All features of plug-in can be accessed under the “Plugins-> Add Reactions” menu.
How to import database reactions
You can import database by three options:
1. SBML file
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.
After press “Ok”, the all the reactions will be loaded into the clipboard.
2. Flat files
If you choose “Flat Files” option in menu, you must indicate the metabolites, fluxes and stoichiometric matrix text files.
3. TXT Files
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.
Select the reactions and metabolites files. Click in “Open” button.
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”.
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).
How to reduce the database of reactions
To reduce the number of reactions in database to optimization process, you can apply a filter giving the target compound and a value of tolerance. The process will found all pathways between the metabolites presented in model and the target compound and calculate the cost for each pathway. Using the tolerance value will be selected the pathways with less cost and others that are in tolerance range.
This process can be accessed in "AddReactions->Database Filter".
How to do a mutant simulation by adding reactions
The mutant simulation with addiction of reactions can be access in “Plugins -> Add Reactions->Simulation” menu.
Select knockouts and added reactions
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.
Select Simulation Method
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.
Objective Function Configuration
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.
Select Environmental Conditions
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.
How to do a mutant optimization by adding reactions
You can access to a mutant optimization with addition of reactions operation under the
“Plugins -> Add Reactions->Optimization”.
The strains optimization process try to find the set of new reactions added to the model to improve the production of specific product. In this process we can search only for a set of reaction to be added or the combination of added reactions and knockouts. With this combination it's possible the production of a desired product while the organism viability are maintained.
In the application interface for optimization process, we can select:
The available optimization algorithms are EAs and SA approaches;
You can select the one of these methods: FBA, MOMA and ROOM. These methods are used in simulation of each solution evaluation;
This function is used to calculate the fitness value of each solution after the phenotype simulation using FBA, MOMA or ROOM. The most used functions are the Biomass-Product Coupled Yield (BPCY) and Product Yield;
Optimization Basic Setup
You can configure the maximum number of solution evaluations (simulations), set up the maximum number knockouts and added reactions in solution and if the genome size should be fixed or have a variable size;
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.
You can define if it is possible to knockout some special type of reactions like drains, transport and critical reactions.