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class="docs-right"><a class="docs-edit-link" href="https://github.com/lcsb-biocore/COBREXA.jl/blob/master/docs/src/notebooks.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Notebooks-and-example-workflows"><a class="docs-heading-anchor" href="#Notebooks-and-example-workflows">Notebooks and example workflows</a><a id="Notebooks-and-example-workflows-1"></a><a class="docs-heading-anchor-permalink" href="#Notebooks-and-example-workflows" title="Permalink"></a></h1><ul><li><a href="1_loading_converting_saving/#Loading,-converting,-and-saving-models">Loading, converting, and saving models</a></li><ul><li><a href="1_loading_converting_saving/#Loading-models">Loading models</a></li><li><a href="1_loading_converting_saving/#Using-the-generic-interface-to-access-model-details">Using the generic interface to access model details</a></li><li><a href="1_loading_converting_saving/#Converting-between-model-types">Converting between model types</a></li><li><a href="1_loading_converting_saving/#Saving-and-exporting-models">Saving and exporting models</a></li></ul><li><a href="2_finding_balance/#Finding-balance-and-variability-of-constraint-based-models">Finding balance and variability of constraint-based models</a></li><ul><li><a href="2_finding_balance/#Optimization-solvers-in-COBREXA">Optimization solvers in <code>COBREXA</code></a></li><li><a href="2_finding_balance/#Flux-balance-analysis-(FBA)">Flux balance analysis (FBA)</a></li><li><a href="2_finding_balance/#Extending-FBA-with-modifications">Extending FBA with modifications</a></li><li><a href="2_finding_balance/#Flux-variability-analysis-(FVA)">Flux variability analysis (FVA)</a></li><li><a href="2_finding_balance/#Parsimonious-flux-balance-analysis-(pFBA)">Parsimonious flux balance analysis (pFBA)</a></li><li><a href="2_finding_balance/#Minimizing-metabolic-adjustment-analysis-(MOMA)">Minimizing metabolic adjustment analysis (MOMA)</a></li><li><a href="2_finding_balance/#Composing-(more-complicated)-modifications">Composing (more complicated) modifications</a></li></ul><li><a href="3_basic_stdmodel_usage/#Basic-usage-of-StandardModel">Basic usage of <code>StandardModel</code></a></li><ul><li><a href="3_basic_stdmodel_usage/#Loading-a-model">Loading a model</a></li><li><a href="3_basic_stdmodel_usage/#Basic-analysis">Basic analysis</a></li><li><a href="3_basic_stdmodel_usage/#Inspecting-the-flux-solution:-atom_fluxes">Inspecting the flux solution: <code>atom_fluxes</code></a></li><li><a href="3_basic_stdmodel_usage/#Inspecting-the-flux-solution:-metabolite_fluxes">Inspecting the flux solution: <code>metabolite_fluxes</code></a></li><li><a href="3_basic_stdmodel_usage/#Internals-of-StandardModel">Internals of <code>StandardModel</code></a></li><li><a href="3_basic_stdmodel_usage/#Genes,-Reactions,-and-Metabolites"><code>Gene</code>s, <code>Reaction</code>s, and <code>Metabolite</code>s</a></li><li><a href="3_basic_stdmodel_usage/#Checking-the-internals-of-StandardModels:-annotation_index">Checking the internals of <code>StandardModel</code>s: <code>annotation_index</code></a></li><li><a href="3_basic_stdmodel_usage/#Checking-the-internals-of-StandardModels:-check_duplicate_reaction">Checking the internals of <code>StandardModel</code>s: <code>check_duplicate_reaction</code></a></li><li><a href="3_basic_stdmodel_usage/#Checking-the-internals-of-StandardModels:-reaction_mass_balanced">Checking the internals of <code>StandardModel</code>s: <code>reaction_mass_balanced</code></a></li></ul><li><a href="4_basic_core_coupled_usage/#Basic-usage-of-CoreModel-and-CoreModelCoupled">Basic usage of <code>CoreModel</code> and <code>CoreModelCoupled</code></a></li><ul><li><a href="4_basic_core_coupled_usage/#Loading-a-CoreModel">Loading a <code>CoreModel</code></a></li><li><a href="4_basic_core_coupled_usage/#Basic-analysis-on-CoreModel">Basic analysis on <code>CoreModel</code></a></li><li><a href="4_basic_core_coupled_usage/#Structure-of-CoreModel">Structure of <code>CoreModel</code></a></li><li><a href="4_basic_core_coupled_usage/#CoreModelCoupled-adds-coupling-constraints-to-CoreModel"><code>CoreModelCoupled</code> adds coupling constraints to <code>CoreModel</code></a></li></ul><li><a href="5_basic_stdmodel_construction/#Model-construction-and-modification">Model construction and modification</a></li><ul><li><a href="5_basic_stdmodel_construction/#Model-construction">Model construction</a></li><li><a href="5_basic_stdmodel_construction/#Modifying-existing-models">Modifying existing models</a></li></ul><li><a href="6_screening/#Exploring-model-variants-with-screen">Exploring model variants with <code>screen</code></a></li><ul><li><a href="6_screening/#Preparing-the-functions">Preparing the functions</a></li><li><a href="6_screening/#Knocking-out-single-reactions">Knocking out single reactions</a></li><li><a href="6_screening/#Knocking-out-reaction-combinations">Knocking out reaction combinations</a></li></ul><li><a href="7_community_model/#Building-and-analysing-a-small-community-model">Building and analysing a small community model</a></li><ul><li><a href="7_community_model/#Load-the-base-model">Load the base model</a></li><li><a href="7_community_model/#Load-the-models-and-inspect-fba-solutions">Load the models and inspect fba solutions</a></li><li><a href="7_community_model/#Build-a-community-model-of-the-cytochrome-oxidase-knockout-and-the-ATP-synthase-knockout-models">Build a community model of the cytochrome oxidase knockout and the ATP synthase knockout models</a></li><li><a href="7_community_model/#Set-exchange-reaction-bounds-of-community-model-based-on-the-bounds-of-the-individual-models">Set exchange reaction bounds of community model based on the bounds of the individual models</a></li><li><a href="7_community_model/#Add-objective-function-to-community-model">Add objective function to community model`</a></li><li><a href="7_community_model/#Perform-community-FBA">Perform community FBA</a></li><li><a href="7_community_model/#Add-the-enolase-knockout-to-the-community-model">Add the enolase knockout to the community model</a></li><li><a href="7_community_model/#Allow-the-mutants-to-rescue-each-other-by-sharing-pyruvate">Allow the mutants to rescue each other by sharing pyruvate</a></li></ul><li><a href="8_custom_model/#Using-a-custom-model-data-structure">Using a custom model data structure</a></li><li><a href="9_max_min_driving_force_analysis/#Maximum-minimum-driving-force-analysis">Maximum-minimum driving force analysis</a></li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../advanced/2_custom_model/">« Working with custom models</a><a class="docs-footer-nextpage" href="1_loading_converting_saving/">Loading, converting, and saving models »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option 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