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| The layer (a) addresses the objective functions at the bioengineering level to be addressed by the MO algorithm, while the layer (b) depicts the constraints of the inner phenotype simulation (cellular level). In this bi-level formulation the strain optimization and the phenotype simulation methods can be chosen independently from all available options (e.g. SPEA2, EA or SA in a) and FBA, MOMA or ROOM in b)). | | The layer (a) addresses the objective functions at the bioengineering level to be addressed by the MO algorithm, while the layer (b) depicts the constraints of the inner phenotype simulation (cellular level). In this bi-level formulation the strain optimization and the phenotype simulation methods can be chosen independently from all available options (e.g. SPEA2, EA or SA in a) and FBA, MOMA or ROOM in b)). |
| The output of phenotype simulation is the set of flux values for all reactions in the model. These are used by the optimization algorithms to compute the fitness value of the solution, using an appropriate objective function. | | The output of phenotype simulation is the set of flux values for all reactions in the model. These are used by the optimization algorithms to compute the fitness value of the solution, using an appropriate objective function. |
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− | = Performing strain optimization in OptFlux =
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− | The operation can be accessed in the menu '''Optimization->Evolutionary...'''
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− | [[File:menu_opt.png]]
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− | == Optimization dialog and preferences ==
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− | [[File:maindialog.png|700px|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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