Commit 4c20f321 authored by Documenter.jl's avatar Documenter.jl
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build based on b584f62e

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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Documentation · SBML.jl</title><link rel="canonical" href="https://lcsb-biocore.github.io/DistributedData.jl/stable/"/><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit">SBML.jl</span></div><form class="docs-search" action="search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Documentation</a><ul class="internal"><li><a class="tocitem" href="#Functions"><span>Functions</span></a></li><li><a class="tocitem" href="#Data-helpers"><span>Data helpers</span></a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Documentation</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Documentation</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/LCSB-BioCore/SBML.jl/blob/master/docs/src/index.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="SBML.jl-—-load-systems-biology-models-from-SBML-files"><a class="docs-heading-anchor" href="#SBML.jl-—-load-systems-biology-models-from-SBML-files">SBML.jl — load systems biology models from SBML files</a><a id="SBML.jl-—-load-systems-biology-models-from-SBML-files-1"></a><a class="docs-heading-anchor-permalink" href="#SBML.jl-—-load-systems-biology-models-from-SBML-files" title="Permalink"></a></h1><p>This package provides a straightforward way to load model- and simulation-relevant information from SBML files.</p><p>The library provides a single function <a href="#SBML.readSBML-Tuple{String}"><code>readSBML</code></a> to load a <a href="#SBML.Model"><code>Model</code></a>:</p><pre><code class="language-julia">julia&gt; using SBML
julia&gt; mdl = readSBML(&quot;Ec_core_flux1.xml&quot;)
Model(…)
julia&gt; mdl.compartments
2-element Array{String,1}:
&quot;Extra_organism&quot;
&quot;Cytosol&quot;</code></pre><p>There are several functions to help you with using the data in the usual COBRA-style workflows, such as <a href="#SBML.getS-Tuple{Model}"><code>getS</code></a>:</p><pre><code class="language-julia">julia&gt; metabolites, reactions, S = getS(mdl)
julia&gt; metabolites
77-element Array{String,1}:
&quot;M_succoa_c&quot;
&quot;M_ac_c&quot;
&quot;M_etoh_c&quot;
julia&gt; S
77×77 Array{Float64,2}:
0.0 1.0 0.0 0.0 0.0 0.0 0.0 … 0.0 0.0 0.0 0.0 0.0 0.0 0.0