test : 00505/00505-settings.txt model : xml, description simulation engine : JVode generated code : _00505_sbml_l3v1.java results : table with results plots : normal status : ok simulation time : 0.125 s.Parameters:
start: 0 duration: 20.0 steps: 50 variables: S1, S2, S3, S4 absolute: 1.000000e-006 relative: 0.0001 amount: S1, S2, S3, S4 concentration:Simulate via BioUML web edition:
The model contains one compartment called C. There are four species called S1, S2, S3 and S4 and three parameters called k1, k2 and p1. Species S4 is labeled as a constant species. The model contains two reactions defined as:
| Reaction | Rate |
| S1 + S2 → S3 | k1 · S1 · S4 · C |
| S3 → S1 + S2 | k2 · S3 · C |
The model contains one initialAssignment:
| Variable | Formula |
| S4 | p1 · 2 |
Note: SBML's InitialAssignment construct override any declared initialvalues. In this case the initial value declared for species S4 isconsistent with the value returned by the InitialAssignment.
The initial conditions are as follows:
| Value | Units | |
| Initial amount of S1 | 0.25 × 10−3 | mole |
| Initial amount of S2 | 2.0 × 10−3 | mole |
| Initial amount of S3 | 1.0 × 10−3 | mole |
| Initial amount of S4 | 1.0 × 10−3 | mole |
| Value of parameter k1 | 0.75 | litre mole-1 second-1 |
| Value of parameter k2 | 0.25 | second-1 |
| Value of parameter p1 | 5 × 10−4 | mole |
| Volume of compartment C | 1 | litre |
The species values are given as amounts of substance to make it easier touse the model in a discrete stochastic simulator, but (as per usual SBMLprinciples) they must be treated as concentrations where they appear inexpressions.
Normal plot
| time | S3 | S4 | S2 | S1 |
| 0.0 |
0.0010 0.0010 |
0.0010 0.0010 |
0.0020 0.0020 |
2.5E-4 2.5E-4 |
| 0.4 |
9.049228145403459E-4 9.049228279408181E-4 |
0.0010 0.0010 |
0.002095077185459654 0.0020950771720591828 |
3.450771854596538E-4 3.450771720591823E-4 |
| 0.8 |
8.189192241351895E-4 8.189192589276177E-4 |
0.0010 0.0010 |
0.00218108077586481 0.0021810807410723833 |
4.310807758648104E-4 4.310807410723826E-4 |
| 1.2 |
7.411232989127843E-4 7.41123321949561E-4 |
0.0010 0.0010 |
0.002258876701087215 0.00225887667805044 |
5.088767010872156E-4 5.088766780504394E-4 |
| 1.6 |
6.707517508019127E-4 6.707517436800805E-4 |
0.0010 0.0010 |
0.002329248249198087 0.00232924825631992 |
5.792482491980872E-4 5.792482563199198E-4 |
| 2.0 |
6.070960386624061E-4 6.070960261947581E-4 |
0.0010 0.0010 |
0.002392903961337593 0.002392903973805242 |
6.429039613375938E-4 6.429039738052423E-4 |
| 2.4 |
5.495152482556701E-4 5.495152275335957E-4 |
0.0010 0.0010 |
0.002450484751744329 0.0024504847724664044 |
7.004847517443299E-4 7.004847724664047E-4 |
| 2.8 |
4.974296220631535E-4 4.974295676804428E-4 |
0.0010 0.0010 |
0.002502570377936846 0.0025025704323195573 |
7.525703779368465E-4 7.525704323195577E-4 |
| 3.2 |
4.503147345227438E-4 4.503146862692105E-4 |
0.0010 0.0010 |
0.002549685265477255 0.0025496853137307895 |
7.996852654772561E-4 7.996853137307897E-4 |
| 3.6 |
4.076962082066309E-4 4.0769616272133015E-4 |
0.0010 0.0010 |
0.002592303791793368 0.00259230383727867 |
8.42303791793369E-4 8.4230383727867E-4 |
| 4.0 |
3.691449178562953E-4 3.691448990716982E-4 |
0.0010 0.0010 |
0.002630855082143704 0.0026308551009283023 |
8.808550821437046E-4 8.808551009283021E-4 |
| 4.4 |
3.342727496678214E-4 3.3427273290340576E-4 |
0.0010 0.0010 |
0.002665727250332177 0.002665727267096595 |
9.157272503321785E-4 9.157272670965944E-4 |
| 4.8 |
3.027285923539072E-4 3.027285585411156E-4 |
0.0010 0.0010 |
0.002697271407646092 0.0026972714414588853 |
9.472714076460927E-4 9.472714414588846E-4 |
| 5.2 |
2.741947829016641E-4 2.741947863674831E-4 |
0.0010 0.0010 |
0.002725805217098335 0.002725805213632518 |
9.758052170983358E-4 9.758052136325171E-4 |
| 5.6 |
2.483840913922515E-4 2.4838410010721493E-4 |
0.0010 0.0010 |
0.002751615908607748 0.002751615899892786 |
0.001001615908607748 0.0010016158998927855 |
| 6.0 |
2.250366226827883E-4 2.250366215901344E-4 |
0.0010 0.0010 |
0.002774963377317211 0.002774963378409867 |
0.001024963377317211 0.0010249633784098658 |
| 6.4 |
2.039172725815789E-4 2.0391729063914938E-4 |
0.0010 0.0010 |
0.00279608272741842 0.002796082709360852 |
0.001046082727418421 0.0010460827093608505 |
| 6.8 |
1.84813438493515E-4 1.8481346138070635E-4 |
0.0010 0.0010 |
0.002815186561506484 0.002815186538619295 |
0.001065186561506485 0.0010651865386192938 |
| 7.2 |
1.675327733709911E-4 1.6753278492976392E-4 |
0.0010 0.0010 |
0.002832467226629008 0.002832467215070237 |
0.001082467226629009 0.001082467215070236 |
| 7.6 |
1.519012567234943E-4 1.5190127264729688E-4 |
0.0010 0.0010 |
0.002848098743276505 0.0028480987273527044 |
0.001098098743276505 0.0010980987273527033 |
| 8.0 |
1.377615105480195E-4 1.37761538006598E-4 |
0.0010 0.0010 |
0.00286223848945198 0.002862238461993403 |
0.00111223848945198 0.001112238461993402 |
| 8.4 |
1.249711844554397E-4 1.2497121412245038E-4 |
0.0010 0.0010 |
0.00287502881554456 0.002875028785877551 |
0.00112502881554456 0.0011250287858775498 |
| 8.8 |
1.134014989556843E-4 1.1340152147027212E-4 |
0.0010 0.0010 |
0.002886598501044315 0.0028865984785297295 |
0.001136598501044315 0.0011365984785297282 |
| 9.2 |
1.029359539384899E-4 1.0293597102285002E-4 |
0.0010 0.0010 |
0.00289706404606151 0.0028970640289771514 |
0.00114706404606151 0.0011470640289771503 |
| 9.6 |
9.346916722720942E-5 9.346918922934625E-5 |
0.0010 0.0010 |
0.00290653083277279 0.0029065308107706555 |
0.00115653083277279 0.001156530810770654 |
| 10.0 |
8.490583339578104E-5 8.490586029695724E-5 |
0.0010 0.0010 |
0.002915094166604219 0.0029150941397030443 |
0.001165094166604219 0.0011650941397030432 |
| 10.4 |
7.715973863353657E-5 7.71597636538017E-5 |
0.0010 0.0010 |
0.002922840261366464 0.0029228402363461995 |
0.001172840261366463 0.0011728402363461988 |
| 10.8 |
7.015288863719308E-5 7.015290796196831E-5 |
0.0010 0.0010 |
0.002929847111362807 0.002929847092038033 |
0.001179847111362807 0.001179847092038032 |
| 11.2 |
6.38147267644823E-5 6.381474419050105E-5 |
0.0010 0.0010 |
0.002936185273235518 0.0029361852558095003 |
0.001186185273235518 0.0011861852558094992 |
| 11.6 |
5.80814357831218E-5 5.8081456669457093E-5 |
0.0010 0.0010 |
0.002941918564216878 0.0029419185433305437 |
0.001191918564216878 0.0011919185433305432 |
| 12.0 |
5.28952974914464E-5 5.289531949422738E-5 |
0.0010 0.0010 |
0.002947104702508553 0.002947104680505774 |
0.001197104702508553 0.001197104680505773 |
| 12.4 |
4.820409688722731E-5 4.820411599592147E-5 |
0.0010 0.0010 |
0.002951795903112773 0.0029517958840040797 |
0.001201795903112772 0.0012017958840040788 |
| 12.8 |
4.396059745287009E-5 4.39606127184122E-5 |
0.0010 0.0010 |
0.00295603940254713 0.002956039387281589 |
0.00120603940254713 0.0012060393872815882 |
| 13.2 |
4.012206840712801E-5 4.012208373517859E-5 |
0.0010 0.0010 |
0.002959877931592872 0.0029598779162648223 |
0.001209877931592872 0.0012098779162648217 |
| 13.6 |
3.664986389230235E-5 3.6649880938442664E-5 |
0.0010 0.0010 |
0.002963350136107698 0.002963350119061558 |
0.001213350136107698 0.0012133501190615577 |
| 14.0 |
3.350902769251707E-5 3.350904414106328E-5 |
0.0010 0.0010 |
0.002966490972307483 0.0029664909558589376 |
0.001216490972307483 0.001216490955858937 |
| 14.4 |
3.066793611903428E-5 3.066794996830664E-5 |
0.0010 0.0010 |
0.002969332063880965 0.002969332050031694 |
0.001219332063880966 0.0012193320500316935 |
| 14.8 |
2.809798089563962E-5 2.809799261873957E-5 |
0.0010 0.0010 |
0.00297190201910436 0.002971902007381261 |
0.00122190201910436 0.0012219020073812605 |
| 15.2 |
2.57732842085579E-5 2.577329657177654E-5 |
0.0010 0.0010 |
0.002974226715791442 0.0029742267034282245 |
0.001224226715791442 0.0012242267034282234 |
| 15.6 |
2.36704426484768E-5 2.3670456541869642E-5 |
0.0010 0.0010 |
0.002976329557351524 0.002976329543458131 |
0.001226329557351523 0.0012263295434581305 |
| 16.0 |
2.176828513669127E-5 2.1768301184486648E-5 |
0.0010 0.0010 |
0.002978231714863309 0.002978231698815514 |
0.001228231714863308 0.0012282316988155133 |
| 16.4 |
2.004765903778458E-5 2.0047677071421145E-5 |
0.0010 0.0010 |
0.002979952340962216 0.00297995232292858 |
0.001229952340962215 0.0012299523229285787 |
| 16.8 |
1.849123818446448E-5 1.849125791806276E-5 |
0.0010 0.0010 |
0.002981508761815536 0.0029815087420819383 |
0.001231508761815535 0.0012315087420819372 |
| 17.2 |
1.708335158172837E-5 1.7083372636959398E-5 |
0.0010 0.0010 |
0.002982916648418272 0.0029829166273630412 |
0.001232916648418271 0.0012329166273630406 |
| 17.6 |
1.580982572852143E-5 1.5809847010444896E-5 |
0.0010 0.0010 |
0.002984190174271479 0.0029841901529895558 |
0.001234190174271478 0.001234190152989555 |
| 18.0 |
1.465783846245739E-5 1.4657859217004478E-5 |
0.0010 0.0010 |
0.002985342161537543 0.0029853421407829966 |
0.001235342161537542 0.0012353421407829957 |
| 18.4 |
1.361579017407215E-5 1.3615810301979968E-5 |
0.0010 0.0010 |
0.002986384209825928 0.002986384189698021 |
0.001236384209825927 0.0012363841896980202 |
| 18.8 |
1.267318776755198E-5 1.2673207979135794E-5 |
0.0010 0.0010 |
0.002987326812232449 0.0029873267920208653 |
0.001237326812232447 0.0012373267920208642 |
| 19.2 |
1.18205413330621E-5 1.1820561618389796E-5 |
0.0010 0.0010 |
0.002988179458666939 0.002988179438381611 |
0.001238179458666937 0.0012381794383816102 |
| 19.6 |
1.10492672107604E-5 1.104928656364516E-5 |
0.0010 0.0010 |
0.002988950732789241 0.0029889507134363558 |
0.001238950732789239 0.0012389507134363549 |
| 20.0 |
1.035159901617304E-5 1.035161732972156E-5 |
0.0010 0.0010 |
0.002989648400983828 0.0029896483826702797 |
0.001239648400983826 0.0012396483826702786 |
Legend:
each cell contains two values:
- value that should be obtained accrding to CSV file;
- value that were approximated for corresponding point by BioUML workbench simulation engine.
Color indicates difference between values:
- simulation results satisfy SBML passing criterion
- relative error (> SBML passing criterion allows and <50%)
- simulation results don't satisfy SBML passing criterion and significantly differs (>50%)