From Optflux
Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.
The edit can be undone.
Please check the comparison below to verify that this is what you want to do, and then save the changes below to finish undoing the edit.
| Latest revision | Your text | ||
| Line 8: | Line 8: | ||
it either through the Project menu or the Toolbar.<br> | it either through the Project menu or the Toolbar.<br> | ||
<br> | <br> | ||
| − | http://sites.google.com/site/optfluxhowtos/howtos/1/newProjectWizard.png | + | http://sites.google.com/site/optfluxhowtos/howtos/1/newProjectWizard.png</div> |
| − | < | + | <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 | ||
| Line 26: | Line 27: | ||
<br> | <br> | ||
<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> | |
<br> | <br> | ||
<br> | <br> | ||