Editing OptFlux3:OPK

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'''Note:''' This plugin has been discontinued in current versions of OptFlux.

=Example file=

You can download it here -> [[Media:OptKnock_toy.zip| OptKnock_toy.zip]]

An illustrative image of this model can be found below.

[[Image:OptKnock_toy_image.png]]

The simple network is constituted of seven reactions. The reactions: Desired, Biomass and substrate represents the production of the biological coumpound of interest, the formation of biomass and the uptake of metabolite M1 from surrounding media, respectively.

The coefficient of reaction <b>R2</b> (M1->M3) are such that two molecules of M1 create one molecule of M3, while the stoichiometric coefficients of all other reactions reflect a one-to-one relationship between molecule quantities.


=Brief tutorial=

This brief tutorial will help you to begin working with OptKnock4OptFlux.

*To start, you will need load a model in OptFlux(see how to [[HowTos| here]]). You must pay attention to select a correct biomass flux.

==Run OptKnock==

* 1 - Start by accessing the menu '''Plugins->OptKnock->OptKnock Optimization'''.

[[Image:OptKnock_menu.png]]

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* 2 - The following dialog will be displayed.

[[Image:OptKnock_dialog.png]]

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<b><i>Select Project and Model</i></b><br>
You can select the model/project to work.
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<b><i>Substrate Definition</i></b><br>
You can select the substrate flux and its uptake value.
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<b><i>Biomass Minimum Value</i></b><br>
You can define the minimum value for the biomass (in %).
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<b><i>Desired Flux Definition</i></b><br>
You can select the reaction representing the production of the desired compound.
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<b><i>Knockouts Definition</i></b><br>
You can define de maximum numbers of knockouts.
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<b><i>Selected Environmental Conditions</i></b><br>
You can define the environmental conditions if you have created any.
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* 3 - After execution, a new datatype will be placed in the clipboard, under the '''Optimizations Results -> OptKnock Optimizations'''. 
[[Image:OptKnock_datatype.png]]

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Pressing it will launch three viewers.

<b>1. <i>OptKnockView</i></b>

[[Image:OptKnock_view.png]]

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<b>2. <i>Drain Fluxes</i></b>

[[Image:OptKnock_DrainsFluxes.png]]

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<b>3. <i>Internal Fluxes</i></b>

[[Image:OptKnock_InterFluxes.png]]
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