sbml3

A single SBML model runs with input from a files and output to a file. This example demonstrates the use of the only_output_final_step model parameter to only get the final output of the simulation.

SBML Version

Model Code:

  1<?xml version="1.0" encoding="UTF-8"?>
  2<sbml xmlns="http://www.sbml.org/sbml/level2" xmlns:jd2="http://www.sys-bio.org/sbml/jd2" level="2" version="1">
  3  <model id="feedback" name="Feedback">
  4    <annotation>
  5      <jd2:JDesignerLayout xmlns:jd2="http://www.sys-bio.org/sbml/jd2" version="2.0" MajorVersion="2" MinorVersion="3" BuildVersion="45">
  6        <jd2:header>
  7          <jd2:VersionHeader JDesignerVersion="1.0"/>
  8          <jd2:ModelHeader ModelTitle="Feedback"/>
  9          <jd2:TimeCourseDetails timeStart="0" timeEnd="25" numberOfPoints="200"/>
 10        </jd2:header>
 11        <jd2:JDGraphicsHeader BackGroundColor="FFFFFFEF"/>
 12        <jd2:listOfCompartments>
 13          <jd2:compartment id="compartment" size="1" visible="false">
 14            <jd2:boundingBox x="0" y="0" w="0" h="0"/>
 15            <jd2:membraneStyle thickness="12" color="FF00A5FF"/>
 16            <jd2:interiorStyle color="FFEEEEFF"/>
 17            <jd2:text value="compartment" visible="true">
 18              <jd2:position rx="-31" ry="-16"/>
 19              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 20            </jd2:text>
 21          </jd2:compartment>
 22        </jd2:listOfCompartments>
 23        <jd2:listOfSpecies>
 24          <jd2:species id="S1" boundaryCondition="false" compartment="compartment" initialConcentration="0">
 25            <jd2:positionLocked value="false"/>
 26            <jd2:boundingBox x="138" y="104"/>
 27            <jd2:displayValue visible="false">
 28              <jd2:position rx="0" ry="0"/>
 29              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 30            </jd2:displayValue>
 31            <jd2:text value="S1" visible="true">
 32              <jd2:position rx="4" ry="6"/>
 33              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 34            </jd2:text>
 35            <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
 36              <jd2:subunit shape="suRoundSquare">
 37                <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
 38                <jd2:text value="S1" visible="false">
 39                  <jd2:position rx="6" ry="5"/>
 40                  <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 41                </jd2:text>
 42                <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
 43                <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
 44              </jd2:subunit>
 45            </jd2:complex>
 46          </jd2:species>
 47          <jd2:species id="S2" boundaryCondition="false" compartment="compartment" initialConcentration="0">
 48            <jd2:positionLocked value="false"/>
 49            <jd2:boundingBox x="234" y="143"/>
 50            <jd2:displayValue visible="false">
 51              <jd2:position rx="0" ry="0"/>
 52              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 53            </jd2:displayValue>
 54            <jd2:text value="S2" visible="true">
 55              <jd2:position rx="4" ry="6"/>
 56              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 57            </jd2:text>
 58            <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
 59              <jd2:subunit shape="suRoundSquare">
 60                <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
 61                <jd2:text value="S1" visible="false">
 62                  <jd2:position rx="6" ry="5"/>
 63                  <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 64                </jd2:text>
 65                <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
 66                <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
 67              </jd2:subunit>
 68            </jd2:complex>
 69          </jd2:species>
 70          <jd2:species id="S3" boundaryCondition="false" compartment="compartment" initialConcentration="0">
 71            <jd2:positionLocked value="false"/>
 72            <jd2:boundingBox x="318" y="178"/>
 73            <jd2:displayValue visible="false">
 74              <jd2:position rx="0" ry="0"/>
 75              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 76            </jd2:displayValue>
 77            <jd2:text value="S3" visible="true">
 78              <jd2:position rx="4" ry="6"/>
 79              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 80            </jd2:text>
 81            <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
 82              <jd2:subunit shape="suRoundSquare">
 83                <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
 84                <jd2:text value="S1" visible="false">
 85                  <jd2:position rx="6" ry="5"/>
 86                  <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 87                </jd2:text>
 88                <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
 89                <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
 90              </jd2:subunit>
 91            </jd2:complex>
 92          </jd2:species>
 93          <jd2:species id="S4" boundaryCondition="false" compartment="compartment" initialConcentration="0">
 94            <jd2:positionLocked value="false"/>
 95            <jd2:boundingBox x="411" y="212"/>
 96            <jd2:displayValue visible="false">
 97              <jd2:position rx="0" ry="0"/>
 98              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
 99            </jd2:displayValue>
100            <jd2:text value="S4" visible="true">
101              <jd2:position rx="4" ry="6"/>
102              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
103            </jd2:text>
104            <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
105              <jd2:subunit shape="suRoundSquare">
106                <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
107                <jd2:text value="S1" visible="false">
108                  <jd2:position rx="6" ry="5"/>
109                  <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
110                </jd2:text>
111                <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
112                <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
113              </jd2:subunit>
114            </jd2:complex>
115          </jd2:species>
116          <jd2:species id="X0" boundaryCondition="true" compartment="compartment" initialConcentration="10">
117            <jd2:positionLocked value="false"/>
118            <jd2:boundingBox x="33" y="60"/>
119            <jd2:displayValue visible="false">
120              <jd2:position rx="0" ry="0"/>
121              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
122            </jd2:displayValue>
123            <jd2:text value="X0" visible="true">
124              <jd2:position rx="4" ry="6"/>
125              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
126            </jd2:text>
127            <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
128              <jd2:subunit shape="suRoundSquare">
129                <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
130                <jd2:text value="S1" visible="false">
131                  <jd2:position rx="6" ry="5"/>
132                  <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
133                </jd2:text>
134                <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
135                <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
136              </jd2:subunit>
137            </jd2:complex>
138          </jd2:species>
139          <jd2:species id="X1" boundaryCondition="true" compartment="compartment" initialConcentration="0">
140            <jd2:positionLocked value="false"/>
141            <jd2:boundingBox x="415" y="292"/>
142            <jd2:displayValue visible="false">
143              <jd2:position rx="0" ry="0"/>
144              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
145            </jd2:displayValue>
146            <jd2:text value="X1" visible="true">
147              <jd2:position rx="4" ry="6"/>
148              <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
149            </jd2:text>
150            <jd2:complex id="DefaultMolecule" w="24" h="24" boundarySpeciesStyle="bsBox" boundaryStyleColor="FF0000FF" captionPosition="npCenter" aliasBoundaryColor="FFFF0000" aliasBoundaryThickness="3">
151              <jd2:subunit shape="suRoundSquare">
152                <jd2:boundingBox rx="0" ry="0" w="24" h="24"/>
153                <jd2:text value="S1" visible="false">
154                  <jd2:position rx="6" ry="5"/>
155                  <jd2:font fontName="Arial" fontSize="8" fontColor="FF000000"/>
156                </jd2:text>
157                <jd2:color scheme="gtHorizLinear" startColor="FFCCFFFF" endColor="FFFFFFFF"/>
158                <jd2:edgeStyle color="FF969696" thickness="1" stroke="dsSolid"/>
159              </jd2:subunit>
160            </jd2:complex>
161          </jd2:species>
162        </jd2:listOfSpecies>
163        <jd2:listOfReactions>
164          <jd2:reaction id="J0" reversible="false">
165            <jd2:listOfReactants>
166              <jd2:speciesReference species="X0" stoichiometry="1"/>
167            </jd2:listOfReactants>
168            <jd2:listOfProducts>
169              <jd2:speciesReference species="S1" stoichiometry="1"/>
170            </jd2:listOfProducts>
171            <jd2:listOfModifierEdges>
172              <jd2:modifierEdge>
173                <jd2:speciesReference species="S4"/>
174                <jd2:destinationReaction name="J0" regulatorType="rtNegative" relativePosition="0.415929203539823" destinationArcId="0" destinationLineSegmentId="0"/>
175                <jd2:display lineThickness="2" lineColor="FF0000FF" lineDashStyle="dsSolid" negativeMarkerStyle="rmBar">
176                  <jd2:lineType type="ltSegmentedLine">
177                    <jd2:pt x="423" y="224" type="modifier" speciesRef="S4"/>
178                    <jd2:pt x="353" y="243"/>
179                    <jd2:pt x="69" y="127"/>
180                    <jd2:pt x="84" y="101"/>
181                  </jd2:lineType>
182                </jd2:display>
183              </jd2:modifierEdge>
184            </jd2:listOfModifierEdges>
185            <jd2:kineticLaw type="explicit">
186              <jd2:rateEquation value="J0_VM1*(X0-S1/J0_Keq1)/(1+X0+S1+pow(S4,J0_h))"/>
187            </jd2:kineticLaw>
188            <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
189              <jd2:lineType type="ltLine">
190                <jd2:edge>
191                  <jd2:pt x="45" y="72" type="substrate" speciesRef="X0"/>
192                  <jd2:pt x="150" y="116" type="product" speciesRef="S1"/>
193                </jd2:edge>
194              </jd2:lineType>
195            </jd2:display>
196          </jd2:reaction>
197          <jd2:reaction id="J1" reversible="false">
198            <jd2:listOfReactants>
199              <jd2:speciesReference species="S1" stoichiometry="1"/>
200            </jd2:listOfReactants>
201            <jd2:listOfProducts>
202              <jd2:speciesReference species="S2" stoichiometry="1"/>
203            </jd2:listOfProducts>
204            <jd2:listOfModifierEdges/>
205            <jd2:kineticLaw type="explicit">
206              <jd2:rateEquation value="(10*S1-2*S2)/(1+S1+S2)"/>
207            </jd2:kineticLaw>
208            <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
209              <jd2:lineType type="ltLine">
210                <jd2:edge>
211                  <jd2:pt x="150" y="116" type="substrate" speciesRef="S1"/>
212                  <jd2:pt x="246" y="155" type="product" speciesRef="S2"/>
213                </jd2:edge>
214              </jd2:lineType>
215            </jd2:display>
216          </jd2:reaction>
217          <jd2:reaction id="J2" reversible="false">
218            <jd2:listOfReactants>
219              <jd2:speciesReference species="S2" stoichiometry="1"/>
220            </jd2:listOfReactants>
221            <jd2:listOfProducts>
222              <jd2:speciesReference species="S3" stoichiometry="1"/>
223            </jd2:listOfProducts>
224            <jd2:listOfModifierEdges/>
225            <jd2:kineticLaw type="explicit">
226              <jd2:rateEquation value="(10*S2-2*S3)/(1+S2+S3)"/>
227            </jd2:kineticLaw>
228            <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
229              <jd2:lineType type="ltLine">
230                <jd2:edge>
231                  <jd2:pt x="246" y="155" type="substrate" speciesRef="S2"/>
232                  <jd2:pt x="330" y="190" type="product" speciesRef="S3"/>
233                </jd2:edge>
234              </jd2:lineType>
235            </jd2:display>
236          </jd2:reaction>
237          <jd2:reaction id="J3" reversible="false">
238            <jd2:listOfReactants>
239              <jd2:speciesReference species="S3" stoichiometry="1"/>
240            </jd2:listOfReactants>
241            <jd2:listOfProducts>
242              <jd2:speciesReference species="S4" stoichiometry="1"/>
243            </jd2:listOfProducts>
244            <jd2:listOfModifierEdges/>
245            <jd2:kineticLaw type="explicit">
246              <jd2:rateEquation value="(10*S3-2*S4)/(1+S3+S4)"/>
247            </jd2:kineticLaw>
248            <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
249              <jd2:lineType type="ltLine">
250                <jd2:edge>
251                  <jd2:pt x="330" y="190" type="substrate" speciesRef="S3"/>
252                  <jd2:pt x="423" y="224" type="product" speciesRef="S4"/>
253                </jd2:edge>
254              </jd2:lineType>
255            </jd2:display>
256          </jd2:reaction>
257          <jd2:reaction id="J4" reversible="false">
258            <jd2:listOfReactants>
259              <jd2:speciesReference species="S4" stoichiometry="1"/>
260            </jd2:listOfReactants>
261            <jd2:listOfProducts>
262              <jd2:speciesReference species="X1" stoichiometry="1"/>
263            </jd2:listOfProducts>
264            <jd2:listOfModifierEdges/>
265            <jd2:kineticLaw type="explicit">
266              <jd2:rateEquation value="J4_V4*S4/(J4_KS4+S4)"/>
267            </jd2:kineticLaw>
268            <jd2:display arrowStyle="ar1" arrowFillColor="FF000000" lineColor="FF838464" lineThickness="2">
269              <jd2:lineType type="ltLine">
270                <jd2:edge>
271                  <jd2:pt x="423" y="224" type="substrate" speciesRef="S4"/>
272                  <jd2:pt x="427" y="304" type="product" speciesRef="X1"/>
273                </jd2:edge>
274              </jd2:lineType>
275            </jd2:display>
276          </jd2:reaction>
277        </jd2:listOfReactions>
278      </jd2:JDesignerLayout>
279    </annotation>
280    <listOfCompartments>
281      <compartment id="compartment" size="1"/>
282    </listOfCompartments>
283    <listOfSpecies>
284      <species id="S1" compartment="compartment" initialConcentration="0"/>
285      <species id="S2" compartment="compartment" initialConcentration="0"/>
286      <species id="S3" compartment="compartment" initialConcentration="0"/>
287      <species id="S4" compartment="compartment" initialConcentration="0"/>
288      <species id="X0" compartment="compartment" initialConcentration="10" boundaryCondition="true"/>
289      <species id="X1" compartment="compartment" initialConcentration="0" boundaryCondition="true"/>
290    </listOfSpecies>
291    <listOfParameters>
292      <parameter id="J0_VM1" value="10"/>
293      <parameter id="J0_Keq1" value="10"/>
294      <parameter id="J0_h" value="10"/>
295      <parameter id="J4_V4" value="2.5"/>
296      <parameter id="J4_KS4" value="0.5"/>
297    </listOfParameters>
298    <listOfReactions>
299      <reaction id="J0" reversible="false">
300        <listOfReactants>
301          <speciesReference species="X0"/>
302        </listOfReactants>
303        <listOfProducts>
304          <speciesReference species="S1"/>
305        </listOfProducts>
306        <listOfModifiers>
307          <modifierSpeciesReference species="S4"/>
308        </listOfModifiers>
309        <kineticLaw>
310          <math xmlns="http://www.w3.org/1998/Math/MathML">
311            <apply>
312              <divide/>
313              <apply>
314                <times/>
315                <ci> J0_VM1 </ci>
316                <apply>
317                  <minus/>
318                  <ci> X0 </ci>
319                  <apply>
320                    <divide/>
321                    <ci> S1 </ci>
322                    <ci> J0_Keq1 </ci>
323                  </apply>
324                </apply>
325              </apply>
326              <apply>
327                <plus/>
328                <cn type="integer"> 1 </cn>
329                <ci> X0 </ci>
330                <ci> S1 </ci>
331                <apply>
332                  <power/>
333                  <ci> S4 </ci>
334                  <ci> J0_h </ci>
335                </apply>
336              </apply>
337            </apply>
338          </math>
339        </kineticLaw>
340      </reaction>
341      <reaction id="J1" reversible="false">
342        <listOfReactants>
343          <speciesReference species="S1"/>
344        </listOfReactants>
345        <listOfProducts>
346          <speciesReference species="S2"/>
347        </listOfProducts>
348        <kineticLaw>
349          <math xmlns="http://www.w3.org/1998/Math/MathML">
350            <apply>
351              <divide/>
352              <apply>
353                <minus/>
354                <apply>
355                  <times/>
356                  <cn type="integer"> 10 </cn>
357                  <ci> S1 </ci>
358                </apply>
359                <apply>
360                  <times/>
361                  <cn type="integer"> 2 </cn>
362                  <ci> S2 </ci>
363                </apply>
364              </apply>
365              <apply>
366                <plus/>
367                <cn type="integer"> 1 </cn>
368                <ci> S1 </ci>
369                <ci> S2 </ci>
370              </apply>
371            </apply>
372          </math>
373        </kineticLaw>
374      </reaction>
375      <reaction id="J2" reversible="false">
376        <listOfReactants>
377          <speciesReference species="S2"/>
378        </listOfReactants>
379        <listOfProducts>
380          <speciesReference species="S3"/>
381        </listOfProducts>
382        <kineticLaw>
383          <math xmlns="http://www.w3.org/1998/Math/MathML">
384            <apply>
385              <divide/>
386              <apply>
387                <minus/>
388                <apply>
389                  <times/>
390                  <cn type="integer"> 10 </cn>
391                  <ci> S2 </ci>
392                </apply>
393                <apply>
394                  <times/>
395                  <cn type="integer"> 2 </cn>
396                  <ci> S3 </ci>
397                </apply>
398              </apply>
399              <apply>
400                <plus/>
401                <cn type="integer"> 1 </cn>
402                <ci> S2 </ci>
403                <ci> S3 </ci>
404              </apply>
405            </apply>
406          </math>
407        </kineticLaw>
408      </reaction>
409      <reaction id="J3" reversible="false">
410        <listOfReactants>
411          <speciesReference species="S3"/>
412        </listOfReactants>
413        <listOfProducts>
414          <speciesReference species="S4"/>
415        </listOfProducts>
416        <kineticLaw>
417          <math xmlns="http://www.w3.org/1998/Math/MathML">
418            <apply>
419              <divide/>
420              <apply>
421                <minus/>
422                <apply>
423                  <times/>
424                  <cn type="integer"> 10 </cn>
425                  <ci> S3 </ci>
426                </apply>
427                <apply>
428                  <times/>
429                  <cn type="integer"> 2 </cn>
430                  <ci> S4 </ci>
431                </apply>
432              </apply>
433              <apply>
434                <plus/>
435                <cn type="integer"> 1 </cn>
436                <ci> S3 </ci>
437                <ci> S4 </ci>
438              </apply>
439            </apply>
440          </math>
441        </kineticLaw>
442      </reaction>
443      <reaction id="J4" reversible="false">
444        <listOfReactants>
445          <speciesReference species="S4"/>
446        </listOfReactants>
447        <listOfProducts>
448          <speciesReference species="X1"/>
449        </listOfProducts>
450        <kineticLaw>
451          <math xmlns="http://www.w3.org/1998/Math/MathML">
452            <apply>
453              <divide/>
454              <apply>
455                <times/>
456                <ci> J4_V4 </ci>
457                <ci> S4 </ci>
458              </apply>
459              <apply>
460                <plus/>
461                <ci> J4_KS4 </ci>
462                <ci> S4 </ci>
463              </apply>
464            </apply>
465          </math>
466        </kineticLaw>
467      </reaction>
468    </listOfReactions>
469  </model>
470</sbml>

Model YAML:

 1model:
 2  name: feedback
 3  language: sbml
 4  args: ./src/sbml3.xml
 5  only_output_final_step: true
 6  inputs:
 7    - name: input
 8      vars: time,S1,S2
 9      default_file:
10        name: ./Input/input.txt
11        filetype: table
12  outputs:
13    - name: output
14      vars: time,S1,S2
15      default_file:
16        name: ./output.txt
17        filetype: table