-
Notifications
You must be signed in to change notification settings - Fork 42
/
model1.xml
154 lines (153 loc) · 6.14 KB
/
model1.xml
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
<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by COPASI version 4.30 (Build 240) on 2021-03-03 15:27 with libSBML version 5.19.0. -->
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model metaid="COPASI0" id="ABC_Example" name="ABC Example">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<pre>Example from:
https://pyabc.readthedocs.io/en/latest/examples/chemical_reaction.html</pre>
</body>
</notes>
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI0">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-03T11:20:00Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfUnitDefinitions>
<unitDefinition id="substance" name="substance">
<listOfUnits>
<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="length" name="length">
<listOfUnits>
<unit kind="metre" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="area" name="area">
<listOfUnits>
<unit kind="metre" exponent="2" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="volume" name="volume">
<listOfUnits>
<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="time" name="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="COPASI1" id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI1">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-03T11:20:53Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="COPASI2" id="X" name="X" compartment="compartment" initialConcentration="40" boundaryCondition="false" constant="false">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI2">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-03T11:20:53Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
</species>
<species metaid="COPASI3" id="Y" name="Y" compartment="compartment" initialConcentration="3" boundaryCondition="false" constant="false">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#Metabolite_0">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-03T11:20:53Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter metaid="COPASI5" id="rate" name="rate" value="2.3" constant="true">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI5">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-03T14:26:22Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
</parameter>
</listOfParameters>
<listOfReactions>
<reaction metaid="COPASI4" id="reaction" name="R1" reversible="false">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI4">
<dcterms:created>
<rdf:Description>
<dcterms:W3CDTF>2021-03-03T11:20:53Z</dcterms:W3CDTF>
</rdf:Description>
</dcterms:created>
</rdf:Description>
</rdf:RDF>
</COPASI>
</annotation>
<listOfReactants>
<speciesReference species="X" stoichiometry="1"/>
<speciesReference species="Y" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="Y" stoichiometry="2"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<ci> rate </ci>
<ci> X </ci>
<ci> Y </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>