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| The operation can be accessed in the menu '''Optimization->Evolutionary...''' | | The operation can be accessed in the menu '''Optimization->Evolutionary...''' |
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− | [[File:menu_opt.png]] | + | [[File:menu_opt.png|thumb]] |
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− | == Optimization dialog and preferences ==
| + | This will launch the optimization dialog |
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− | [[File:maindialog.png|700px|thumb]] | + | [[File:maindialog.png|400px|thumb]] |
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− | * '''Select Simulation method''' - The method used to perform the phenotype simulation layer.
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− | ** FBA, pFBA, MOMA, LinearMOMA, ROOM and MIMBL are available.
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− | * '''Select Environmental Conditions''' - The list of available environmental conditions available for this project.
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− | * '''Select the objective functions'''
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− | ** OptFlux support multiple-criteria optimisation, this means that you can select several objective functions to optimize at the same time.
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− | *** BPCY: Biomass-product coupled yield
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− | *** YIELD: Product Yield with minimum biomass
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− | *** Max/Min of reaction flux value
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− | *** Max/Min of the number of knockouts
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− | *** Max/Min of the sum of flux measures
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− | ** You must configure each objective function individually and then press the '''Add>>''' button to add it to the list (on the right).
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− | * '''Select Optimization Algorithm''' - The optimization method to use
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− | ** Evolutionary Algorithm (EA)
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− | ** Simulated Annealing (SA)
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− | ** Strength Pareto Evolutionary Algorithm 2 (SPEA2) - This method is natively multi-objective, thus prone to provide better solutions when multiple objective functions are used.
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− | * '''Knockout Type'''
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− | ** Reactions or Genes
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− | ** Perform Under/Over expression based optimization. This option allows to compute regulations for the activity of reactions/expression of genes instead of simple deletion.
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− | * '''Optimization Basic Setup'''
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− | ** Maximum Number of Solution Evaluations - The number of simulations allowed for this optimization. The larger the number, the better the chances of finding optimal solutions, but the longer it will take.
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− | ** Maximum Number of Knockouts - The maximum number of deletions/regulations allowed.
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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.
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− | * '''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 ==
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− | When performing optimizations, one of the following dialogs will be displayed, depending on whether you select only one objective function (Left) or several (Right)
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− | [[File: run_single.png]]
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− | [[File: run_multi.png]]
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− | In the case of single-objective optimization, the chart displays the best solution found relative to the number of evaluation
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− | functions performed. In the event of multi-objective optimization, the chart displays the current state of the pareto-front,
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− | 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.
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− | == Analysing optimization solutions ==
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− | [[File:opt_view.png|600px|thumb]]
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− | When the optimization procedure completes, the solutions will be sent to the OptFlux clipboard:
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− | [[File:clip.png]]
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− | Clicking it will launch the view on the right:
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− | * The optimization view contains three distinct sections:
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− | ** (TOP) The List of solutions and respective fitnesses
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− | ** (BOTTOM-LEFT) The decoded solution (you must select a solution either in the list or in the chart). This list will display the suggested gene/reaction) deletions or over/under regulations for the selected solution
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− | ** (BOTOM-RIGHT) The chart displaying the trade-of solutions (This chart is displayed as a pareto front when multiple objective functions were used, otherwise, the solutions will be ploted with the single objective function as the Y axis only)
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− | *** '''You can zoom-in or out of the chart using the mouse.'''
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− | *** '''You can click any point and the corresponding solution will be highlighted in the top list.'''
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− | * Pressing the '''<< Add to simulation results''' button, will send the selected solutions to the list of simulations in the clipboard
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− | [[File:clip_opt.png]][[File:addtosim.png]]
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− | '''Aftewards, each simulation can be individually analysed with full detail using the simulation view.'''
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− | [[File:sim_view.png]]
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