CellDesigner Simulation
Curated BioModel Database (checked 2008/07/25)
CellDesigner 4.0.0(Released 2008/08/04)
- BioModels (release_25Sep2007_sbmls.tar.gz/curated/).
- All tests run from 0 to 10 seconds with output time step 0.01 seconds.
Legends
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OK. |  |
NG. |  |
including "events" in the KineticLaws. |
- *1 : may not be able to run simulation if the global parameter constant changed to "true".
- *2 : Error message "Couldn't create log plot: Data contains negative value or zero." displayed when you convert the display to [Log].
- *3 : When you run simulation with SOSlib, SOSlib and CellDesigner hang.
| BIOMODEL ID | BioModel name | EVENTS | SOSlib | COPASI | Exception | Comments | ||
|---|---|---|---|---|---|---|---|---|
| RAW | LOG | RAW | LOG | |||||
| BIOMD0000000001 | Edelstein1996_EPSP_AChEvent |
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Simulation Failed: The SBML_odeSolver implementation of events is not fully SBML conformant. | |
| BIOMD0000000002 | Edelstein1996_EPSP_AChSpecies |
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*2 | |
| BIOMD0000000003 | Goldbeter1991_MinMitOscil |
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*1 | |
| BIOMD0000000004 | Goldbeter1991_MinMitOscil_ExplInact |
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*1 | |
| BIOMD0000000005 | Tyson1991_CellCycle_6var |
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*2 | |
| BIOMD0000000006 | Tyson1991_CellCycle_2var |
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*2 | |
| BIOMD0000000007 | Novak1997_CellCycle |
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initial Quantity value (initialAmount or initialConcertration) is undefined in the following Species: | *1 |
| BIOMD0000000008 | Gardner1998_CellCycle_Goldbeter |
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*1 *2 | |
| BIOMD0000000009 | Huang1996_MAPK_ultrasens |
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*2 | |
| BIOMD0000000010 | Kholodenko2000_MAPK_feedback |
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| BIOMD0000000011 | Levchenko2000_MAPK_noScaffold |
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*2 | |
| BIOMD0000000012 | Elowitz2000_Repressilator |
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*2 | |
| BIOMD0000000013 | Poolman2004_CalvinCycle |
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| BIOMD0000000014 | Levchenko2000_MAPK_Scaffold |
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*2 | |
| BIOMD0000000015 | Curto1998_purineMetabol |
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| BIOMD0000000016 | Goldbeter1995_CircClock |
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| BIOMD0000000017 | Hoefnagel2002_PyruvateBranches |
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*2 | |
| BIOMD0000000018 | Morrison1989_FolateCycle |
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*2 | |
| BIOMD0000000020 | hodgkin-huxley squid-axon 1952 |
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- | - | - | - | There is no Species. | |
| BIOMD0000000021 | Leloup1999_CircClock |
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*1 *2 | |
| BIOMD0000000022 | Ueda2001_CircClock |
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*2 | |
| BIOMD0000000023 | Rohwer2001_Sucrose |
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*2 | |
| BIOMD0000000024 | Scheper1999_CircClock |
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*3 | |
| BIOMD0000000025 | Smolen2002_CircClock |
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*3 | |
| BIOMD0000000026 | Markevich2004_MAPK_orderedElementary |
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| BIOMD0000000027 | Markevich2004_MAPK_orderedMM |
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*2 | |
| BIOMD0000000028 | Markevich2004_MAPK_phosphoRandomElementary |
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| BIOMD0000000029 | Markevich2004_MAPK_phosphoRandomMM |
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| BIOMD0000000030 | Markevich2005_MAPK_AllRandomElementary |
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*2 | |
| BIOMD0000000031 | Markevich2004_MAPK_orderedMM2kinases |
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| BIOMD0000000032 | Kofahl2004_pheromone |
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*2 | |
| BIOMD0000000033 | Brown2004_NGF_EGF_signaling |
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*2 | |
| BIOMD0000000034 | Smolen2004_CircClock |
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*3 | *1 |
| BIOMD0000000035 | Vilar2002_Oscillator |
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| BIOMD0000000036 | Tyson1999_CircClock |
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*2 | |
| BIOMD0000000037 | Marwan_Genetics_2003 |
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*2 | |
| BIOMD0000000038 | Rohwer2000_Phosphotransferase_System |
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| BIOMD0000000039 | Marhl2000_CaOscillations |
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| BIOMD0000000040 | Field1974_Oregonator |
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Simulation failed: Integration not successful. | |
| BIOMD0000000041 | Kongas2001_creatine |
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*2 | |
| BIOMD0000000042 | Nielsen1998_Glycolysis |
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*2 | |
| BIOMD0000000043 | Borghans1997_CaOscillation_model1 |
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| BIOMD0000000044 | Borghans1997_CaOscillation_model2 |
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| BIOMD0000000045 | Borghans1997_CaOscillation_model3 |
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*2 | |
| BIOMD0000000046 | Olsen2003_peroxidase |
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*2 | |
| BIOMD0000000047 | Oxhamre2005_Ca_oscillation |
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*1 *2 | |
| BIOMD0000000048 | Kholodenko1999_EGFRsignaling |
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*2 | |
| BIOMD0000000049 | Sasagawa2005_MAPK |
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| BIOMD0000000050 | Martins2003_AmadoriDegradation |
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| BIOMD0000000051 | Chassagnole2002_Carbon_Metabolism |
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*3 | *1 |
| BIOMD0000000052 | Brands2002_MonosaccharideCasein |
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*2 | |
| BIOMD0000000053 | Ferreira2003_CML_generation2 |
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*2 | |
| BIOMD0000000054 | Ataullahkhanov1996_Adenylate |
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Error: no message. | |
| BIOMD0000000055 | Locke2005_CircClock |
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Simulation Control Panel cannot be launched. There are following errors. | |
| BIOMD0000000056 | Chen2004_CellCycle |
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initial Quantity value (initialAmount or initialConcertration) is undefined in the following Species: | *1 |
| BIOMD0000000057 | Sneyd2002_IP3_Receptor |
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*1 *2 | |
| BIOMD0000000058 | Bindschadler2001_coupled_Ca_oscillators |
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*1 | |
| BIOMD0000000059 | Fridlyand2003_Calcium_flux |
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*1 | |
| BIOMD0000000060 | Keizer1996_Ryanodine_receptor_adaptation |
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| BIOMD0000000061 | Hynne2001 Glycolysis |
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| BIOMD0000000062 | bhartiya2003 tryptophan operon |
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| BIOMD0000000063 | Galazzo1990_pathway_kinetics |
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| BIOMD0000000064 | Teusink2000_Glycolysis |
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initial Quantity value (initialAmount or initialConcertration) is undefined in the following Species: | *1 |
| BIOMD0000000065 | Yildirim2003_Lac_Operon |
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*2 | |
| BIOMD0000000066 | Chassagnole2001_Threonine Synthesis |
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| BIOMD0000000067 | Fung2005_Metabolic_Oscillator |
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| BIOMD0000000068 | Curien2003_MetThr_synthesis |
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| BIOMD0000000069 | Fuss2006_MitoticActivation |
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*1 *2 | |
| BIOMD0000000070 | Holzhutter2004_Erythrocyte_Metabolism |
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*2 | |
| BIOMD0000000071 | Bakker2001_Glycolysis |
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| BIOMD0000000072 | Yi2003_GproteinCycle |
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| BIOMD0000000073 | Leloup2003_CircClock_DD |
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| BIOMD0000000074 | Leloup2003_CircClock_DD_REV-ERBalpha |
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| BIOMD0000000075 | Xu2003_Phosphoinositide_turnover |
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*3 | *1 |
| BIOMD0000000076 | Cronwright2002_Glycerol_Synthesis |
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| BIOMD0000000077 | Blum2000_LHsecretion_1 |
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| BIOMD0000000078 | Leloup2003_CircClock_LD |
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*3 | *1 |
| BIOMD0000000079 | Goldbeter2006_weightCycling |
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| BIOMD0000000080 | Thomsen1989_AdenylateCyclase |
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| BIOMD0000000081 | Suh2004_KCNQ_Regulation |
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*3 | *1 |
| BIOMD0000000082 | Thomsen1988_AdenylateCyclase_Inhibition |
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| BIOMD0000000083 | Leloup2003_CircClock_LD_REV-ERBalpha |
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*3 | *1 |
| BIOMD0000000084 | Hornberg2005_ERKcascade |
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| BIOMD0000000085 | Maurya2005_GTPaseCycle_reducedOrder |
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*1 *2 | |
| BIOMD0000000086 | Bornheimer2004_GTPaseCycle |
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*1 *2 | |
| BIOMD0000000087 | Proctor2006_telomere |
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| BIOMD0000000088 | Maeda2006_MyosinPhosphorylation |
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| BIOMD0000000089 | Locke2006_CircClock_LL |
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| BIOMD0000000090 | Wolf2001 respiratory oscillations |
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| BIOMD0000000091 | Hsp90model_basis510 |
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| BIOMD0000000092 | Fuentes2005_ZymogenActivation |
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| BIOMD0000000093 | Yamada2003_JAK_STAT_pathway |
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| BIOMD0000000094 | Yamada2003_JAK_STAT_SOCS1_knockout |
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| BIOMD0000000095 | Zeilinger2006_PRR7-PRR9-Y |
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| BIOMD0000000096 | Zeilinger2006_PRR7-PRR9light-Y |
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Simulation Failed: The SBML_odeSolver implementation of events is not fully SBML conformant. | |
| BIOMD0000000097 | Zeilinger2006_PRR7-PRR9light-Yprime |
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Simulation Failed: The SBML_odeSolver implementation of events is not fully SBML conformant. | |
| BIOMD0000000098 | Goldbeter1990_Ca_Oscillations |
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| BIOMD0000000099 | Laub1998_SpontaneousOscillations |
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| BIOMD0000000100 | Rozi2003_GlycogenPhosphorylase_Activation |
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*2 | |
| BIOMD0000000101 | Vilar2006_TGFbeta |
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| BIOMD0000000102 | Legewie2006_apoptosis_WT |
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| BIOMD0000000103 | Legewie2006_apoptosis_NC |
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| BIOMD0000000104 | Klipp2002_MetabolicOptimization_linearPathway(n=2) |
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Simulation Failed: The SBML_odeSolver implementation of events is not fully SBML conformant. | |
| BIOMD0000000105 | Proctor2007_ubiquitine |
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*2 | |
| BIOMD0000000106 | Yang2007_ArachidonicAcid |
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*2 | |
| BIOMD0000000107 | Novak1993_M_phase_control |
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*1 *2 | |
| BIOMD0000000108 | Kowald2006_SOD |
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*1 *2 | |
| BIOMD0000000109 | Haberichter2007_cellcycle |
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initial Quantity value (initialAmount or initialConcertration) is undefined in the following Species: | |
| BIOMD0000000110 | Qu2003_CellCycle |
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*2 | |
| BIOMD0000000111 | Novak2001_FissionYeast_CellCycle |
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Simulation Failed: The SBML_odeSolver implementation of events is not fully SBML conformant. | *1 |
| BIOMD0000000112 | Clarke2006_Smad_signalling |
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*1 *2 | |
| BIOMD0000000113 | Dupont1992_Ca_dpt_protein_phospho |
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initial Quantity value (initialAmount or initialConcertration) is undefined in the following Species: | *1 |
| BIOMD0000000114 | Somogyi1990_CaOscillations |
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*1 | |
| BIOMD0000000115 | Somogyi1990_CaOscillations_SingleCaSpike |
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*1 | |
| BIOMD0000000116 | McClean2007?_CrossTalk |
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| BIOMD0000000117 | Dupont1991_CaOscillation |
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*1 | |
| BIOMD0000000118 | Golomb2006_SomaticBursting |
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- | - | - | - | There is no Species. | |
| BIOMD0000000119 | Golomb2006_SomaticBursting_nonzero[Ca] |
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*1 | |
| BIOMD0000000120 | Chan2004_TCell_receptor_activation |
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Simulation Failed: The SBML_odeSolver implementation of events is not fully SBML conformant. | |
| BIOMD0000000121 | Clancy2001_Kchannel |
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Simulation failed. | *1 |
| BIOMD0000000122 | Fisher2006_Ca_Oscillation_dpdnt_NFAT_dynamics |
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| BIOMD0000000123 | Fisher2006_NFAT_Activation |
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| BIOMD0000000124 | Wu2006_K+Channel |
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*1 | |
| BIOMD0000000125 | Komarova2005_TheoreticalFramework_BasicArchitecture |
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*2 | |
| BIOMD0000000126 | Clancy2002_CardiacSodiumChannel_WT |
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Simulation failed. | *1 |
| BIOMD0000000127 | Izhikevich2003_SpikingNeuron |
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- | - | - | - | There is no Species. | |
| BIOMD0000000128 | Bertram2006_Endothelin |
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*1 | |
| BIOMD0000000129 | Izhikevich2004_SpikingNeurons_inhibitionInducedSpiking |
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- | - | - | - | There is no Species. | |