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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. | 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. | ||
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* Removing External Metabolites | * Removing External Metabolites | ||
| − | + | By removing external metabolites (metabolites in the external compartment) the model is, by consequence, unbalanced, thus making possible to perform simulation methods. | |
* Creating Drains | * Creating Drains | ||
| − | + | By identifying the external metabolites it's possible to create "unbalanced" reactions for these metabolites, therefore unbalancing the model. | |
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In order to create drains, in both methods, there is the necessity to detect the external metabolites. | In order to create drains, in both methods, there is the necessity to detect the external metabolites. | ||
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* Compartment Heuristic | * Compartment Heuristic | ||
| − | + | If the model has compartment information, and OptFlux can detect the external compartment. | |
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[[Image: Drainsheuristic.png]] | [[Image: Drainsheuristic.png]] | ||
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* Using Regular Expressions | * Using Regular Expressions | ||
| − | + | Using regular expressions to determine which metabolites are the external.<br> | |
| − | + | BIGG database uses this approach for instance. | |
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[[Image: BiggRegexp.png]] | [[Image: BiggRegexp.png]] | ||
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After choosing the method for drain detection/creation, press "Next" and follow up to the biomass detection step. | After choosing the method for drain detection/creation, press "Next" and follow up to the biomass detection step. | ||
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| − | <i>Return to [[ | + | <i>Return to [[NewProjectOptflux3]]</i> |