test : 00408/00408-settings.txt model : xml, description simulation engine : JVode generated code : _00408_sbml_l3v1.java results : table with results plots : normal status : ok simulation time : 0.11 s.Parameters:
start: 0 duration: 3 steps: 50 variables: S1, S2, S3, S4 absolute: 1.000000e-007 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 calledS1, S2, S3 and S4 and two parameters called k1 and k2. The model containstwo reactions defined as:
| Reaction | Rate |
| S1 + S2 → S3 + S4 | k1 · S1 · S2 · C |
| S3 + S4 → S1 + S2 | k2 · S3 · S4 · C |
The model contains one event that assigns a value to species S1:
| Trigger | Delay | Assignments | |
| Event1 | S4 > S2 | 1 | S1 → 2 × 10−4 |
The initial conditions are as follows:
| Value | Units | |
| Initial amount of S1 | 1.0 × 10−4 | mole |
| Initial amount of S2 | 1.0 × 10−4 | mole |
| Initial amount of S3 | 2.0 × 10−4 | mole |
| Initial amount of S4 | 1.0 × 10−4 | mole |
| Value of parameter k1 | 0.75 × 104 | litre mole-1 second-1 |
| Value of parameter k2 | 0.25 × 104 | litre mole-1 second-1 |
| 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) their symbols represent their values in concentration unitswhere they appear in expressions.
Normal plot
| time | S3 | S4 | S2 | S1 |
| 0.0 |
2.0E-4 2.0E-4 |
1.0E-4 1.0E-4 |
1.2E-4 1.2E-4 |
1.0E-4 1.0E-4 |
| 0.06 |
2.02236E-4 2.0223575344362264E-4 |
1.02236E-4 1.0223575344362266E-4 |
1.17764E-4 1.1776424655637734E-4 |
9.77643E-5 9.776424655637735E-5 |
| 0.12 |
2.04174E-4 2.0417413545956674E-4 |
1.04174E-4 1.0417413545956679E-4 |
1.15826E-4 1.1582586454043322E-4 |
9.5826E-5 9.582586454043322E-5 |
| 0.18 |
2.05857E-4 2.0585674213075784E-4 |
1.05857E-4 1.0585674213075789E-4 |
1.14143E-4 1.1414325786924212E-4 |
9.41434E-5 9.414325786924212E-5 |
| 0.24 |
2.07319E-4 2.0731879035104496E-4 |
1.07319E-4 1.0731879035104503E-4 |
1.12681E-4 1.1268120964895498E-4 |
9.26813E-5 9.268120964895498E-5 |
| 0.3 |
2.0859E-4 2.085903139708943E-4 |
1.0859E-4 1.0859031397089436E-4 |
1.1141E-4 1.1140968602910565E-4 |
9.14097E-5 9.140968602910565E-5 |
| 0.36 |
2.09697E-4 2.0969698163790428E-4 |
1.09697E-4 1.096969816379043E-4 |
1.10303E-4 1.103030183620957E-4 |
9.0303E-5 9.03030183620957E-5 |
| 0.42 |
2.10661E-4 2.1066081225351357E-4 |
1.10661E-4 1.1066081225351361E-4 |
1.09339E-4 1.093391877464864E-4 |
8.93392E-5 8.93391877464864E-5 |
| 0.48 |
2.11501E-4 2.1150070051893498E-4 |
1.11501E-4 1.1150070051893505E-4 |
1.08499E-4 1.0849929948106495E-4 |
8.84993E-5 8.849929948106495E-5 |
| 0.54 |
2.12233E-4 2.1223297534615036E-4 |
1.12233E-4 1.1223297534615044E-4 |
1.07767E-4 1.0776702465384957E-4 |
8.7767E-5 8.776702465384957E-5 |
| 0.6 |
2.12872E-4 2.128717257526927E-4 |
1.12872E-4 1.128717257526928E-4 |
1.07128E-4 1.071282742473072E-4 |
8.71283E-5 8.71282742473072E-5 |
| 0.66 |
2.13429E-4 2.1342909557597054E-4 |
1.13429E-4 1.1342909557597063E-4 |
1.06571E-4 1.0657090442402938E-4 |
8.6571E-5 8.657090442402938E-5 |
| 0.72 |
2.13916E-4 2.139156152865253E-4 |
1.13916E-4 1.1391561528652533E-4 |
1.06084E-4 1.0608438471347468E-4 |
8.60844E-5 8.608438471347468E-5 |
| 0.78 |
2.1434E-4 2.1434041545198224E-4 |
1.1434E-4 1.1434041545198226E-4 |
1.0566E-4 1.0565958454801775E-4 |
8.56596E-5 8.565958454801775E-5 |
| 0.84 |
2.14711E-4 2.1471142354950303E-4 |
1.14711E-4 1.1471142354950304E-4 |
1.05289E-4 1.0528857645049697E-4 |
8.52886E-5 8.528857645049697E-5 |
| 0.9 |
2.15035E-4 2.1503552405467913E-4 |
1.15035E-4 1.1503552405467915E-4 |
1.04965E-4 1.0496447594532087E-4 |
8.49645E-5 8.496447594532087E-5 |
| 0.96 |
2.15319E-4 2.1531869974986793E-4 |
1.15319E-4 1.1531869974986794E-4 |
1.04681E-4 1.0468130025013209E-4 |
8.46813E-5 8.468130025013209E-5 |
| 1.02 |
2.15566E-4 2.1556615735430525E-4 |
1.15566E-4 1.1556615735430527E-4 |
1.04434E-4 1.0443384264569477E-4 |
8.44339E-5 8.443384264569475E-5 |
| 1.08 |
2.15782E-4 2.1578243510406576E-4 |
1.15782E-4 1.1578243510406577E-4 |
1.04218E-4 1.0421756489593426E-4 |
8.42176E-5 8.421756489593425E-5 |
| 1.14 |
2.15971E-4 2.1597148892743196E-4 |
1.15971E-4 1.1597148892743195E-4 |
1.04029E-4 1.0402851107256808E-4 |
8.40285E-5 8.402851107256807E-5 |
| 1.2 |
2.16137E-4 2.161367655912685E-4 |
1.16137E-4 1.1613676559126846E-4 |
1.03863E-4 1.0386323440873158E-4 |
8.38633E-5 8.386323440873157E-5 |
| 1.26 |
2.16281E-4 2.1628126923332094E-4 |
1.16281E-4 1.1628126923332093E-4 |
1.03719E-4 1.037187307666791E-4 |
8.37188E-5 8.371873076667909E-5 |
| 1.32 |
2.16408E-4 2.1640762094609037E-4 |
1.16408E-4 1.1640762094609036E-4 |
1.03592E-4 1.0359237905390967E-4 |
8.35924E-5 8.35923790539101E-5 |
| 1.38 |
2.16699E-4 2.1669954736065744E-4 |
1.16699E-4 1.1669954736065747E-4 |
1.03301E-4 1.0330045263934257E-4 |
1.99815E-4 1.9981509069358654E-4 |
| 1.44 |
2.21715E-4 2.2171541869348953E-4 |
1.21715E-4 1.2171541869348952E-4 |
9.82849E-5 9.828458130651049E-5 |
1.94799E-4 1.9479921936075618E-4 |
| 1.5 |
2.2589E-4 2.258904095077251E-4 |
1.2589E-4 1.2589040950772507E-4 |
9.41098E-5 9.410959049227497E-5 |
1.90624E-4 1.9062422854652063E-4 |
| 1.56 |
2.29374E-4 2.2937432005934176E-4 |
1.29374E-4 1.2937432005934174E-4 |
9.06258E-5 9.062567994065821E-5 |
1.8714E-4 1.8714031799490396E-4 |
| 1.62 |
2.32288E-4 2.3228766152492186E-4 |
1.32288E-4 1.3228766152492184E-4 |
8.77125E-5 8.77123384750781E-5 |
1.84227E-4 1.8422697652932386E-4 |
| 1.68 |
2.34728E-4 2.3472811344295606E-4 |
1.34728E-4 1.3472811344295604E-4 |
8.5272E-5 8.527188655704386E-5 |
1.81787E-4 1.8178652461128966E-4 |
| 1.74 |
2.36775E-4 2.367754709439121E-4 |
1.36775E-4 1.3677547094391207E-4 |
8.32247E-5 8.322452905608788E-5 |
1.79739E-4 1.7973916711033362E-4 |
| 1.8 |
2.38495E-4 2.3849517349324887E-4 |
1.38495E-4 1.3849517349324886E-4 |
8.1505E-5 8.150482650675111E-5 |
1.7802E-4 1.7801946456099684E-4 |
| 1.86 |
2.39941E-4 2.3994116351757472E-4 |
1.39941E-4 1.399411635175747E-4 |
8.0059E-5 8.005883648242526E-5 |
1.76574E-4 1.76573474536671E-4 |
| 1.92 |
2.41158E-4 2.4115804559806962E-4 |
1.41158E-4 1.411580455980696E-4 |
7.88421E-5 7.884195440193033E-5 |
1.75357E-4 1.753565924561761E-4 |
| 1.98 |
2.42183E-4 2.4218288472080578E-4 |
1.42183E-4 1.4218288472080573E-4 |
7.78172E-5 7.781711527919418E-5 |
1.74332E-4 1.7433175333343996E-4 |
| 2.04 |
2.43046E-4 2.4304652198994003E-4 |
1.43046E-4 1.4304652198993999E-4 |
7.69536E-5 7.695347801005994E-5 |
1.73468E-4 1.734681160643057E-4 |
| 2.1 |
2.43775E-4 2.437746827252247E-4 |
1.43775E-4 1.4377468272522466E-4 |
7.62253E-5 7.622531727477527E-5 |
1.7274E-4 1.7273995532902104E-4 |
| 2.16 |
2.44389E-4 2.4438889304524827E-4 |
1.44389E-4 1.443888930452482E-4 |
7.56111E-5 7.561110695475171E-5 |
1.72126E-4 1.721257450089975E-4 |
| 2.22 |
2.44907E-4 2.4490718595903023E-4 |
1.44907E-4 1.4490718595903016E-4 |
7.50928E-5 7.509281404096976E-5 |
1.71607E-4 1.7160745209521556E-4 |
| 2.28 |
2.45345E-4 2.4534467841273076E-4 |
1.45345E-4 1.453446784127307E-4 |
7.46553E-5 7.465532158726923E-5 |
1.7117E-4 1.71169959641515E-4 |
| 2.34 |
2.45714E-4 2.457140589525953E-4 |
1.45714E-4 1.457140589525953E-4 |
7.42859E-5 7.428594104740462E-5 |
1.70801E-4 1.708005791016504E-4 |
| 2.4 |
2.46026E-4 2.460260007566351E-4 |
1.46026E-4 1.4602600075663504E-4 |
7.3974E-5 7.39739992433649E-5 |
1.70489E-4 1.7048863729761065E-4 |
| 2.46 |
2.46289E-4 2.4628948719366677E-4 |
1.46289E-4 1.4628948719366678E-4 |
7.37105E-5 7.371051280633315E-5 |
1.70225E-4 1.7022515086057892E-4 |
| 2.52 |
2.46512E-4 2.465120800666765E-4 |
1.46512E-4 1.4651208006667647E-4 |
7.34879E-5 7.348791993332343E-5 |
1.70003E-4 1.7000255798756923E-4 |
| 2.58 |
2.467E-4 2.4670015052189305E-4 |
1.467E-4 1.4670015052189303E-4 |
7.32998E-5 7.329984947810688E-5 |
1.69814E-4 1.6981448753235266E-4 |
| 2.64 |
2.46859E-4 2.468590708113686E-4 |
1.46859E-4 1.4685907081136857E-4 |
7.31409E-5 7.314092918863137E-5 |
1.69656E-4 1.6965556724287713E-4 |
| 2.7 |
2.46993E-4 2.469933725261951E-4 |
1.46993E-4 1.469933725261952E-4 |
7.30066E-5 7.300662747380475E-5 |
1.69521E-4 1.695212655280505E-4 |
| 2.76 |
2.47107E-4 2.4710687819825584E-4 |
1.47107E-4 1.4710687819825593E-4 |
7.28931E-5 7.289312180174399E-5 |
1.69408E-4 1.6940775985598976E-4 |
| 2.82 |
2.47203E-4 2.472028144967884E-4 |
1.47203E-4 1.4720281449678843E-4 |
7.27972E-5 7.279718550321152E-5 |
1.69312E-4 1.6931182355745726E-4 |
| 2.88 |
2.47284E-4 2.472839056972496E-4 |
1.47284E-4 1.4728390569724968E-4 |
7.27161E-5 7.271609430275026E-5 |
1.69231E-4 1.6923073235699602E-4 |
| 2.94 |
2.47352E-4 2.473524524077422E-4 |
1.47352E-4 1.4735245240774222E-4 |
7.26475E-5 7.264754759225772E-5 |
1.69162E-4 1.6916218564650348E-4 |
| 3.0 |
2.4741E-4 2.47410397506718E-4 |
1.4741E-4 1.4741039750671813E-4 |
7.25896E-5 7.258960249328183E-5 |
1.69104E-4 1.6910424054752756E-4 |
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%)