-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathtutorial.html
285 lines (207 loc) · 12.4 KB
/
tutorial.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
<title>Tutorial — BioSimulators-COBRApy 0.1.23 documentation</title>
<link href="_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
<link href="_static/styles/pydata-sphinx-theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
<link rel="stylesheet"
href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
<link rel="preload" as="font" type="font/woff2" crossorigin
href="_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
<link rel="preload" as="font" type="font/woff2" crossorigin
href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
<link rel="stylesheet" type="text/css" href="_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="_static/styles/pydata-sphinx-theme.css" />
<link rel="stylesheet" type="text/css" href="_static/css/biosimulators.css" />
<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf">
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<link rel="author" title="About these documents" href="about.html" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="biosimulators_cobrapy package" href="source/biosimulators_cobrapy.html" />
<link rel="prev" title="Installation instructions" href="installation.html" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="docsearch:language" content="en">
<link rel="icon" sizes="16x16" href="https://github.com/biosimulations/biosimulations/raw/dev/libs/shared/assets/src/assets/icons/favicon-16x16.png">
<link rel="icon" sizes="32x32" href="https://github.com/biosimulations/biosimulations/raw/dev/libs/shared/assets/src/assets/icons/favicon-32x32.png">
<!-- Google Analytics -->
</head>
<body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
<div class="container-fluid" id="banner"></div>
<nav class="navbar navbar-light navbar-expand-lg bg-light fixed-top bd-navbar" id="navbar-main"><div class="container-xl">
<div id="navbar-start">
<a class="navbar-brand" href="index.html">
<img src="_static/biosimulators-logo.svg" class="logo" alt="logo">
</a>
</div>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbar-collapsible" aria-controls="navbar-collapsible" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar-collapsible" class="col-lg-9 collapse navbar-collapse">
<div id="navbar-center" class="mr-auto">
</div>
<div id="navbar-end">
<div class="navbar-end-item">
<ul id="navbar-icon-links" class="navbar-nav" aria-label="Quick links">
<li class="nav-item">
<a class="nav-link" href="https://github.com/biosimulators/Biosimulators_COBRApy" rel="noopener" target="_blank" title="GitHub"><span><i class="fab fa-github"></i></span>
<label class="sr-only">GitHub</label></a>
</li>
<li class="nav-item">
<a class="nav-link" href="https://twitter.com/biosimulators" rel="noopener" target="_blank" title="Twitter"><span><i class="fab fa-twitter"></i></span>
<label class="sr-only">Twitter</label></a>
</li>
<li class="nav-item">
<a class="nav-link" href="mailto:[email protected]" rel="noopener" target="_blank" title="Email"><span><i class="fas fa-envelope"></i></span>
<label class="sr-only">Email</label></a>
</li>
</ul>
</div>
</div>
</div>
</div>
</nav>
<div class="container-xl">
<div class="row">
<!-- Only show if we have sidebars configured, else just a small margin -->
<div class="col-12 col-md-3 bd-sidebar">
<div class="sidebar-start-items"><form class="bd-search d-flex align-items-center" action="search.html" method="get">
<i class="icon fas fa-search"></i>
<input type="search" class="form-control" name="q" id="search-input" placeholder="Enter text to search for ..." aria-label="Enter text to search for ..." autocomplete="off" >
</form><nav class="bd-links" id="bd-docs-nav" aria-label="Main navigation">
<div class="bd-toc-item active">
</div>
</nav>
</div>
<div class="sidebar-end-items">
</div>
</div>
<div class="d-none d-xl-block col-xl-2 bd-toc">
<div class="toc-item">
<div class="tocsection onthispage pt-5 pb-3">
<i class="fas fa-list"></i> On this page
</div>
<nav id="bd-toc-nav">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry">
<a class="reference internal nav-link" href="#creating-combine-omex-archives-and-encoding-simulation-experiments-into-sed-ml">
Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML
</a>
<ul class="visible nav section-nav flex-column">
<li class="toc-h3 nav-item toc-entry">
<a class="reference internal nav-link" href="#sed-ml-targets-for-simulation-predictions">
SED-ML targets for simulation predictions
</a>
</li>
</ul>
</li>
<li class="toc-h2 nav-item toc-entry">
<a class="reference internal nav-link" href="#command-line-program">
Command-line program
</a>
</li>
<li class="toc-h2 nav-item toc-entry">
<a class="reference internal nav-link" href="#docker-image-with-a-command-line-entrypoint">
Docker image with a command-line entrypoint
</a>
</li>
</ul>
</nav>
</div>
<div class="toc-item">
<div class="tocsection editthispage">
<a href="https://github.com/biosimulators/Biosimulators_COBRApy/edit/dev/docs-src/tutorial.rst">
<i class="fas fa-pencil-alt"></i> Edit this page
</a>
</div>
</div>
</div>
<main class="col-12 col-md-9 col-xl-7 py-md-5 pl-md-5 pr-md-4 bd-content" role="main">
<div>
<section id="tutorial">
<h1>Tutorial<a class="headerlink" href="#tutorial" title="Permalink to this headline">¶</a></h1>
<p>BioSimulators-COBRApy is available as a command-line program and as a command-line program encapsulated into a Docker image.</p>
<section id="creating-combine-omex-archives-and-encoding-simulation-experiments-into-sed-ml">
<h2>Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML<a class="headerlink" href="#creating-combine-omex-archives-and-encoding-simulation-experiments-into-sed-ml" title="Permalink to this headline">¶</a></h2>
<p>Information about how to create COMBINE/OMEX archives which can be executed by BioSimulators-COBRApy is available <a class="reference external" href="https://docs.biosimulations.org/users/creating-projects/">here</a>.</p>
<p>A list of the algorithms and algorithm parameters supported by COBRApy is available at <a class="reference external" href="https://biosimulators.org/simulators/cobrapy">BioSimulators</a>.</p>
<section id="sed-ml-targets-for-simulation-predictions">
<h3>SED-ML targets for simulation predictions<a class="headerlink" href="#sed-ml-targets-for-simulation-predictions" title="Permalink to this headline">¶</a></h3>
<p>BioSimulators-COBRApy recognizes the following targets for simulation predictions:</p>
<ul class="simple">
<li><p>FBA (<code class="docutils literal notranslate"><span class="pre">KISAO_0000437</span></code>), parsimonious FBA (<code class="docutils literal notranslate"><span class="pre">KISAO_0000528</span></code>), geometric FBA (<code class="docutils literal notranslate"><span class="pre">KISAO_0000527</span></code>):</p>
<ul>
<li><p>Objective: <code class="docutils literal notranslate"><span class="pre">fbc:objective/@value</span></code></p></li>
<li><p>Reaction flux: <code class="docutils literal notranslate"><span class="pre">sbml:reaction/@flux</span></code></p></li>
<li><p>Reaction reduced cost: <code class="docutils literal notranslate"><span class="pre">sbml:reaction/@reducedCost</span></code></p></li>
<li><p>Species shadow price: <code class="docutils literal notranslate"><span class="pre">sbml:species/@shadowPrice</span></code></p></li>
</ul>
</li>
<li><p>FVA (<code class="docutils literal notranslate"><span class="pre">KISAO_0000526</span></code>):</p>
<ul>
<li><p>Minimum reaction flux: <code class="docutils literal notranslate"><span class="pre">sbml:reaction/@minFlux</span></code></p></li>
<li><p>Maximum reaction flux: <code class="docutils literal notranslate"><span class="pre">sbml:reaction/@maxFlux</span></code></p></li>
</ul>
</li>
</ul>
<p>Please see <a class="reference external" href="https://docs.biosimulations.org/concepts/conventions/simulation-experiments/">https://docs.biosimulations.org</a> for more information.</p>
</section>
</section>
<section id="command-line-program">
<h2>Command-line program<a class="headerlink" href="#command-line-program" title="Permalink to this headline">¶</a></h2>
<p>The command-line program can be used to execute COMBINE/OMEX archives that describe simulations as illustrated below.</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>usage: biosimulators-cobrapy [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]
BioSimulators-compliant command-line interface to the COBRApy <https://opencobra.github.io/cobrapy/> simulation program.
optional arguments:
-h, --help show this help message and exit
-d, --debug full application debug mode
-q, --quiet suppress all console output
-i ARCHIVE, --archive ARCHIVE
Path to OMEX file which contains one or more SED-ML-
encoded simulation experiments
-o OUT_DIR, --out-dir OUT_DIR
Directory to save outputs
-v, --version show program's version number and exit
</pre></div>
</div>
<p>For example, the following command could be used to execute the simulations described in <code class="docutils literal notranslate"><span class="pre">./modeling-study.omex</span></code> and save their results to <code class="docutils literal notranslate"><span class="pre">./</span></code>:</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>biosimulators-cobrapy -i ./modeling-study.omex -o ./
</pre></div>
</div>
</section>
<section id="docker-image-with-a-command-line-entrypoint">
<h2>Docker image with a command-line entrypoint<a class="headerlink" href="#docker-image-with-a-command-line-entrypoint" title="Permalink to this headline">¶</a></h2>
<p>The entrypoint to the Docker image supports the same command-line interface described above.</p>
<p>For example, the following command could be used to use the Docker image to execute the same simulations described in <code class="docutils literal notranslate"><span class="pre">./modeling-study.omex</span></code> and save their results to <code class="docutils literal notranslate"><span class="pre">./</span></code>:</p>
<div class="highlight-text notranslate"><div class="highlight"><pre><span></span>docker run \
--tty \
--rm \
--mount type=bind,source="$(pwd),target=/tmp/working-dir \
ghcr.io/biosimulators/cobrapy:latest \
-i /tmp/working-dir/modeling-study.omex \
-o /tmp/working-dir
</pre></div>
</div>
</section>
</section>
</div>
</main>
</div>
</div>
<script src="_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf"></script>
<footer class="footer mt-5 mt-md-0">
<div class="container">
<div class="footer-item">
<p class="copyright">
© Copyright 2022, BioSimulators Team.<br>
</p>
</div>
</div>
</footer>
</body>
</html>