diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py index 8d9cc3d..06d4b59 100644 --- a/biosimulators_test_suite/_version.py +++ b/biosimulators_test_suite/_version.py @@ -1 +1 @@ -__version__ = '0.1.85' +__version__ = '0.1.86' diff --git a/examples/README.md b/examples/README.md index a3d1b4f..d155d24 100644 --- a/examples/README.md +++ b/examples/README.md @@ -50,7 +50,8 @@ The archives in this directory involve the following model formats: | [SBML flux balance constraints package](http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/fbc) | SBML-fbc | [format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) | | [SBML qualitative modeling package](http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/qual) | SBML-qual | [format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) | | [SBML MASS schema](https://masspy.readthedocs.io/en/stable/tutorials/reading_writing_models.html) | | | -| [XPP Language](http://www.math.pitt.edu/~bard/xpp/xpp.html) | | | +| [Virtual Cell Markup Language](https://vcell.org/) | VCML | | +| [XPP ODE format](http://www.math.pitt.edu/~bard/xpp/xpp.html) | | | Note, more specific EDAM terms have SBML-fbc, SBML-qual, and other formats have been requested. @@ -89,9 +90,10 @@ Below is information about the compatibility of a selection of archives. | [Lorenz system](https://github.com/opencor/opencor/blob/master/models/tests/cellml/lorenz.cellml) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/cellml/Lorenz-system.omex)| [`.h5`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/cellml/Lorenz-system/reports.h5) | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | OpenCOR | [OpenCOR](https://biosimulators.org/simulators/opencor) | | [Lotka-Volterra model (Smoldyn Team)](http://www.smoldyn.org/archive/examples/S8_reactions/lotvolt/lotvolt.txt) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/smoldyn/Lotka-Volterra.omex)| [`.h5`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/smoldyn/Lotka-Volterra/reports.h5) | | spatial discrete ([0000294](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000294)) | Smoluchowski method ([0000057](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057)) | Smoldyn | [Smoldyn](https://biosimulators.org/simulators/smoldyn) | | [Parmar *BMC Syst Biol*](https://doi.org/10.1186/s12918-017-0431-3) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex) | [`.h5`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/reports.h5) | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [PySCeS](https://biosimulators.org/simulators/pysces), [tellurium](https://biosimulators.org/simulators/tellurium), [VCell](https://biosimulators.org/simulators/vcell) | +| [Powers *Pflugers Arch*](https://doi.org/10.1007/s00424-016-1893-7) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex) | | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | VCML | [VCell](https://biosimulators.org/simulators/vcell) | | [Szymanska *J Theor Biol*](https://doi.org/10.1016/j.jtbi.2009.03.021) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex) | [`.h5`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/reports.h5) | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODES ([0000496](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [AMICI](https://biosimulators.org/simulators/amici) | [Tomida *EMBO J*](https://doi.org/10.1093/emboj/cdg381) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex) | [`.h5`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/reports.h5) | [`.json`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/Figure_3c.vg.json) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | LSODA/LSODAR ([0000560](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [COPASI](https://biosimulators.org/simulators/copasi) | | [Saglam toy gene regulatory network](https://github.com/biosimulators/Biosimulators_BioNetGen/blob/dev/tests/fixtures/test.bngl) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/bngl/test-bngl.omex) | [`.h5`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/bngl/test-bngl/reports.h5) | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | BNGL ([format_3972](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972)) | [BioNetGen](https://biosimulators.org/simulators/bionetgen) | | [Varusai *Sci Rep*](https://doi.org/10.1038/s41598-017-18400-z) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex) | [`.h5`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/reports.h5) | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | LSODA/LSODAR ([0000560](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [COPASI](https://biosimulators.org/simulators/copasi) | | [Vilar *PNAS*](https://doi.org/10.1073/pnas.092133899) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex) | | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)), non-spatial discrete ([0000295](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000295)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) and NRM ([0000027](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [VCell](https://biosimulators.org/simulators/vcell) | -| [Wu *Biochem Pharmacol*](https://doi.org/10.1016/j.bcp.2005.11.016) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells.omex) | | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | XPP | [XPP](https://biosimulators.org/simulators/xpp) | +| [Wu *Biochem Pharmacol*](https://doi.org/10.1016/j.bcp.2005.11.016) | [`.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells.omex) | | | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | XPP ODE | [XPP](https://biosimulators.org/simulators/xpp) | diff --git a/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex new file mode 100644 index 0000000..fa7563f Binary files /dev/null and b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex differ diff --git a/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/Figure6.webp b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/Figure6.webp new file mode 100644 index 0000000..e93d322 Binary files /dev/null and b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/Figure6.webp differ diff --git a/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/biomodel_100596964.sedml b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/biomodel_100596964.sedml new file mode 100644 index 0000000..03523dd --- /dev/null +++ b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/biomodel_100596964.sedml @@ -0,0 +1,112 @@ + + + + + + +

Actual Solver Name : 'Combined Stiff Solver (IDA/CVODE)'.

+ + + + + + + + + + + + + + + + + + + + + + + t_tsk_0_0 + + + + + + + + GluR_plasma_membrane_tsk_0_0 + + + + + + + + Leak_plasma_membrane_tsk_0_0 + + + + + + + + ion_muscle_tsk_0_0 + + + + + + + + Sion_Extracellular_tsk_0_0 + + + + + + + + ion_Extracellular_tsk_0_0 + + + + + + + + Sion_muscle_tsk_0_0 + + + + + + +

Plot of all variables and output functions from application 'compartment' ; simulation 'Simulation1' in VCell model

+ + + + + + + + + + + + +

Report of all variables and output functions from application 'compartment' ; simulation 'Simulation1' in VCell model

+ + + + + + + + + + + + + + diff --git a/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/biomodel_100596964.vcml b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/biomodel_100596964.vcml new file mode 100644 index 0000000..57fe0f1 --- /dev/null +++ b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/biomodel_100596964.vcml @@ -0,0 +1,2 @@ + +-0.00116-63.07.290.0-1.00.00.00.0065(gL * (Voltage_plasma_membrane - VL))((I / (carrierValence * _F_)) * unitFactor)1.0(8.388606999999999E15 / 8388607.0)-63.0-0.00116 - (Gs * (Voltage_plasma_membrane - Vs) * K * (exp( - ((t - onset) / t2)) - exp( - ((t - onset) / t1))) * (t > onset))0.01.01.480.0010.009100000.00.0100000.00.0100000.00.0100000.00.00.00.00.00.096480.09.648E-51.0E-96.02E113.1415926535897938314.0300.00.00.041761.01.00.00.0-0.00116-0.001160.07.290.0100000.0100000.01.481000.0(1.0 / 602.0)0.00.00.0065100000.0100000.01000000.01057352.0105735.00.0010.009-63.0-63.0-63.0-1.0(C_plasma_membrane * Size_plasma_membrane)( - (I * Size_plasma_membrane) - LumpedI)(K_GluR_plasma_membrane_total / (Size_plasma_membrane * UnitFactor_uM_um3_molecules_neg_1))(gL_leak * (Voltage_plasma_membrane - VL_leak))ion_Extracellular_init_uMion_muscle_init_uM((I / (carrierValence_leak * _F_)) * unitFactor)(Size_plasma_membrane * UnitFactor_uM_um3_molecules_neg_1 * GluR_plasma_membrane_init_molecules_um_2)(Size_plasma_membrane * UnitFactor_uM_um3_molecules_neg_1 * Leak_plasma_membrane_init_molecules_um_2)(K_Leak_plasma_membrane_total / (Size_plasma_membrane * UnitFactor_uM_um3_molecules_neg_1)) - (Gs * (Voltage_plasma_membrane - Vs) * K * (exp( - ((t - onset) / t2)) - exp( - ((t - onset) / t1))) * (t > onset))Sion_Extracellular_init_uMSion_muscle_init_uM(1.0E9 / 1.0)(1000.0 / 1.0)(1.0 / 602.0)((UnitFactor_mV_pF_s_neg_1_pA_neg_1 / device_plasma_membrane.Capacitance) * (I_plasma_membrane - ( - (I * Size_plasma_membrane) - LumpedI)))Voltage_plasma_membrane_init1 diff --git a/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/expected-results.json b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/expected-results.json new file mode 100644 index 0000000..efafea4 --- /dev/null +++ b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/expected-results.json @@ -0,0 +1,74 @@ +{ + "name": "Regulation of quantal currents determines synaptic strength at neuromuscular synapses in larval Drosophila", + "filename": "Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex", + "taskRequirements": [ + { + "modelFormat": "format_9000", + "modelFormatFeatures": [], + "simulationAlgorithm": "KISAO_0000019" + } + ], + "skippedSimulators": [], + "expectedReports": [ + { + "id": "biomodel_100596964.sedml/report_Simulation1", + "dataSets": [ + { + "id": "__data_set__plot2d_Simulation1time_tsk_0_0", + "label": "time_tsk_0_0" + }, + { + "id": "__data_set__plot2d_Simulation1dataGen_tsk_0_0_GluR_plasma_membrane", + "label": "dataGen_tsk_0_0_GluR_plasma_membrane" + }, + { + "id": "__data_set__plot2d_Simulation1dataGen_tsk_0_0_Leak_plasma_membrane", + "label": "dataGen_tsk_0_0_Leak_plasma_membrane" + }, + { + "id": "__data_set__plot2d_Simulation1dataGen_tsk_0_0_ion_muscle", + "label": "dataGen_tsk_0_0_ion_muscle" + }, + { + "id": "__data_set__plot2d_Simulation1dataGen_tsk_0_0_Sion_Extracellular", + "label": "dataGen_tsk_0_0_Sion_Extracellular" + }, + { + "id": "__data_set__plot2d_Simulation1dataGen_tsk_0_0_ion_Extracellular", + "label": "dataGen_tsk_0_0_ion_Extracellular" + }, + { + "id": "__data_set__plot2d_Simulation1dataGen_tsk_0_0_Sion_muscle", + "label": "dataGen_tsk_0_0_Sion_muscle" + } + ], + "points": [ + 5001 + ], + "values": [ + { + "id": "__data_set__plot2d_Simulation1time_tsk_0_0", + "label": "time_tsk_0_0", + "value": { + "0": 0, + "5000": 0.2 + } + } + ] + } + ], + "expectedPlots": [ + { + "id": "biomodel_100596964.sedml/plot2d_Simulation1" + } + ], + "runtimeFailureAlertType": "exception", + "author": "Andrew S. Powers, Jeffrey Grizzaffi, Richard Ribchester & Gregory A. Lnenicka", + "identifiers": [ + { + "namespace": "url", + "id": "http://identifiers.org/vcell:100596964", + "url": "https://identifiers.org/vcell:100596964" + } + ] +} \ No newline at end of file diff --git a/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/manifest.xml b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/manifest.xml new file mode 100644 index 0000000..36dea4a --- /dev/null +++ b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/manifest.xml @@ -0,0 +1,10 @@ + + + + + + + + + + diff --git a/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/metadata.rdf b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/metadata.rdf new file mode 100644 index 0000000..b04d002 --- /dev/null +++ b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/metadata.rdf @@ -0,0 +1,120 @@ + + + + Regulation of quantal currents determines synaptic strength at neuromuscular synapses in larval Drosophila + The model captures the generation of minEPSPs using a single compartment with membrane reactions describing the currents resulting from the synaptic and resting conductances as in our previous study. The time course of the synaptic conductance (G syn) was simulated using the equation: G syn = K(e −t/τ2 − e −t/τ1)G syn peak; where K is the scaling constant, τ 1 is the rise time constant, τ 2 is the decay time constant, and G syn peak is the peak G syn. G syn peak was calculated from the minEPSCs amplitude using a reversal potential of −1 mV. Values for K, τ 1, and τ 2 were chosen to give the best fit to the minEPSC waveform. Simulations demonstrated that the increase in minEPSC size resulted in a 129% increase in minEPSP amplitude for third-instar larvae; this was mainly due to the increase in minEPSC duration. + synapse + homeostasis + neuromuscular junction + + + + + + Drosophila melanogaster + + + + + + + vcell:100596964 + + + + + + + Daniel M. Gertner, Sunil Desai & Gregory A. Lnenicka. Synaptic excitation is regulated by the postsynaptic dSK channel at the Drosophila larval NMJ. J Neurophysiol 111 (12), 2533-2543 (2014). + + + + + + Andrew S. Powers + Andrew S. Powers + + + + + Jeffrey Grizzaffi + Jeffrey Grizzaffi + + + + + Richard Ribchester + Richard Ribchester + + + + + + + Gregory A. Lnenicka + Gregory A. Lnenicka + + + + + + Dan Vasilescu + Dan Vasilescu + + + + + Michael Blinov + Michael Blinov + + + + + + + Ion Moraru + Ion Moraru + + + + + + + + Jonathan Karr + + Jonathan Karr + + + + + + + Andrew S. Powers, Jeffrey Grizzaffi, Richard Ribchester & Gregory A. Lnenicka. Regulation of quantal currents determines synaptic strength at neuromuscular synapses in larval Drosophila. Pflugers Arch 468 (11-12), 2031-2040 (2016). + + + + + + + 2016-10-25 + + + + + + 2022-02-25 + + + + \ No newline at end of file diff --git a/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/reports.h5 b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/reports.h5 new file mode 100644 index 0000000..98c63f1 Binary files /dev/null and b/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/reports.h5 differ