Editing OverUnder4OptFlux

Documentation regarding the plug-in can also be downloaded [http://darwin.di.uminho.pt/optflux/files/HowTosOU.pdf here!]
== How to do a mutant simulation - Reactions Regulations ==
<br>
<br>
You can access the under/overexpression reaction simulation option under the “Plugins -> Under and Overexpression -> Reaction Simulation…”.
<br>
[[Image:Menu.png]]
<br><br>
In the Reaction Simulation you can select the model/project to work, and set up your configuration.
<br>
[[Image:ReactionSimulationMenu.png]]
<br>
<b>1. Reaction Regulations Set Up</b><br>
Selecting in the Reactions list and defining an expression value in Expression Value box you can add/remove (using the arrows buttons) reactions regulations. On the right side appear the Reactions Regulations list and the respective Expression Value. <br>
<br>
<b>2. Select Simulation Method</b><br>
OptFlux can use several simulation methods for knockout simulations, namely: Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA
<br>
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>
<br>
<b>3. Objective Function Configuration</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.<br>
<br>
<b>4. Select Environmental Conditions</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.<br>
<br>
Finally, you can press Ok button and the results will be loaded into the clipboard.
<br>
[[Image:ReactionSimulationClipboard.png]]
<br>
<br>
Double-click on the Simulation Result will show the results panel.<br>
[[Image:ReactionSimulationPainel.png]]

== How to do a mutant simulation - Genes Regulations ==
<br><br>
You can access the under/overexpression reaction simulation option under the “Plugins -> Under and Overexpression -> Gene Simulation…”. 
<br>
[[Image:Menu.png]]
<br><br>
In the Gene Simulation you can select the model/project to work, and set up your configuration.
<br>
[[Image:GeneSimulationMenu.png]]
<br><br>
<b>1. Gene Regulations Set Up</b><br>
Selecting in the Genes list and defining an expression value in Expression Value box you can add/remove (using the arrows buttons) reactions regulations. On the right side appear the Genes Regulations list and the respective Expression Value, and also the influenced reactions regulations.<br>
<br>
<b>2. Select Simulation Method </b><br>
OptFlux can use several simulation methods for knockout simulations, namely: Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA<br>
<br>
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>
<br>
<b>3. Objective Function Configuration</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.<br>
<br>
<b>4. Select Environmental Conditions</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.<br>
<br>
Finally, you can press Ok button and the results will be loaded into the clipboard.<br>
<br>
[[Image:GeneSimulationClipboard.png]]
<br><br>
Double-click on the Gene Simulation Result will show the results panel.
<br>
[[Image:GeneSimulationPanel.png]]
<br><br>

== How to do a Strain Optimization – Reactions Regulations ==
You can access the under/overexpression reaction optimization option under the “Plugins -> Under and Overexpression -> Reaction Optimization…”. 
<br>
[[Image:Menu.png]]
<br><br>
You can select the model/project to work and set up your optimization.
<br>
[[Image:ReactionOptimizationMenu.png]]
<br><br>
<b>1. Select Project and Model</b><br>
In the Project combo box select the project where you want to perform the optimization, in the Model combo box select the model within the project that you want to use (if you have performed model simplification, the simplified models will be easier to handle by the optimization algorithms).<br>
<br>
<b>2. Select Simulation Method</b><br>
OptFlux can use several simulation methods for knockout simulations, namely: Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA<br>
<br>
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>
<br>
<b>3. Select Environmental Conditions</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.<br>
<br>
<b>4. Select Objective Function</b><br>
OptFlux can use two types of objective function:<br>
BPCY - Biomass-Product Coupled Yield, YIELD - Product Yield with Minimum Biomass.<br>
The first calculates the product of the biomass flux and the compound production flux; the second, returns the value of the target compound production flux divided by the substrate consumption flux, if the biomass is larger than a minimum value, defined by the user.<br>
<br>
<b>5. Objective Function Configuration</b><br>
Here you can select the flux to be optimize (the compound you wish to produce), the flux that represents the biomass and the substrate that is in use. <br>
<br>
<b>6. Select Optimization Algorithm </b><br>
OptFlux allows you to perform optimizations using one of the following algorithms:<br>
Cellular Genetic Algorithm, Evolutionary Algorithm, Simulated Annealing. <br>
<br>
<b>7. Optimization Basic Setup</b><br>
Here you can configure the maximum number of solution evaluations (Simulations) and check the expected time to perform that number of evaluations. You can also set up the maximum number of regulations and if the set of regulations should be static or have a variable size.<br>
<br>
<b>8. Essential Information</b><br>
You can define if it is possible to regulate some special type of reactions like drains, transport and critical reactions (if you have loaded/created this information).<br>
<br>
<br>
Finally, you can press Ok button and the results will be loaded into the clipboard.<br>
[[Image:ReactionOptimizationClipboard.png]]
<br><br>
Double-click on the Optimization Result will show the results panel.<br>
[[Image:ReactionOptimizationPanel.png]]

== How to do a Strain Optimization – Genes Regulations ==
You can access the under/overexpression reaction optimization option under the “Plugins -> Under and Overexpression -> Gene Optimization…”. <br>
[[Image:Menu.png]]
<br><br>
You can select the model/project to work and set up your optimization.<br>
[[Image:GeneOptimizationMenu.png]]
<br><br>
<b>1. Select Project and Model</b><br>
In the Project combo box select the project where you want to perform the optimization, in the Model combo box select the model within the project that you want to use (if you have performed model simplification, the simplified models will be easier to handle by the optimization algorithms).<br>
<br>
<b>2. Select Simulation Method</b><br>
OptFlux can use several simulation methods for knockout simulations, namely: Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA<br>
<br>
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>
<br>
<b>3. Select Environmental Conditions</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.<br>
<br>
<b>4. Select Objective Function</b><br>
OptFlux can use two types of objective function:<br>
BPCY - Biomass-Product Coupled Yield, YIELD - Product Yield with Minimum Biomass.<br>
The first calculates the product of the biomass flux and the compound production flux; the second, returns the value of the target compound production flux divided by the substrate consumption flux, if the biomass is larger than a minimum value, defined by the user. <br>
<br>
<b>5. Objective Function Configuration</b><br>
Here you can select the flux to be optimize (the compound you wish to produce), the flux that represents the biomass and the substrate that is in use. <br>
<br>
<b>6. Select Optimization Algorithm </b><br>
OptFlux allows you to perform optimizations using one of the following algorithms:<br>
Cellular Genetic Algorithm;<br> Evolutionary Algorithm;<br> Simulated Annealing; <br>
<br>
<b>7. Optimization Basic Setup</b><br>
Here you can configure the maximum number of solution evaluations (Simulations) and check the expected time to perform that number of evaluations. You can also set up the maximum number of regulations and if the set of regulations should be static or have a variable size.<br>
<br>
<b>8. Essential Information</b><br>
You can define if it is possible to regulate some special type of reactions like drains, transport and critical reactions (if you have loaded/created this information).<br>
<br>
<br>
Finally, you can press Ok button and the results will be loaded into the clipboard.<br>
[[Image:GeneOptimizationClipboard.png]]
<br><br>
Double-click on the Gene Optimization Result will show the results panel.
<br>
[[Image:GeneOptimizationPanel.png]]