know more about the SBML format check http://www.sbml.org.<br>
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Start the
creation of a new project using the <i>New Project Wizard</i>. You can access
it either through the Project menu or the Toolbar.<br>
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http://sites.google.com/site/optfluxhowtos/howtos/1/newProjectWizard.png
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<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>
<div style="display: block; text-align: left;">
http://sites.google.com/site/optfluxhowtos/howtos/1/Step1NewProjectSBML.png</div><br>
<b>2nd step</b><br>
OptFlux
allows you to load Standard SBML files and also CellDesigner SBML files.<br>
In
the 2nd step, you have to define the type of the file, and also choose
the name and location of the file you want to load.<br>
If you want to load GPR
(gene-protein-reaction) information from the SBML file, choose the option
"Load GPR information if available".<br>
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[[Image:Step2 sbml.png]]
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<b>3th step</b><br>
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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[[Image:Step3 sbml.png]]
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<b>4th step</b><br>
The identification of the reaction corresponding to biomass formation is an essential task for performing simulations. In this step you have to validate the biomass/ growth reaction automatically detected. You can change it if the heuristic used in the detection did not work.<br>
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[[Image:Step4.png]]
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And that's all! After created, the new Project will be available in the clipboard and you can enjoy the OptFlux features.<br>
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<div style="display: block; text-align: left; margin-right: auto;">http://sites.google.com/site/optfluxhowtos/howtos/1/newProjectSBML.png</div>
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@@ Line 29: / Line 29: @@
 </b><br><br>
 <b>3th step</b><br>
-To allow OptFlux to determine the external metabolites you can choose to use "Use compartments heuristics" or "Use regular expressions".
+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>
-<br>
-The first detects external metabolites based on the definitions of the compartments contained in the SBML file.
-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>
-You can also load the most commonly used regular expressions using the option "Load common regexps".
-<br>
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 [[Image:Step3 sbml.png]]