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== Optimization dialog and preferences == | == Optimization dialog and preferences == | ||
− | [[File:maindialog.png| | + | [[File:maindialog.png|600px|thumb]] |
* '''Select Simulation method''' - The method used to perform the phenotype simulation layer. | * '''Select Simulation method''' - The method used to perform the phenotype simulation layer. | ||
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** Variable size solution. When selected, the size of the solutions is not fixed and can vary up to the maximum previously configured. | ** Variable size solution. When selected, the size of the solutions is not fixed and can vary up to the maximum previously configured. | ||
* '''Essential Information''' - Depending on whether this is a Reaction of Gene optimization, you can select a set of reactions/genes that must never be considered for deletion. This set can be computed automatically by OptFlux (see [[OptFlux3:OPT:Critical | Determine Critical Genes/Reactions]]) | * '''Essential Information''' - Depending on whether this is a Reaction of Gene optimization, you can select a set of reactions/genes that must never be considered for deletion. This set can be computed automatically by OptFlux (see [[OptFlux3:OPT:Critical | Determine Critical Genes/Reactions]]) | ||
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== Execution and options == | == Execution and options == | ||
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[[File: run_multi.png]] | [[File: run_multi.png]] | ||
− | In the case of single-objective optimization, the chart displays the best solution found relative to the number of evaluation | + | In the case of single-objective optimization, the chart displays the best solution found relative to the number of evaluation functions performed. In the event of multi-objective optimization, the chart displays the current state of the pareto-front, that is the trade-off between the selected objectives for solutions kept in the archive. |
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In both cases you can stop the optimization process at any time, and this will call the solution simplification process immediately. | In both cases you can stop the optimization process at any time, and this will call the solution simplification process immediately. | ||
== Analysing optimization solutions == | == Analysing optimization solutions == | ||
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When the optimization procedure completes, the solutions will be sent to the OptFlux clipboard: | When the optimization procedure completes, the solutions will be sent to the OptFlux clipboard: | ||
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[[File:clip.png]] | [[File:clip.png]] | ||
− | Clicking it will launch the view | + | Clicking it will launch the view: |
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− | [[File: | + | [[File:opt_view.png]] |