Editing How to create a new model/project from text files

<b>How to create a new model/project from text files</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 a set of text files contemplating the distinct components of a model: a list of reactions and limits for the fluxes, a list of metabolites and a matrix with the reactions stoichiometry.<br>
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Start the
creation of a new project using the New Project Wizard. You can access
it either through the Project menu or the Toolbar.<br>
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<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/2/newProjectWizard.png</div>
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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 "Flat files" as the model source input.<br>
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<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/2/Step1NewProjectFlatFiles.png</div>
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<b>2nd step</b><br>
In
the 2nd step you have to define the input files for the Fluxes,
Stoichiometric Matrix (and choose the matrix format: full or sparse)
and for the Metabolites.<br>
It is also possible to load the GPR
(gene-protein-reaction) information from a flat file using the "Load
GPR information?" option.<br>
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<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/2/Step2NewProjectFlatFiles.png</div>
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<b>3rd step</b><br>
After choosing the
input flat files, you have to define the first index (0 or 1) and
the field delimiters for each of the files (comma, tab, white space or user
defined).<br>
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<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/2/Step3NewProjectFlatFiles.png</div>
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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 the 4th 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;">http://sites.google.com/site/optfluxhowtos/howtos/2/newProjectSBML.png</div>
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