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http://sites.google.com/site/optfluxhowtos/howtos/1/newProjectWizard.png | http://sites.google.com/site/optfluxhowtos/howtos/1/newProjectWizard.png | ||
− | + | <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> | ||
+ | <b> | ||
<div style="display: block; text-align: left;"> | <div style="display: block; text-align: left;"> | ||
− | http://sites.google.com/site/optfluxhowtos/howtos/1/Step1NewProjectSBML.png</div | + | http://sites.google.com/site/optfluxhowtos/howtos/1/Step1NewProjectSBML.png</div> |
− | + | </b><br> | |
OptFlux | OptFlux | ||
− | allows you to load | + | 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> | ||
− | + | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/1/Step2NewProjectSBML.png</div> | |
− | </b | + | </b><br> |
− | <b> | + | <b>3rd step</b><br> |
− | To allow OptFlux to determine the external metabolites you can choose to use "Use compartments heuristics" or "Use regular expressions". | + | To allow |
+ | OptFlux to determine the external metabolites you can choose to use | ||
+ | "Use compartments heuristics" or "Use regular expressions".<br> | ||
<br> | <br> | ||
− | The first detects external metabolites based on the definitions of the compartments contained in the SBML file. | + | The first detects external metabolites based on the definitions of the compartments contained in the SBML file.<br> |
− | 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> | + | Using |
− | You can also load the most commonly used regular expressions using the option "Load common regexps". | + | 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> | ||
<br> | <br> | ||
+ | <div style="display: block; text-align: left;"> | ||
+ | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/1/Step3NewProjectSBML.png</div> | ||
<br> | <br> | ||
− | + | </div> | |
<br> | <br> | ||
+ | <b>4th step</b><br> | ||
+ | In the 4th step, you can validate the information regarding external metabolites / drains detected by OptFlux adding or removing elements to the original list.<br> | ||
<br> | <br> | ||
− | <b> | + | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/1/Step4NewProjectSBML.png</div> |
− | + | <br> | |
+ | <br> | ||
+ | <b>5th step</b><br> | ||
+ | In the 5th step, you have to validate the biomass/ growth flux automaticaly detected. You can change it if the heuristic used in the detection did not work.<br> | ||
<br> | <br> | ||
− | + | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/1/Step5NewProjectSBML.png</div> | |
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