| Model | BioModel? | >1 Sim? | ODE? | PDE? | SBML Conversion? | Comments |
|---|
| Byung Chang Suh |  |  | | | | Already submitted to the database |
| Mathew Holt | | | | | | |
| Fridlyand | | | | | | Already submitted to the database |
| Alicia E Smith | | | | | | Completed and submitted to the database |
| Anton Burakov | | | | | | |
| Chang Xu | | | | | | Already submitted to the database |
| Fink CC (Two models) | | | | | | |
| Lukas TJ | | | | | | Contains fast reactions |
| Lan Ma | | | | | | |
| Ali Agah | | | | | | Contacted the authors for clarification regarding discrepancy between simulation result and plots in the paper. Yet to hear from the authors |
| Roy P | | | | | | |
| Slepchenko BM, Cyclin aggregation | | | | | | Completed, matches with the simulation on virtual cell. However, doesn't match with that in publication. There is a Math Model that does a reasonable job of replicating the figure in the paper. Need a SBML export of this Math Model. |
| Slepchenko BM, Bioswitches | | | | | | Same as above. Cyclin aggregation and Bioswitches are one and the same model. |
| Pomorski | | | | | | Need clarificaion regarding model accesibility |
| Horowitz LP | | | | | | Electric current not handled by SBML export |
| Mayya | | | | | | Completed the model, Submitted to Biomodels database. |
| Hernjak N | | | | | | Completed, submitted to the Biomodels database. |
| Schneider IC | | | | | | |
| Kalab P | | | | | | Completed, ready for submission. Need some clarification from the authors. |
| JJ Saucerman | | | | | | Completed the model, submitted to the Biomodels database. |
| Moissoqlu K | | | | | | |
| Eungdamrong NJ | | | | | | Completed, submitted the model to the Biomodels database. |
| Fridlyand LE | | | | | | |
| Slepchenko BM 2007 | | | | | | |
| Haugh JM | | | | | | Simulation result matches with that of a figure in the supplement of the paper. |
| Paul A | | | | | | Model not given in the main paper but in the supplementary material, however it is not elaborate. Difficult to make a correspondence between material and the model on VCell. Fig S2 does not match with any of the results on VCell. |
| Coatesworth W | | | | | | Simulation matches with the figures in the paper. |
| Duman JG | | | | | | Simulation result matches with those of plots in Fig 1A but not those in Fig 9. |
| Suh 2006 | | | | | | Simulation result matches with the figure in the paper but electric current not handled by SBML export |
| Shen 2008 | | | | | | Simulation result for small area and large area FRAP and FLIP at tight junction, FLIP intracellular depicted in Fig 6 match with simulation result. However, I did see that the simulation result for ZO1 for intracellular bleach FLIP was a little steeper in VCell simulation. |
| Brown 2008 | | | | | | Simulation result match with the figures in the paper, figure 3 is helpful in figuring out the coordinates of simulation points. |
| Neves2008 | | | | | | Compartmental model submitted to the Biomodels database. Had issues with correspondence of plot in the paper to simulation result. I contacted the author, Dr Neves, she is submitting an errata to the publishers. Simulation result of spatial models works fine. |
'Successful import' implies being able to import into the Virtual Cell and running simulations and comparing the results to results generated for the same models using another tool (in this case,
). The table shows PASS/FAIL for the comparison of simulation results (Copasi-VCell,
| BIOMODEL ID | BioModel name | _PASS / FAIL_ | Relative Error | Exception |
|---|
| BIOMD0000000001 | Edelstein1996_EPSP_AChEvent | | ()()(1.66) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000002 | Edelstein1996_EPSP_AChSpecies | | (7.24E-7)(16.6)(16.6) | |
| BIOMD0000000003 | Goldbeter1991_MinMitOscil | | (1.02E-3)(1.56E-3)(1.74E-3) | |
| BIOMD0000000004 | Goldbeter1991_MinMitOscil_ExplInact | | (1.04E-3)(1.55E-3)(1.74E-3) | |
| BIOMD0000000005 | Tyson1991_CellCycle_6var | | ()()(1.44E-2) | VCELL SBML Import Error: An assignment rule for species YT contains another species in the model, this is not allowed for a non-spatial model in VCell |
| BIOMD0000000006 | Tyson1991_CellCycle_2var | | ()()(1.14E-3) | VCELL Error adding species context; cannot use a reserved symbol ('x','y','z','t') as a Species common name |
| BIOMD0000000007 | Novak1997_CellCycle | | ()()(0.327) | VCELL SBML Import Error: Rate rules are not handled in the Virtual Cell at this time |
| BIOMD0000000008 | Gardner1998_CellCycle_Goldbeter | | (0.114)(8.51E-3)(0.109) | |
| BIOMD0000000009 | Huang1996_MAPK_ultrasens | | (1.49E-2)()() | mathSBML For input string: "(P_KKK)[0.]" |
| BIOMD0000000010 | Kholodenko2000_MAPK_feedback | | (8.05E-2)()() | mathSBML For input string: "(MKKK_P)[0.]" |
| BIOMD0000000011 | Levchenko2000_MAPK_noScaffold | | (9.86E-4)(2.03E-3)(2.12E-3) | |
| BIOMD0000000012 | Elowitz2000_Repressilator | | (0.186)(3.81E-2)(0.187) | |
| BIOMD0000000013 | Poolman2004_CalvinCycle | | ()()() | mathSBML For input string: "(x_CO2)[0.]" VCELL Error adding Feature to vcModel there is more than one top-level feature |
| BIOMD0000000014 | Levchenko2000_MAPK_Scaffold | | (1.62E-4)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000015 | Curto1998_purineMetabol | | (0.128)(3.23E-4)(0.128) | |
| BIOMD0000000016 | Goldbeter1995_CircClock | | ()()(0.209) | VCELL SBML Import Error: An assignment rule for species Pt contains another species in the model, this is not allowed for a non-spatial model in VCell |
| BIOMD0000000017 | Hoefnagel2002_PyruvateBranches | | (0.066)(6.03E-3)(0.072) | |
| BIOMD0000000018 | Morrison1989_FolateCycle | | ()()() | VCELL SBML Import Error: An assignment rule for species FH2b contains another species in the model, this is not allowed for a non-spatial model in VCell COMPARE COPASI/mSBML variable 'CH2FH4' not found in test dataset |
| BIOMD0000000019 | Schoeberl2002_EGF_MAPK | | ()()() | mathSBML For input string: "(Raf_act)[0.]" VCELL SBML Import Error: An assignment rule for species Ras_GTP contains another species in the model, this is not allowed for a non-spatial model in VCell |
| BIOMD0000000020 | hodgkin-huxley squid-axon 1952 | | ()()() | COPASI COPASI model doesn't have metabolites - skipping VCELL SBML Import Error: Rate rules are not handled in the Virtual Cell at this time |
| BIOMD0000000021 | Leloup1999_CircClock | | ()()(0.325) | VCELL null |
| BIOMD0000000022 | Ueda2001_CircClock | | ()()() | mathSBML For input string: "(12.*(species))[0.]"_ VCELL Error adding Feature to vcModel there is more than one top-level feature |
| BIOMD0000000023 | Rohwer2001_Sucrose | | ()()(0.266) | VCELL SBML Import Error: Unable to interpret Kinetic rate for reaction : v11 Cannot interpret non-linear function of compartment size |
| BIOMD0000000026 | Markevich2004_MAPK_orderedElementary | | (0.27)()() | mathSBML For input string: "(M_MAPKK)[0.]" |
| BIOMD0000000027 | Markevich2004_MAPK_orderedMM | | (0.572)(0.572)(1.63E-2) | |
| BIOMD0000000028 | Markevich2004_MAPK_phosphoRandomElementary | | (0.466)()() | mathSBML For input string: "(MpY?_MEK)[0.]" |
| BIOMD0000000029 | Markevich2004_MAPK_phosphoRandomMM | | (0.368)(0.368)(2.38E-3) | |
| BIOMD0000000030 | Markevich2005_MAPK_AllRandomElementary | | (0.494)()() | mathSBML For input string: "(MpY?_MAPKK)[0.]" |
| BIOMD0000000031 | Markevich2004_MAPK_orderedMM2kinases | | (0.396)(0.396)(1.59E-2) | |
| BIOMD0000000032 | Kofahl2004_pheromone | | ()()(0.18) | VCELL null |
| BIOMD0000000033 | Brown2004_NGF_EGF_signaling | | ()()(2.16) | VCELL NativeIDASolver: IDA_TOO_MUCH_WORK: The solver took mxstep internal steps but could not reach tout. The default value for mxstep is MXSTEP_DEFAULT = 5000 |
| BIOMD0000000035 | Vilar2002_Oscillator | | (1.13)(2.68E-2)(1.11) | |
| BIOMD0000000036 | Tyson1999_CircClock | | ()()(1.55) | VCELL Error adding Feature to vcModel there is more than one top-level feature |
| BIOMD0000000037 | Marwan_Genetics_2003 | | (0.185)(2.85E-2)(0.185) | |
| BIOMD0000000038 | Rohwer2000_Phosphotransferase_System | | (2.06E-7)(1.26E-5)(1.27E-5) | |
| BIOMD0000000039 | Marhl2000_CaOscillations | | ()()() | mathSBML For input string: "(Ca_cyt)[0.]" VCELL SBML Import Error: Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time. |
| BIOMD0000000040 | Field1974_Oregonator | | ()()(5.11E-3) | VCELL SBML Import Error: Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time. |
| BIOMD0000000041 | Kongas2001_creatine | | ()()(6.32E-2) | VCELL Error adding Feature to vcModel there is more than one top-level feature |
| BIOMD0000000042 | Nielsen1998_Glycolysis | | (0.099)(1.42E-2)(9.04E-2) | |
| BIOMD0000000043 | Borghans1997_CaOscillation_model1 | | ()()() | mathSBML For input string: "(_Channels*(Fraction_Inactive))[0.]" VCELL null |
| BIOMD0000000044 | Borghans1997_CaOscillation_model2 | | ()()() | mathSBML For input string: "(_IP3*_of*_production*(Agonist_stimulated))[0.]" VCELL null |
| BIOMD0000000045 | Borghans1997_CaOscillation_model3 | | ()()(1.49E-2) | VCELL null |
| BIOMD0000000046 | Olsen2003_peroxidase | | (4.45E-3)(4.88E-3)(6.58E-4) | |
| BIOMD0000000047 | Oxhamre2005_Ca_oscillation | | ()()() | mathSBML For input string: "(Ca_Cyt)[0.]" VCELL SBML Import Error: Rate rules are not handled in the Virtual Cell at this time |
| BIOMD0000000048 | Kholodenko1999_EGFRsignaling | | (0.941)(0.928)(0.054) | |
| BIOMD0000000049 | Sasagawa2005_MAPK | | ()()() | mathSBML For input string: "(L_EGFR)[0.]" VCELL null |
| BIOMD0000000050 | Martins2003_AmadoriDegradation | | (8.14E-3)()() | mathSBML mathSBML output file C:\SBMLRelated\SBML_Testing\release_21August2008_sbmls\Results4.6_IDA_8_21_08\BIOMD0000000050.csv not found |
| BIOMD0000000051 | Chassagnole2002_Carbon_Metabolism | | ()()() | VCELL null COMPARE COPASI/mSBML variable 'cfdp' not found in test dataset |
| BIOMD0000000052 | Brands2002_MonosaccharideCasein | | (1.76E-3)()() | mathSBML For input string: "(Formic_acid)[0.]" |
| BIOMD0000000053 | Ferreira2003_CML_generation2 | | (8.46E-7)(3.62E-4)(3.62E-4) | |
| BIOMD0000000054 | Ataullahkhanov1996_Adenylate | | ()()(0.213) | VCELL new variable (Function(11139111) = 'Expression@f1572492 '((P * J_U1) * sbmlRateFactor_U1)'') conflicts with existing var (Constant(14870151) = 'Expression@2c90b73 '100.0'' |
| BIOMD0000000055 | Locke2005_CircClock | | (3.40E4)(3.40E4)(1.26E-2) | |
| BIOMD0000000056 | Chen2004_CellCycle | | ()()() | mathSBML For input string: "(BCK2)[0.]"_ VCELL SBML Import Error: Algebraic rules are not handled in the Virtual Cell at this time |
| BIOMD0000000057 | Sneyd2002_IP3_Receptor | | (3.05E-2)(2.74E-3)(3.18E-2) | |
| BIOMD0000000058 | Bindschadler2001_coupled_Ca_oscillators | | (0.415)(2.84E-2)(0.403) | |
| BIOMD0000000059 | Fridlyand2003_Calcium_flux | | ()()() | mathSBML For input string: "(Ca_cyt)[0.]" VCELL SBML Import Error: Rate rules are not handled in the Virtual Cell at this time |
| BIOMD0000000060 | Keizer1996_Ryanodine_receptor_adaptation | | (3.53E-2)(3.25E-3)(3.26E-2) | |
| BIOMD0000000061 | Hynne2001 Glycolysis | | ()()() | VCELL null COMPARE COPASI/mSBML variable 'FBP' not found in test dataset |
| BIOMD0000000062 | bhartiya2003 tryptophan operon | | ()()(3.55E-4) | VCELL SBML Import Error: An assignment rule for species Tt contains another species in the model, this is not allowed for a non-spatial model in VCell |
| BIOMD0000000063 | Galazzo1990_pathway_kinetics | | ()()() | VCELL SBML Import Error: Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time. COMPARE COPASI/mSBML variable 'FDP' not found in test dataset |
| BIOMD0000000064 | Teusink2000_Glycolysis | | ()()() | mathSBML For input string: "(SUM_P)[0.]" VCELL SBML Import Error: An assignment rule for species ADP contains another species in the model, this is not allowed for a non-spatial model in VCell |
| BIOMD0000000065 | Yildirim2003_Lac_Operon | | (1.01E-2)()() | mathSBML For input string: "(L_e)[0.]" |
| BIOMD0000000066 | Chassagnole2001_Threonine Synthesis | | (3.15E-3)(1.55E-3)(3.02E-3) | |
| BIOMD0000000067 | Fung2005_Metabolic_Oscillator | | (0.352)()() | mathSBML For input string: "(HOAc:Blank[2.718281828459045])[0.]" |
| BIOMD0000000068 | Curien2003_MetThr_synthesis | | (2.70E-3)(2.78E-3)(6.62E-4) | |
| BIOMD0000000069 | Fuss2006_MitoticActivation | | (5.82E-4)()() | mathSBML For input string: "(_CSK*(Cbp_P))[0.]" |
| BIOMD0000000070 | Holzhutter2004_Erythrocyte_Metabolism | | ()()() | VCELL NativeIDASolver: IDA_CONV_FAIL: Convergence test failures occurred too many times (= MXNCF = 10) during one internal step. COMPARE COPASI/mSBML variable 'Fru16P2' not found in test dataset |
| BIOMD0000000071 | Bakker2001_Glycolysis | | ()()() | VCELL SBML Import Error: Cannot resolve location of reaction : vGlcTr COMPARE COPASI/mSBML variable 'Fru16BP' not found in test dataset |
| BIOMD0000000072 | Yi2003_GproteinCycle | | ()()(0.406) | VCELL NativeIDASolver: IDA_CONV_FAIL: Convergence test failures occurred too many times (= MXNCF = 10) during one internal step. |
| BIOMD0000000073 | Leloup2003_CircClock_DD | | (0.402)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000074 | Leloup2003_CircClock_DD_REV-ERBalpha | | (6.76E-2)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000075 | Xu2003_Phosphoinositide_turnover | | ()()() | mathSBML For input string: "(_PM*(PIP2_PHGFP))[0.]" VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000076 | Cronwright2002_Glycerol_Synthesis | | (8.08E-3)(1.61E-3)(6.70E-3) | |
| BIOMD0000000077 | Blum2000_LHsecretion_1 | | ()()() | mathSBML For input string: "0.[0.]" VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000078 | Leloup2003_CircClock_LD | | (4.62E4)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000079 | Goldbeter2006_weightCycling | | (0.42)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000080 | Thomsen1989_AdenylateCyclase | | (2.50E-9)()() | mathSBML For input string: "(DRG_GDP)[0.]" |
| BIOMD0000000081 | Suh2004_KCNQ_Regulation | | ()()() | mathSBML For input string: "(GTPgS?_C)[0.]" VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000082 | Thomsen1988_AdenylateCyclase_Inhibition | | (1.37E-8)()() | mathSBML For input string: "(DRG_GDP)[0.]" |
| BIOMD0000000083 | Leloup2003_CircClock_LD_REV-ERBalpha | | (1.86E4)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000084 | Hornberg2005_ERKcascade | | (14.5)(14.6)(0.065) | |
| BIOMD0000000085 | Maurya2005_GTPaseCycle_reducedOrder | | (1.12E-7)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000086 | Bornheimer2004_GTPaseCycle | | (2.69E-8)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000087 | Proctor2006_telomere | | ()()(5.00E4) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000088 | Maeda2006_MyosinPhosphorylation | | ()()(9.59E-3) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000089 | Locke2006_CircClock_LL | | (4.04E-2)(3.65E-2)(8.74E-3) | |
| BIOMD0000000090 | Wolf2001 respiratory oscillations | | ()()() | mathSBML For input string: "(sul_ex)[0.]" VCELL SBML Import Error: An assignment rule for species A2c contains another species in the model, this is not allowed for a non-spatial model in VCell |
| BIOMD0000000091 | Hsp90model_basis510 | | ()()(0.224) | VCELL NativeIDASolver: IDA_TOO_MUCH_WORK: The solver took mxstep internal steps but could not reach tout. The default value for mxstep is MXSTEP_DEFAULT = 5000 |
| BIOMD0000000092 | Fuentes2005_ZymogenActivation | | ()()(2.18E-6) | VCELL Error adding species context; cannot use a reserved symbol ('x','y','z','t') as a Species common name |
| BIOMD0000000093 | Yamada2003_JAK_STAT_pathway | | ()()() | mathSBML For input string: "(IFNRJ2_star)[0.]" VCELL null |
| BIOMD0000000094 | Yamada2003_JAK_STAT_SOCS1_knockout | | ()()() | mathSBML For input string: "(IFNRJ2_star)[0.]" VCELL null |
| BIOMD0000000095 | Zeilinger2006_PRR7-PRR9-Y | | ()()(0.172) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000096 | Zeilinger2006_PRR7-PRR9light-Y | | ()()(3.34E-2) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000097 | Zeilinger2006_PRR7-PRR9light-Yprime | | ()()(3.42E4) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000098 | Goldbeter1990_Ca_Oscillations | | ()()(49.9) | VCELL Error adding Feature to vcModel there is more than one top-level feature |
| BIOMD0000000099 | Laub1998_SpontaneousOscillations | | ()()() | mathSBML For input string: "0.[0.]" VCELL null |
| BIOMD0000000100 | Rozi2003_GlycogenPhosphorylase_Activation | | ()()(0.652) | VCELL null |
| BIOMD0000000101 | Vilar2006_TGFbeta | | ()()() | mathSBML For input string: "(lRIRII_endo)[0.]" VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000102 | Legewie2006_apoptosis_WT | | (1.16)()() | mathSBML For input string: "(C3_star)[0.]" |
| BIOMD0000000103 | Legewie2006_apoptosis_NC | | (1.26)()() | mathSBML For input string: "(C3_star)[0.]" |
| BIOMD0000000104 | Klipp2002_MetabolicOptimization_linearPathway(n=2) | | ()()() | mathSBML For input string: "0.[0.]" VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000105 | Proctor2007_ubiquitine | | (4.95)()() | mathSBML For input string: "(E1_Ub)[0.]" |
| BIOMD0000000106 | Yang2007_ArachidonicAcid | | (0.184)(0.013)(0.177) | |
| BIOMD0000000107 | Novak1993_M_phase_control | | ()()() | mathSBML For input string: "(dimer_p)[0.]" VCELL SBML Import Error: An assignment rule for species cdc2 contains another species in the model, this is not allowed for a non-spatial model in VCell |
| BIOMD0000000108 | Kowald2006_SOD | | (1.15E-7)()() | mathSBML For input string: "(species)[0.]"_ |
| BIOMD0000000109 | Haberichter2007_cellcycle | | ()()(0.741) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000110 | Qu2003_CellCycle | | ()()(2.86) | VCELL SBML Import Error: An assignment rule for species c contains another species in the model, this is not allowed for a non-spatial model in VCell |
| BIOMD0000000111 | Novak2001_FissionYeast_CellCycle | | ()()(0.169) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000112 | Clarke2006_Smad_signalling | | (9.21E3)()() | mathSBML For input string: "(_cyt*(R_smad))[0.]" |
| BIOMD0000000113 | Dupont1992_Ca_dpt_protein_phospho | | ()()() | mathSBML For input string: "(W_star)[0.]" VCELL null |
| BIOMD0000000114 | Somogyi1990_CaOscillations | | ()()(6.15E-2) | VCELL Error adding Feature to vcModel there is more than one top-level feature |
| BIOMD0000000115 | Somogyi1990_CaOscillations_SingleCaSpike | | ()()(8.53) | VCELL Error adding Feature to vcModel there is more than one top-level feature |
| BIOMD0000000116 | McClean2007?_CrossTalk | | (2.92E-2)()() | mathSBML For input string: "0.[0.]" |
| BIOMD0000000117 | Dupont1991_CaOscillation | | ()()(4.62E4) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000118 | Golomb2006_SomaticBursting | | ()()() | COPASI COPASI model doesn't have metabolites - skipping VCELL SBML Import Error: Rate rules are not handled in the Virtual Cell at this time |
| BIOMD0000000119 | Golomb2006_SomaticBursting_nonzero[Ca] | | ()()() | COPASI null VCELL SBML Import Error: Rate rules are not handled in the Virtual Cell at this time |
| BIOMD0000000120 | Chan2004_TCell_receptor_activation | | ()()() | mathSBML For input string: "(lck_inactive)[0.]" VCELL SBML Import Error: VCell doesn't support Events at this time |
| BIOMD0000000121 | Clancy2001_Kchannel | | ()()(2.96E-3) | VCELL SBML Import Error: VCell doesn't support Events at this time |
| |
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