CORE:Readers:Drains

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In order to be possible to make simulations with a model there must be an "unbalance", where reactants enter the network and product are produced. This extra cellular infomation is provided by the drains of the model.

Considering that sometimes models dont bring information about the drains, OptFlux has the tools to create those drains.
When creating a new project, OptFlux tries do determine the best way to identify/create the drains of the model (in case it's needed).
There are several options.
If the files/source of the model already have correct drain information then OptFlux can just ignore this step and don't create drains.

DontDoDrains.png

If the creation of drains is necessary, then there are 2 methods to do so:

  • Removing External Metabolites
Removing external metabolites (metabolites in the external compartment) unbalances the model allowing the usage of simulation methods.
  • Creating Drains
Identifying the external metabolites and creatin "unbalanced" reactions for them unbalances the model.



In order to create drains, in both methods, there is the necessity to detect the external metabolites.

This can be made following two approaches

  • Compartment Heuristic
If the model has compartment information, and OptFlux can detect the external compartment.


Drainsheuristic.png

  • Using Regular Expressions
Using regular expressions to determine which metabolites are the external.
BIGG database uses this approach for instance.


BiggRegexp.png

In all cases OptFlux allways tries to identify the method of drain detection/creation.
After choosing the method for drain detection/creation, press "Next" and follow up to the biomass detection step.


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