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All features of plug-in can be accessed under the “Plugins-> Add Reactions” menu. | All features of plug-in can be accessed under the “Plugins-> Add Reactions” menu. | ||
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− | [[Image:AddReactionsMenu.png | + | [[Image:AddReactionsMenu.png]] |
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== How to import database reactions == | == How to import database reactions == | ||
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Choose the option “SBML File” in menu. It will be appear a new window when you can choose the project, SBML file and the name of database. | Choose the option “SBML File” in menu. It will be appear a new window when you can choose the project, SBML file and the name of database. | ||
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− | [[Image:AddReactionsSBML.png | + | [[Image:AddReactionsSBML.png]] |
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After press “Ok”, the all the reactions will be loaded into the clipboard. | After press “Ok”, the all the reactions will be loaded into the clipboard. | ||
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− | [[Image:AddReactionsClipboard.png | + | [[Image:AddReactionsClipboard.png]] |
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<br><b>2. Flat files</b><br> | <br><b>2. Flat files</b><br> | ||
If you choose “Flat Files” option in menu, you must indicate the metabolites, fluxes and stoichiometric matrix text files. | If you choose “Flat Files” option in menu, you must indicate the metabolites, fluxes and stoichiometric matrix text files. | ||
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− | [[Image:AddReactionsFF.png | + | [[Image:AddReactionsFF.png]] |
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<br><b>3. TXT Files</b><br> | <br><b>3. TXT Files</b><br> | ||
This is a new format representation for reactions and metabolites. In this case, you must indicate the metabolites and reactions text files. More information about files format can be found here. | This is a new format representation for reactions and metabolites. In this case, you must indicate the metabolites and reactions text files. More information about files format can be found here. | ||
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− | [[Image:AddReactionsTXT.png | + | [[Image:AddReactionsTXT.png]] |
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<br><b><i>Choose Files</i></b><br> | <br><b><i>Choose Files</i></b><br> | ||
Select the reactions and metabolites files. Click in “Open” button. | Select the reactions and metabolites files. Click in “Open” button. | ||
− | + | <br><b><i>Apply Filters</i></b><br> | |
You can select, by applying filters, a subset of reactions. For do this, click in “Add” to insert a new filter. When you have all filters that you want apply, click in “Apply” button. The filters can be applied in conjunction or disjunction of them. You can remove or edit a filter by select it and click in button “Remove” or “Edit”. | You can select, by applying filters, a subset of reactions. For do this, click in “Add” to insert a new filter. When you have all filters that you want apply, click in “Apply” button. The filters can be applied in conjunction or disjunction of them. You can remove or edit a filter by select it and click in button “Remove” or “Edit”. | ||
− | + | <br><b><i>Import Reactions</i></b><br> | |
When all reactions that you want import are present in reactions table, you need select the Project, a name for database and press the “Save” button. A new database will be created in selected project with the reactions visible in table (2). | When all reactions that you want import are present in reactions table, you need select the Project, a name for database and press the “Save” button. A new database will be created in selected project with the reactions visible in table (2). | ||
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The mutant simulation with addiction of reactions can be access in “Plugins -> Add Reactions->Simulation” menu. | The mutant simulation with addiction of reactions can be access in “Plugins -> Add Reactions->Simulation” menu. | ||
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<br><br><b><i>Select knockouts and added reactions</i></b><br> | <br><br><b><i>Select knockouts and added reactions</i></b><br> | ||
After choose the database, you can select a set of reactions from “Reactions” list using the buttons (arrows). The reactions that will be added to the model appear in the “Add Reactions” box. The same process is used to select the list of knockouts. | After choose the database, you can select a set of reactions from “Reactions” list using the buttons (arrows). The reactions that will be added to the model appear in the “Add Reactions” box. The same process is used to select the list of knockouts. | ||
− | + | <br><b><i>Select Simulation Method</i></b><br> | |
OptFlux can use several simulation methods, namely: Flux Balance Analysis, ROOM-LP, ROOM-MILP and MOMA. When you only add reactions to the model, only the FBA method should be used. | OptFlux can use several simulation methods, namely: Flux Balance Analysis, ROOM-LP, ROOM-MILP and MOMA. When you only add reactions to the model, only the FBA method should be used. | ||
ROOM-LP stands for the Regulatory On-Off Minimization Method (ROOM), using a linear programming (LP) relaxation; ROOM-MILP is the original ROOM that uses a Mixed Integer LP (MILP) method; MOMA stands for the Minimization of Metabolic Adjustment method that uses quadratic programming. | ROOM-LP stands for the Regulatory On-Off Minimization Method (ROOM), using a linear programming (LP) relaxation; ROOM-MILP is the original ROOM that uses a Mixed Integer LP (MILP) method; MOMA stands for the Minimization of Metabolic Adjustment method that uses quadratic programming. | ||
− | + | <br><b><i>Objective Function Configuration</i></b><br> | |
Here you can select the reaction to optimize (biomass, by default), and you can also define if you will be maximizing or minimizing the flux. | Here you can select the reaction to optimize (biomass, by default), and you can also define if you will be maximizing or minimizing the flux. | ||
− | + | <br><b><i>Select Environmental Conditions</i></b><br> | |
If you have created environmental conditions you can select them to be used as constrains in the simulation. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced. | If you have created environmental conditions you can select them to be used as constrains in the simulation. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced. | ||
Finally, you can press Ok button and the results will be loaded into the clipboard. | Finally, you can press Ok button and the results will be loaded into the clipboard. | ||
== How to do a mutant optimization by adding reactions == | == How to do a mutant optimization by adding reactions == | ||
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