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Warning under construction...

VCDB Curation

Putting public models from VCDB into BMDB...

List of public VC models to be curated/submitted to BMDB

Model BioModel? >1 Sim? ODE? PDE? SBML Conversion? Comments
Byung Chang Suh DONE No DONE No   Already submitted to the database
Mathew Holt       DONE    
Fridlyand DONE No DONE No   Already submitted to the database
Alicia E Smith DONE   DONE     Completed and submitted to the database
Anton Burakov No          
Chang Xu DONE No DONE     Already submitted to the database
Fink CC (Two models) No          
Lukas TJ DONE         Contains fast reactions
Lan Ma DONE     DONE    
Ali Agah DONE   DONE   DONE Contacted the authors for clarification regarding discrepancy between simulation result and plots in the paper. Yet to hear from the authors
Roy P DONE     DONE    
Slepchenko BM, Cyclin aggregation DONE   DONE   DONE 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 DONE   DONE   DONE Same as above. Cyclin aggregation and Bioswitches are one and the same model.
Pomorski           Need clarificaion regarding model accesibility
Horowitz LP DONE       No Electric current not handled by SBML export
Mayya DONE   DONE No DONE Completed the model, Submitted to Biomodels database.
Hernjak N DONE   DONE No DONE Completed, submitted to the Biomodels database.
Schneider IC DONE     DONE    
Kalab P DONE DONE DONE     Completed, ready for submission. Need some clarification from the authors.
JJ Saucerman DONE   DONE No DONE Completed the model, submitted to the Biomodels database.
Moissoqlu K No          
Eungdamrong NJ DONE         Completed, submitted the model to the Biomodels database.
Fridlyand LE No          
Slepchenko BM 2007 No          
Haugh JM DONE     DONE   Simulation result matches with that of a figure in the supplement of the paper.
Paul A DONE     DONE   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 DONE     DONE   Simulation matches with the figures in the paper.
Duman JG DONE     DONE   Simulation result matches with those of plots in Fig 1A but not those in Fig 9.
Suh 2006 DONE       No Simulation result matches with the figure in the paper but electric current not handled by SBML export
Shen 2008 DONE DONE   DONE No 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 DONE DONE   DONE No Simulation result match with the figures in the paper, figure 3 is helpful in figuring out the coordinates of simulation points.
Neves2008 DONE DONE DONE DONE DONE 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.

VCML Support

Making BMDB create VCell format...

Tools

VCML/SBML exporter/importer...

Validation testing

List of Biomodels.net models that were tried to be imported into the VCell

'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, COPASI & MathSBML). The table shows PASS/FAIL for the comparison of simulation results (Copasi-VCell, MathSBML-VCell, Copasi-MathBML); and reasons for failing, if any.

Curated BioModel Database (03/27/2009)

  • VCell 4.6 Beta, Anu's eclipse workspace (updated to Subversion 4475)
  • Reference solutions from CopasiSE.exe (Version 4.4 Build 26) (with help from Stefan Hoops, Sven Sahle and Frank Bergman).
  • Reference solutions from MathSBML (via JLink; Version 2.9; using Mathematica 7.0).
  • BioModels (release_3Dec2008_sbmls/curated/).
  • All tests run from 0 to 10 seconds with output time step 0.01 seconds.
  • Relative Error computed using "new" algorithm with abs/rel tolerances both 1e-5 and pass at < 1.0.

BIOMODEL ID BioModel name _PASS / FAIL_ Relative Error Exception
BIOMD0000000001 Edelstein1996_EPSP_AChEvent No No No ()()(1.66) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000002 Edelstein1996_EPSP_AChSpecies DONE No No (7.28E-7)(16.6)(16.6)  
BIOMD0000000003 Goldbeter1991_MinMitOscil DONE DONE DONE (1.01E-3)(1.56E-3)(1.74E-3)  
BIOMD0000000004 Goldbeter1991_MinMitOscil_ExplInact DONE DONE DONE (1.01E-3)(1.56E-3)(1.74E-3)  
BIOMD0000000005 Tyson1991_CellCycle_6var No No DONE ()()(1.44E-2) VCELL_RT 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 No No DONE ()()(1.14E-3) VCELL_RT Error adding species context; cannot use a reserved symbol ('x','y','z','t') as a Species common name
BIOMD0000000007 Novak1997_CellCycle No No DONE ()()(0.327) VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000008 Gardner1998_CellCycle_Goldbeter DONE DONE DONE (0.114)(8.53E-3)(0.109)  
BIOMD0000000009 Huang1996_MAPK_ultrasens DONE No No (5.18E-5)()() mathSBML For input string: "(P_KKK)[0.]"
BIOMD0000000010 Kholodenko2000_MAPK_feedback DONE No No (7.95E-2)()() mathSBML For input string: "(MKKK_P)[0.]"
BIOMD0000000011 Levchenko2000_MAPK_noScaffold DONE DONE DONE (9.86E-4)(2.04E-3)(2.12E-3)  
BIOMD0000000012 Elowitz2000_Repressilator DONE DONE DONE (0.185)(3.82E-2)(0.187)  
BIOMD0000000013 Poolman2004_CalvinCycle No No No ()()() mathSBML For input string: "(x_CO2)[0.]" VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000014 Levchenko2000_MAPK_Scaffold DONE No No (1.61E-4)()() mathSBML For input string: "0.[0.]"
BIOMD0000000015 Curto1998_purineMetabol No No DONE ()()(0.128) VCELL_RT cannot use a reserved symbol ('x','y','z','t') as a Reaction name
BIOMD0000000016 Goldbeter1995_CircClock No No DONE ()()(0.209) VCELL_RT 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 DONE DONE DONE (6.61E-2)(5.96E-3)(0.072)  
BIOMD0000000018 Morrison1989_FolateCycle No No No ()()() VCELL_RT 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 No No No ()()() mathSBML For input string: "(Raf_act)[0.]" VCELL_RT 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 No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000021 Leloup1999_CircClock DONE DONE DONE (0.34)(3.32E-2)(0.325)  
BIOMD0000000022 Ueda2001_CircClock No No No ()()() mathSBML For input string: "(12.*(species))[0.]"_ VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000023 Rohwer2001_Sucrose No No DONE ()()(0.266) VCELL_RT SBML Import Error: Unable to interpret Kinetic rate for reaction : v11 Cannot interpret non-linear function of compartment size
BIOMD0000000024 Scheper1999_CircClock No No No ()()() VCELL_RT SBML Import Error: cannot translate csymbol-delay from MathML
BIOMD0000000025 Smolen2002_CircClock No No No ()()() VCELL_RT SBML Import Error: cannot translate csymbol-delay from MathML
BIOMD0000000026 Markevich2004_MAPK_orderedElementary DONE No No (0.198)()() mathSBML For input string: "(M_MAPKK)[0.]"
BIOMD0000000027 Markevich2004_MAPK_orderedMM DONE DONE DONE (1.73E-3)(1.65E-2)(1.63E-2)  
BIOMD0000000028 Markevich2004_MAPK_phosphoRandomElementary DONE No No (0.112)()() mathSBML For input string: "(MpY_MEK)[0.]"
BIOMD0000000029 Markevich2004_MAPK_phosphoRandomMM DONE DONE DONE (3.72E-4)(2.41E-3)(2.39E-3)  
BIOMD0000000030 Markevich2005_MAPK_AllRandomElementary DONE No No (6.27E-2)()() mathSBML For input string: "(MpY_MAPKK)[0.]"
BIOMD0000000031 Markevich2004_MAPK_orderedMM2kinases DONE DONE DONE (7.81E-4)(1.59E-2)(1.59E-2)  
BIOMD0000000032 Kofahl2004_pheromone DONE DONE DONE (0.171)(0.112)(0.176)  
BIOMD0000000033 Brown2004_NGF_EGF_signaling DONE No No (1.96E4)(1.96E4)(2.17)  
BIOMD0000000034 Smolen2004_CircClock No No No ()()() VCELL_RT SBML Import Error: cannot translate csymbol-delay from MathML
BIOMD0000000035 Vilar2002_Oscillator No DONE No (1.13)(3.53E-2)(1.1)  
BIOMD0000000036 Tyson1999_CircClock No No No ()()(1.55) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000037 Marwan_Genetics_2003 DONE DONE DONE (0.185)(2.85E-2)(0.185)  
BIOMD0000000038 Rohwer2000_Phosphotransferase_System DONE DONE DONE (2.08E-7)(6.58E-6)(6.68E-6)  
BIOMD0000000039 Marhl2000_CaOscillations No No No ()()() mathSBML For input string: "(Ca_cyt)[0.]" VCELL_RT SBML Import Error: Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.
BIOMD0000000040 Field1974_Oregonator No No DONE ()()(5.11E-3) VCELL_RT SBML Import Error: Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.
BIOMD0000000041 Kongas2001_creatine No No DONE ()()(0.065) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000042 Nielsen1998_Glycolysis DONE DONE DONE (9.96E-2)(1.47E-2)(9.04E-2)  
BIOMD0000000043 Borghans1997_CaOscillation_model1 DONE No No (4.65E2)()() mathSBML For input string: "(_Channels*(Fraction_Inactive))[0.]"
BIOMD0000000044 Borghans1997_CaOscillation_model2 DONE No No (3.14E2)()() mathSBML For input string: "(_IP3*_of*_production*(Agonist_stimulated))[0.]"
BIOMD0000000045 Borghans1997_CaOscillation_model3 DONE DONE DONE (1.77E-2)(1.23E-2)(1.49E-2)  
BIOMD0000000046 Olsen2003_peroxidase DONE DONE DONE (2.07E-5)(6.58E-4)(6.58E-4)  
BIOMD0000000047 Oxhamre2005_Ca_oscillation No No No ()()() mathSBML For input string: "(Ca_Cyt)[0.]" VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000048 Kholodenko1999_EGFRsignaling DONE DONE DONE (9.59E-2)(0.109)(0.054)  
BIOMD0000000049 Sasagawa2005_MAPK DONE No No (1.72E-2)()() mathSBML For input string: "(L_EGFR)[0.]"
BIOMD0000000050 Martins2003_AmadoriDegradation DONE No No (8.14E-3)()() mathSBML mathSBML output file C:\SBMLRelated\SBML_Testing\release_03December2008_sbmls\Rountrip_4.6_CVODE_3_24_09\BIOMD0000000050.csv not found
BIOMD0000000051 Chassagnole2002_Carbon_Metabolism No DONE No ()(3.41E-3)() COMPARE VC/COPASI variable 'cfdp' not found in test dataset COMPARE COPASI/mSBML variable 'cfdp' not found in test dataset
BIOMD0000000052 Brands2002_MonosaccharideCasein DONE No No (1.76E-3)()() mathSBML For input string: "(Formic_acid)[0.]"
BIOMD0000000053 Ferreira2003_CML_generation2 DONE DONE DONE (8.48E-7)(3.62E-4)(3.62E-4)  
BIOMD0000000054 Ataullahkhanov1996_Adenylate No No DONE (8.10E3)(8.10E3)(0.213)  
BIOMD0000000055 Locke2005_CircClock No No DONE (3.40E4)(3.40E4)(1.26E-2)  
BIOMD0000000056 Chen2004_CellCycle No No No ()()(9.73E4) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000057 Sneyd2002_IP3_Receptor DONE DONE DONE (3.05E-2)(2.87E-3)(3.27E-2)  
BIOMD0000000058 Bindschadler2001_coupled_Ca_oscillators No No DONE (9.57E4)(9.57E4)(0.403)  
BIOMD0000000059 Fridlyand2003_Calcium_flux No No No ()()() mathSBML For input string: "(Ca_cyt)[0.]" VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000060 Keizer1996_Ryanodine_receptor_adaptation No No DONE ()()(3.26E-2) VCELL_RT Error adding species context; Unable to scale the species unit from: cbit.vcell.units.VCUnitDefinition@16ac : symbol=[litre-1] -> uM
BIOMD0000000061 Hynne2001 Glycolysis No DONE No ()(0.135)() COMPARE VC/COPASI variable 'FBP' not found in test dataset COMPARE COPASI/mSBML variable 'FBP' not found in test dataset
BIOMD0000000062 bhartiya2003 tryptophan operon No No DONE ()()(3.55E-4) VCELL_RT 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 No No No ()()() VCELL_RT 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 No No No ()()() mathSBML For input string: "(SUM_P)[0.]" VCELL_RT 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 DONE No No (1.02E-2)()() mathSBML For input string: "(L_e)[0.]"
BIOMD0000000066 Chassagnole2001_Threonine Synthesis DONE DONE DONE (3.15E-3)(1.55E-3)(3.02E-3)  
BIOMD0000000067 Fung2005_Metabolic_Oscillator DONE No No (0.352)()() mathSBML For input string: "(HOAc:Blank[2.718281828459045])[0.]"
BIOMD0000000068 Curien2003_MetThr_synthesis DONE DONE DONE (2.40E-4)(6.62E-4)(6.61E-4)  
BIOMD0000000069 Fuss2006_MitoticActivation DONE No No (5.74E-4)()() mathSBML For input string: "(_CSK*(Cbp_P))[0.]"
BIOMD0000000070 Holzhutter2004_Erythrocyte_Metabolism No DONE No ()(3.14E-3)() COMPARE VC/COPASI variable 'Fru16P2' not found in test dataset COMPARE COPASI/mSBML variable 'Fru16P2' not found in test dataset
BIOMD0000000071 Bakker2001_Glycolysis No No No ()()() VCELL_RT SBML Import Error: An assignment rule for species ATPg contains another species in the model, this is not allowed for a non-spatial model in VCell COMPARE COPASI/mSBML variable 'Fru16BP' not found in test dataset
BIOMD0000000072 Yi2003_GproteinCycle No No DONE ()()(0.406) VCELL_RT NativeCVOdeSolver: CV_TOO_MUCH_WORK: took mxstep internal steps but could not reach tout
BIOMD0000000073 Leloup2003_CircClock_DD DONE No No (0.374)()() mathSBML For input string: "0.[0.]"
BIOMD0000000074 Leloup2003_CircClock_DD_REV-ERBalpha DONE No No (4.63E-2)()() mathSBML For input string: "0.[0.]"
BIOMD0000000075 Xu2003_Phosphoinositide_turnover DONE No No (0.939)()() mathSBML For input string: "(_PM*(PIP2_PHGFP))[0.]"
BIOMD0000000076 Cronwright2002_Glycerol_Synthesis DONE DONE DONE (8.06E-3)(1.56E-3)(6.70E-3)  
BIOMD0000000077 Blum2000_LHsecretion_1 No No No ()()() mathSBML For input string: "0.[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000078 Leloup2003_CircClock_LD No No No (4.62E4)()() mathSBML For input string: "0.[0.]"
BIOMD0000000079 Goldbeter2006_weightCycling DONE No No (0.414)()() mathSBML For input string: "0.[0.]"
BIOMD0000000080 Thomsen1989_AdenylateCyclase DONE No No (3.79E-11)()() mathSBML For input string: "(DRG_GDP)[0.]"
BIOMD0000000081 Suh2004_KCNQ_Regulation No No No ()()() mathSBML For input string: "(GTPgS_C)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000082 Thomsen1988_AdenylateCyclase_Inhibition DONE No No (1.37E-8)()() mathSBML For input string: "(DRG_GDP)[0.]"
BIOMD0000000083 Leloup2003_CircClock_LD_REV-ERBalpha No No No (1.86E4)()() mathSBML For input string: "0.[0.]"
BIOMD0000000084 Hornberg2005_ERKcascade DONE No DONE (96.4)(96.4)(0.065)  
BIOMD0000000085 Maurya2005_GTPaseCycle_reducedOrder DONE No No (1.12E-7)()() mathSBML For input string: "0.[0.]"
BIOMD0000000086 Bornheimer2004_GTPaseCycle DONE No No (2.52E-8)()() mathSBML For input string: "0.[0.]"
BIOMD0000000087 Proctor2006_telomere No No No ()()(5.00E4) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000088 Maeda2006_MyosinPhosphorylation No No DONE ()()(8.85E-3) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000089 Locke2006_CircClock_LL DONE DONE DONE (1.83E-2)(1.74E-2)(8.74E-3)  
BIOMD0000000090 Wolf2001 respiratory oscillations No No No ()()() mathSBML For input string: "(sul_ex)[0.]" VCELL_RT 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 No No DONE ()()(0.224) VCELL_RT NativeCVOdeSolver: CV_TOO_MUCH_WORK: took mxstep internal steps but could not reach tout
BIOMD0000000092 Fuentes2005_ZymogenActivation No No DONE ()()(2.18E-6) VCELL_RT Error adding species context; cannot use a reserved symbol ('x','y','z','t') as a Species common name
BIOMD0000000093 Yamada2003_JAK_STAT_pathway DONE No No (2.52E-2)()() mathSBML For input string: "(IFNRJ2_star)[0.]"
BIOMD0000000094 Yamada2003_JAK_STAT_SOCS1_knockout DONE No No (2.52E-2)()() mathSBML For input string: "(IFNRJ2_star)[0.]"
BIOMD0000000095 Zeilinger2006_PRR7-PRR9-Y No No DONE ()()(0.173) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000096 Zeilinger2006_PRR7-PRR9light-Y No No DONE ()()(3.34E-2) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000097 Zeilinger2006_PRR7-PRR9light-Yprime No No No ()()(3.42E4) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000098 Goldbeter1990_Ca_Oscillations No No No ()()(49.9) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000099 Laub1998_SpontaneousOscillations DONE No No (0.164)()() mathSBML For input string: "0.[0.]"
BIOMD0000000100 Rozi2003_GlycogenPhosphorylase_Activation DONE DONE DONE (0.724)(8.69E-2)(0.652)  
BIOMD0000000101 Vilar2006_TGFbeta No No No ()()() mathSBML For input string: "(lRIRII_endo)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000102 Legewie2006_apoptosis_WT DONE No No (1.63E-3)()() mathSBML For input string: "(C3_star)[0.]"
BIOMD0000000103 Legewie2006_apoptosis_NC DONE No No (2.80E-4)()() mathSBML For input string: "(C3_star)[0.]"
BIOMD0000000104 Klipp2002_MetabolicOptimization_linearPathway(n=2) No No No ()()() mathSBML For input string: "0.[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000105 Proctor2007_ubiquitine DONE No No (44.8)()() mathSBML For input string: "(E1_Ub)[0.]"
BIOMD0000000106 Yang2007_ArachidonicAcid DONE DONE DONE (0.185)(1.12E-2)(0.174)  
BIOMD0000000107 Novak1993_M_phase_control No No No ()()() mathSBML For input string: "(dimer_p)[0.]" VCELL_RT 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 DONE No No (1.29E-7)()() mathSBML For input string: "(species)[0.]"_
BIOMD0000000109 Haberichter2007_cellcycle No No DONE ()()(0.741) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000110 Qu2003_CellCycle No No No ()()() COPASI C:\SBMLRelated\SBML_Testing\release_03December2008_sbmls\Rountrip_4.6_CVODE_3_24_09\BIOMD0000000110.orig.cps (The system cannot find the file specified) VCELL_RT 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 No No DONE ()()(0.169) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000112 Clarke2006_Smad_signalling No No No (9.20E3)()() mathSBML For input string: "(_cyt*(R_smad))[0.]"
BIOMD0000000113 Dupont1992_Ca_dpt_protein_phospho No No No (1.00E5)()() mathSBML For input string: "(W_star)[0.]"
BIOMD0000000114 Somogyi1990_CaOscillations No No DONE ()()(6.15E-2) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000115 Somogyi1990_CaOscillations_SingleCaSpike No No No ()()(8.53) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000116 McClean2007_CrossTalk DONE No No (2.91E-2)()() mathSBML For input string: "0.[0.]"
BIOMD0000000117 Dupont1991_CaOscillation No No No ()()(4.62E4) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000118 Golomb2006_SomaticBursting No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000119 Golomb2006_SomaticBursting_nonzero[Ca] No No No ()()() COPASI null VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000120 Chan2004_TCell_receptor_activation No No No ()()() mathSBML For input string: "(lck_inactive)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000121 Clancy2001_Kchannel No No DONE ()()(2.96E-3) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000122 Fisher2006_Ca_Oscillation_dpdnt_NFAT_dynamics No No No ()()() mathSBML For input string: "(Ca_Nuc)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000123 Fisher2006_NFAT_Activation DONE No No (1.46E-3)()() mathSBML For input string: "(Ca_Nuc)[0.]"
BIOMD0000000124 Wu2006_K+Channel No No DONE ()()(1.76E-6) VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000125 Komarova2005_TheoreticalFramework_BasicArchitecture No No No ()()(3.98E5) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000126 Clancy2002_CardiacSodiumChannel_WT No No No ()()(9.10E4) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000127 Izhikevich2003_SpikingNeuron No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000128 Bertram2006_Endothelin No No DONE ()()(1.17E-4) VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000129 Izhikevich2004_SpikingNeurons_inhibitionInducedSpiking No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000130 Izhikevich2004_SpikingNeurons_integrator No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000131 Izhikevich2004_SpikingNeurons_reboundBurst No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000132 Izhikevich2004_SpikingNeurons_reboundSpike No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000133 Izhikevich2004_SpikingNeurons_resonator No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000134 Izhikevich2004_SpikingNeurons_SpikeLatency No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000135 Izhikevich2004_SpikingNeurons_subthresholdOscillations No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000136 Izhikevich2004_SpikingNeurons_thresholdVariability No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000137 Sedaghat2002_InsulinSignalling_noFeedback No No No ()()() VCELL_RT SBML Import Error: VCell doesn't support Events at this time COMPARE COPASI/mSBML variable 'x13' not found in test dataset
BIOMD0000000138 Tabak2007_dopamine No No DONE ()()(5.75E-5) VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000139 Hoffmann2002_KnockOut_IkBNFkB_Signaling No No No ()()() mathSBML For input string: "(IkBalpha_NFkB)[0.]" VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000140 Hoffmann2002_WT_IkBNFkB_Signaling No No No ()()() mathSBML For input string: "(IkBalpha_NFkB)[0.]" VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000141 Izhikevich2004_SpikingNeurons_Class1Excitable No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000142 Izhikevich2004_SpikingNeurons_Class2Excitable No No No ()()() COPASI COPASI model doesn't have metabolites - skipping VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000143 Olsen2003_neutrophil_oscillatory_metabolism DONE No No (2.73E-2)()() mathSBML For input string: "(H2O2_p)[0.]"
BIOMD0000000144 Calzone2007_CellCycle No No No ()()() mathSBML For input string: "(IEa)[0.]"_ VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000145 Wang2007_ATP_induced_Ca_Oscillation No No No ()()() mathSBML For input string: "(Galpha_GTP)[0.]" VCELL_RT SBML Import Error: An assignment rule for species DG contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000146 Hatakeyama2003_MAPK DONE No No (5.21E-2)()() mathSBML For input string: "(P:Blank[0. + 1.*I])[0.]"
BIOMD0000000147 ODea2007_IkappaB No No No ()()() mathSBML For input string: "(IkBa_mRNA)[0.]" VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000148 Komarova2003_BoneRemodeling No No No ()()() mathSBML For input string: "(x1_bar)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000149 Kim2007_Wnt_ERK_Crosstalk No No DONE ()()(6.17E-3) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000150 Morris2002_CellCycle_CDK2Cyclin DONE No No (2.79E-8)()() mathSBML For input string: "(_*(CDK2cycA_star))[0.]"
BIOMD0000000151 Singh2006_IL6_Signal_Transduction No No DONE ()()(2.38E-2) VCELL_RT SBML Import Error: Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.
BIOMD0000000152 Fernandez2006_ModelA No No No ()()() mathSBML For input string: "(D_CDK5)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000153 Fernandez2006_ModelB No No No ()()() mathSBML For input string: "(D_CDK5)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000154 Zatorsky2006_p53_Model3 No No No ()()() VCELL_RT SBML Import Error: cannot translate csymbol-delay from MathML
BIOMD0000000155 Zatorsky2006_p53_Model6 No No No ()()() VCELL_RT SBML Import Error: cannot translate csymbol-delay from MathML
BIOMD0000000156 Zatorsky2006_p53_Model5 No No DONE ()()(0.212) VCELL_RT Error adding species context; cannot use a reserved symbol ('x','y','z','t') as a Species common name
BIOMD0000000157 Zatorsky2006_p53_Model4 No No DONE ()()(0.315) VCELL_RT Error adding species context; cannot use a reserved symbol ('x','y','z','t') as a Species common name
BIOMD0000000158 Zatorsky2006_p53_Model2 No No No ()()(1.40E4) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000159 Zatorsky2006_p53_Model1 No No DONE ()()(0.153) VCELL_RT Error adding species context; cannot use a reserved symbol ('x','y','z','t') as a Species common name
BIOMD0000000160 Xie2007_CircClock DONE DONE DONE (0.135)(0.121)(0.059)  
BIOMD0000000161 Eungdamrong2007_Ras_Activation DONE No No (0.335)()() mathSBML For input string: "(_GM*(RasGTP_Golgi))[0.]"
BIOMD0000000162 Hernjak2005_Calcium_Signaling No No No ()()() mathSBML For input string: "(ERDensity_ERM)[0.]" VCELL_RT NativeCVOdeSolver: CV_ERR_FAILURE: error test failures occurred too many times during one internal step
BIOMD0000000163 Zi2007_TGFbeta_signaling DONE No No (7.62E-2)()() mathSBML For input string: "(T1R_Surf)[0.]"
BIOMD0000000164 SmithAE2002_RanTransport No No No (2.09E5)()() mathSBML For input string: "(Carrier_Cytosol)[0.]"
BIOMD0000000165 Saucerman2006_PKA DONE No No (2.75E-3)()() mathSBML For input string: "(Gsbg_cell)[0.]"
BIOMD0000000166 Zhu2007_TF_modulated_by_Calcium No No No ()()(53.5) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000167 Mayya2005_STATmodule No No No ()()() mathSBML For input string: "(stat_sol)[0.]" VCELL_RT Error adding Feature to vcModel membrane 'nm' should have inside and outside features
BIOMD0000000168 Obeyesekere1999_CellCycle No No No ()()() mathSBML For input string: "(D)[0.]"_ VCELL_RT SBML Import Error: An assignment rule for species E2F_1 contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000169 Aguda1999_CellCycle DONE No No (3.75E-2)()() mathSBML For input string: "(Y3)[0.]"_
BIOMD0000000170 Weimann2004_CircadianOscillator No No DONE ()()(8.54E-2) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000171 Leloup1998_CircClock_LD No No No ()()() mathSBML For input string: "(M_T)[0.]" VCELL_RT 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
BIOMD0000000172 Pritchard2002_glycolysis No No No ()()() VCELL_RT Error adding Feature to vcModel there is more than one top-level feature COMPARE COPASI/mSBML variable 'F16bP' not found in test dataset
BIOMD0000000173 Schmierer_2008_Smad_Tgfb No No No ()()() mathSBML For input string: "(S2:Blank[{0. -> 0." VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000174 Del_Conte_Zerial2008_Rab5_Rab7_cut_out_switch DONE DONE DONE (9.03E-3)(1.84E-3)(9.10E-3)  
BIOMD0000000175 Birtwistle2007_ErbB_Signalling No No No ()()() mathSBML For input string: "(E_E1)[0.]" VCELL_RT SBML Import Error: An assignment rule for species norm_Akt_star contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000176 Conant2007_WGD_glycolysis_2A3AB No DONE No ()(2.73E-3)() COMPARE VC/COPASI variable 'F26bP' not found in test dataset COMPARE COPASI/mSBML variable 'F26bP' not found in test dataset
BIOMD0000000177 Conant2007_glycolysis_2C No No No ()()() VCELL_RT Error adding Feature to vcModel there is more than one top-level feature COMPARE COPASI/mSBML variable 'F26bP' not found in test dataset
BIOMD0000000178 Lebeda2008_bot_tox_paralysis No No No ()()() COPASI C:\SBMLRelated\SBML_Testing\release_03December2008_sbmls\Rountrip_4.6_CVODE_3_24_09\BIOMD0000000178.orig.cps (The system cannot find the file specified) VCELL_RT SBML Import Error: An assignment rule for species BoNT contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000179 TaeHwanKim2007_Cellular_Memory_Asymmetric_Model DONE No No (10.9)()() mathSBML For input string: "(P1_prime)[0.]"
BIOMD0000000180 TaeHwanKim2007_Cellular_Memory_Symmetric_Model DONE No No (13.6)()() mathSBML For input string: "(P1_prime)[0.]"
BIOMD0000000181 Sriram2007_CellCycle DONE DONE DONE (1.25E-2)(1.07E-2)(1.32E-2)  
BIOMD0000000182 Neves2008_Cell_Shape DONE No No (2.71)()() mathSBML For input string: "(_cyto*_mem*(AC_active))[0.]"
BIOMD0000000183 Stefan2008_calmodulin_allostery DONE No No (2.76E-8)()() mathSBML For input string: "0.[0.]"
BIOMD0000000184 Lavrentovich2008_Ca_Oscillations No No DONE ()()(6.49E-2) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000185 Locke2008_Circadian_Clock DONE DONE DONE (0.274)(1.59E-2)(0.284)  
BIOMD0000000186 Ibrahim2008_Spindle_Assembly_Checkpoint_dissociation No No No ()()() mathSBML For input string: "(Mad1_CMad2)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000187 Ibrahim2008_Spindle_Assembly_Checkpoint_convey No No No ()()() mathSBML For input string: "(Mad1_CMad2)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000188 Proctor2003_p53_Mdm2_ATM No No No ()()() mathSBML For input string: "(Mdm2_p53)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000189 Proctor2008_p53_Mdm2_ARF No No No ()()() mathSBML For input string: "(Mdm2_p53)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000190 Rodriguez-Caso2006_Polyamine_Metabolism No No DONE ()()(3.28E-2) VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000191 Montañez2008_Arginine_catabolism No No DONE ()()(0.082) VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000192 Görlich2003_RanGTP_gradient No No No ()()() mathSBML For input string: "(RanGDP_nuc)[0.]" VCELL_RT Error adding Feature to vcModel there is more than one top-level feature
BIOMD0000000193 Ibrahim2008_MCC assembly model KDM No No No ()()() mathSBML For input string: "(Mad1_CMad2)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000194 Ibrahim2008_Cdc20 Sequestring Template Model No No No ()()() mathSBML For input string: "(Mad1_CMad2)[0.]" VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000195 Tyson2001_Cell_Cycle_Regulation No No No ()()() COPASI C:\SBMLRelated\SBML_Testing\release_03December2008_sbmls\Rountrip_4.6_CVODE_3_24_09\BIOMD0000000195.orig.cps (The system cannot find the file specified) VCELL_RT SBML Import Error: VCell doesn't support Events at this time
BIOMD0000000196 Srividhya2006_CellCycle No No No ()()() VCELL_RT SBML Import Error: cannot translate Event-delay from MathML; Algebraic Rules
BIOMD0000000197 Bartholome2007_MDCKII No No No ()()() mathSBML For input string: "(BSP_tot)[0.]" VCELL_RT SBML Import Error: An assignment rule for species BSP_tot contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000198 Stone1996_NOsGC No No No ()()() mathSBML For input string: "(NO_sGCfast)[0.]" VCELL_RT SBML Import Error: An assignment rule for species NO_sGC_5coord_tot contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000199 Santolini2001_nNOS_Mechanism_Regulation No No No ()()() mathSBML For input string: "(FeII_O2)[0.]" VCELL_RT SBML Import Error: An assignment rule for species FeIII_t contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000200 bray1995_chemotaxis_receptorlinkedcomplex DONE DONE DONE (2.98E-7)(7.29E-4)(7.29E-4)  
BIOMD0000000201 Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF No No DONE ()()(0.589) VCELL_RT SBML Import Error: An assignment rule for species AK contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000202 ChenXF2008_CICR No No No ()()() mathSBML For input string: "(Ca_Cyt)[0.]" VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000203 Chickarmane2006_StemCell_Switchreversible No No No ()()() mathSBML For input string: "(OCT4_Gene)[0.]" VCELL_RT Error adding species context; Unable to scale the species unit from: cbit.vcell.units.VCUnitDefinition@16ac : symbol=[litre-1] -> uM
BIOMD0000000204 Chickarmane2006_StemCell_Switchirreversible No No No ()()() mathSBML For input string: "(OCT4_Gene)[0.]" VCELL_RT Error adding species context; Unable to scale the species unit from: cbit.vcell.units.VCUnitDefinition@16ac : symbol=[litre-1] -> uM
BIOMD0000000205 Ung2008_EGFR_Endocytosis DONE No No (6.43E-3)()() mathSBML For input string: "0.[0.]"
BIOMD0000000206 Wolf2000_Glycolytic_Oscillations No No No ()()(9.97E2) VCELL_RT SBML Import Error: Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.
BIOMD0000000207 Romond1999_CellCycle No No DONE ()()(3.82E-2) VCELL_RT SBML Import Error: Rate rules are not handled in the Virtual Cell at this time
BIOMD0000000208 Deineko2003_CellCycle DONE DONE DONE (4.17E-2)(4.27E-3)(3.85E-2)  

Curated Biomodels Database models Import at a glance (Results from 03/27/2009)
  • No. of models that were successfully imported into VCell and compared well with Copasi and/or MathSBML = 82
  • No. of models that were imported but failed to compare well with Copasi and/or MathSBML results = 11
  • No. of models that failed to import due to features not supported in VCell = 115

BIOMODEL ID BioModel name PASS Rel Error/Comments
BIOMD0000000001 Edelstein1996_EPSP_AChEvent No Events
BIOMD0000000002 Edelstein1996_EPSP_AChSpecies DONE 4.846960224425041E-5
BIOMD0000000003 Goldbeter1991_MinMitOscil DONE 0.04186745114057356
BIOMD0000000004 Goldbeter1991_MinMitOscil_ExplInact DONE 0.04186781946399379
BIOMD0000000005 Tyson1991_CellCycle_6var No species has 'hasOnlySubstanceUnits'
BIOMD0000000006 Tyson1991_CellCycle_2var No species has 'hasOnlySubstanceUnits'
BIOMD0000000007 Novak1997_CellCycle No Algebraic or Rate rule
BIOMD0000000008 Gardner1998_CellCycle_Goldbeter DONE 0.20799998769931177
BIOMD0000000009 Huang1996_MAPK_ultrasens DONE 0.23188857033057056
BIOMD0000000010 Kholodenko2000_MAPK_feedback DONE 0.5035438885019772
BIOMD0000000011 Levchenko2000_MAPK_noScaffold No species has 'hasOnlySubstanceUnits'
BIOMD0000000012 Elowitz2000_Repressilator No species has 'hasOnlySubstanceUnits'
BIOMD0000000013 Poolman2004_CalvinCycle No species has 'hasOnlySubstanceUnits'
BIOMD0000000014 Levchenko2000_MAPK_Scaffold No species has 'hasOnlySubstanceUnits'
BIOMD0000000015 Curto1998_purineMetabol No species has 'hasOnlySubstanceUnits'
BIOMD0000000016 Goldbeter1995_CircClock No 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 No species has 'hasOnlySubstanceUnits'
BIOMD0000000018 Morrison1989_FolateCycle No An assignment rule for species FH2b contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000020 hodgkin-huxley squid-axon 1952 No Algebraic or Rate rule
BIOMD0000000021 Leloup1999_CircClock DONE 0.5646482777596599
BIOMD0000000022 Ueda2001_CircClock No More than one top-level feature
BIOMD0000000023 Rohwer2001_Sucrose No Unable to interpret Kinetic rate for reaction : v11 Cannot interpret non-linear function of compartment size
BIOMD0000000024 Scheper1999_CircClock No Import is null : delay term in one reaction; mathML returned by libSBML 2.3.4 convenience methods is wrong, hence ExpressionMathMLParser doesn't throw proper expression
BIOMD0000000025 Smolen2002_CircClock No Events
BIOMD0000000026 Markevich2004_MAPK_orderedElementary DONE 0.5068514931958289
BIOMD0000000027 Markevich2004_MAPK_orderedMM DONE 0.24001060371129077
BIOMD0000000028 Markevich2004_MAPK_phosphoRandomElementary DONE 0.39291728977753126
BIOMD0000000029 Markevich2004_MAPK_phosphoRandomMM DONE 0.4213306609624102
BIOMD0000000030 Markevich2005_MAPK_AllRandomElementary DONE 0.38429592553232345
BIOMD0000000031 Markevich2004_MAPK_orderedMM2kinases DONE 0.22026656500557254
BIOMD0000000032 Kofahl2004_pheromone DONE 0.7472814140516087
BIOMD0000000033 Brown2004_NGF_EGF_signaling No Unable to scale the unit for species concentration: uM 1000.0 item.m-3
BIOMD0000000034 Smolen2004_CircClock No Algebraic or Rate rule
BIOMD0000000035 Vilar2002_Oscillator No species has 'hasOnlySubstanceUnits'
BIOMD0000000036 Tyson1999_CircClock No More than one top-level feature
BIOMD0000000037 Marwan_Genetics_2003 DONE 0.3908122459741909
BIOMD0000000038 Rohwer2000_Phosphotransferase_System No NativeIDASolver: Unknown exception
BIOMD0000000039 Marhl2000_CaOscillations No Non-integer stoichiometry
BIOMD0000000040 Field1974_Oregonator No Non-integer stoichiometry
BIOMD0000000041 Kongas2001_creatine No More than one top-level feature
BIOMD0000000042 Nielsen1998_Glycolysis DONE 0.28206495506936263
BIOMD0000000043 Borghans1997_CaOscillation_model1 No 38487.63828792418
BIOMD0000000044 Borghans1997_CaOscillation_model2 No 114318.7674962251
BIOMD0000000045 Borghans1997_CaOscillation_model3 No 53666.58337222832
BIOMD0000000046 Olsen2003_peroxidase DONE 0.2046512482971659
BIOMD0000000047 Oxhamre2005_Ca_oscillation No Algebraic or Rate rule
BIOMD0000000048 Kholodenko1999_EGFRsignaling No 1.7994228812326536
BIOMD0000000049 Sasagawa2005_MAPK No JDOMParseException : doc not well-formed
BIOMD0000000050 Martins2003_AmadoriDegradation DONE 0.22085006954762595
BIOMD0000000051 Chassagnole2002_Carbon_Metabolism No 61785.622954556726
BIOMD0000000052 Brands2002_MonosaccharideCasein DONE 0.41057759279241635
BIOMD0000000053 Ferreira2003_CML_generation2 DONE 0.03804169290181448
BIOMD0000000054 Ataullahkhanov1996_Adenylate No new variable (Function = 'Expression(P * J_U1 * sbmlRateFactor_U1)'') conflicts with existing var (Constant) = 'Expression '100.0''
BIOMD0000000055 Locke2005_CircClock No 34936.14510623187
BIOMD0000000056 Chen2004_CellCycle No Algebraic or Rate rule
BIOMD0000000057 Sneyd2002_IP3_Receptor DONE 0.05301210053046178
BIOMD0000000058 Bindschadler2001_coupled_Ca_oscillators DONE 0.41183508253869267
BIOMD0000000059 Fridlyand2003_Calcium_flux No Algebraic or Rate rule
BIOMD0000000060 Keizer1996_Ryanodine_receptor_adaptation DONE 0.1060340104924619
BIOMD0000000061 Hynne2001 Glycolysis No 4.087591709464351
BIOMD0000000062 bhartiya2003 tryptophan operon No 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 No Non-integer stoichiometry
BIOMD0000000064 Teusink2000_Glycolysis DONE 0.4442576229191075
BIOMD0000000065 Yildirim2003_Lac_Operon DONE 0.04570667521278065
BIOMD0000000066 Chassagnole2001_Threonine Synthesis DONE 0.1902042521803032
BIOMD0000000067 Fung2005_Metabolic_Oscillator DONE 0.415226196542508
BIOMD0000000068 Curien2003_MetThr_synthesis No 90600.94282434192
BIOMD0000000069 Fuss2006_MitoticActivation No 128.84316012171877
BIOMD0000000070 Holzhutter2004_Erythrocyte_Metabolism No NativeIDASolver: Unknown exception
BIOMD0000000071 Bakker2001_Glycolysis No reaction 'vGlcTr' has reaction participants in innermost and ourtermost comaprtments of a 3-compartment model; reaction not allowed in Vcell topology
BIOMD0000000072 Yi2003_GproteinCycle No Unable to scale the unit for species concentration: uM 1000.0 item.m-3
BIOMD0000000073 Leloup2003_CircClock_DD DONE 0.4875566257919786
BIOMD0000000074 Leloup2003_CircClock_DD_REV-ERBalpha DONE 0.22661573257620818
BIOMD0000000075 Xu2003_Phosphoinositide_turnover No Events
BIOMD0000000076 Cronwright2002_Glycerol_Synthesis DONE 0.034345473160881296
BIOMD0000000077 Blum2000_LHsecretion_1 No Events
BIOMD0000000078 Leloup2003_CircClock_LD No  
BIOMD0000000079 Goldbeter2006_weightCycling DONE 0.4368680781160297
BIOMD0000000080 Thomsen1989_AdenylateCyclase DONE 4.767865595737549E-7
BIOMD0000000081 Suh2004_KCNQ_Regulation No Events
BIOMD0000000082 Thomsen1988_AdenylateCyclase_Inhibition DONE 4.995365967159909E-7
BIOMD0000000083 Leloup2003_CircClock_LD_REV-ERBalpha No  
BIOMD0000000084 Hornberg2005_ERKcascade No  
BIOMD0000000085 Maurya2005_GTPaseCycle_reducedOrder DONE 1.2803215751323163E-4
BIOMD0000000086 Bornheimer2004_GTPaseCycle DONE 1.255232861384703E-4
BIOMD0000000087 Proctor2006_telomere No Events
BIOMD0000000088 Maeda2006_MyosinPhosphorylation No Events
BIOMD0000000089 Locke2006_CircClock_LL DONE 0.43824281126201803
BIOMD0000000090 Wolf2001 respiratory oscillations No 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 No species has 'hasOnlySubstanceUnits'
BIOMD0000000092 Fuentes2005_ZymogenActivation No species name is x,y,z,t
BIOMD0000000093 Yamada2003_JAK_STAT_pathway DONE 0.2315551674395519
BIOMD0000000094 Yamada2003_JAK_STAT_SOCS1_knockout DONE 0.2315551674395519
BIOMD0000000095 Zeilinger2006_PRR7-PRR9-Y No Events
BIOMD0000000096 Zeilinger2006_PRR7-PRR9light-Y No Events
BIOMD0000000097 Zeilinger2006_PRR7-PRR9light-Yprime No Events
BIOMD0000000098 Goldbeter1990_Ca_Oscillations No More than one top-level feature
BIOMD0000000099 Laub1998_SpontaneousOscillations DONE 0.3214876212794411
BIOMD0000000100 Rozi2003_GlycogenPhosphorylase_Activation No 39269.856234090206
BIOMD0000000101 Vilar2006_TGFbeta No Events
BIOMD0000000102 Legewie2006_apoptosis_WT DONE 0.3787492324678153
BIOMD0000000103 Legewie2006_apoptosis_NC DONE 0.3814149399515042
BIOMD0000000104 Klipp2002_MetabolicOptimization_linearPathway(n=2) No Events
BIOMD0000000105 Proctor2007_ubiquitine No species has 'hasOnlySubstanceUnits'
BIOMD0000000106 Yang2007_ArachidonicAcid DONE 0.40634364549351826
BIOMD0000000107 Novak1993_M_phase_control No 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 DONE 0.023345885142666445
BIOMD0000000109 Haberichter2007_cellcycle No Events
BIOMD0000000110 Qu2003_CellCycle No 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 No Events
BIOMD0000000112 Clarke2006_Smad_signalling No species has 'hasOnlySubstanceUnits'
BIOMD0000000113 Dupont1992_Ca_dpt_protein_phospho No 49999.99999999999
BIOMD0000000114 Somogyi1990_CaOscillations No More than one top-level feature
BIOMD0000000115 Somogyi1990_CaOscillations_SingleCaSpike No More than one top-level feature
BIOMD0000000116 McClean2007_CrossTalk DONE 0.15688640023909456
BIOMD0000000117 Dupont1991_CaOscillation No Events
BIOMD0000000118 Golomb2006_SomaticBursting No Algebraic or Rate rule
BIOMD0000000119 Golomb2006_SomaticBursting_nonzero[Ca] No Algebraic or Rate rule
BIOMD0000000120 Chan2004_TCell_receptor_activation No Events
BIOMD0000000121 Clancy2001_Kchannel No Events
BIOMD0000000122 Fisher2006_Ca_Oscillation_dpdnt_NFAT_dynamics No Events
BIOMD0000000123 Fisher2006_NFAT_Activation DONE 0.026970348026926487
BIOMD0000000124 Wu2006_K+Channel No Algebraic or Rate rule
BIOMD0000000125 Komarova2005_TheoreticalFramework_BasicArchitecture No Events
BIOMD0000000126 Clancy2002_CardiacSodiumChannel_WT No Events
BIOMD0000000127 Izhikevich2003_SpikingNeuron No Algebraic or Rate rule
BIOMD0000000128 Bertram2006_Endothelin No Algebraic or Rate rule
BIOMD0000000129 Izhikevich2004_SpikingNeurons_inhibitionInducedSpiking No Algebraic or Rate rule
BIOMD0000000130 Izhikevich2004_SpikingNeurons_integrator No Algebraic or Rate rule
BIOMD0000000131 Izhikevich2004_SpikingNeurons_reboundBurst No Algebraic or Rate rule
BIOMD0000000132 Izhikevich2004_SpikingNeurons_reboundSpike No Algebraic or Rate rule
BIOMD0000000133 Izhikevich2004_SpikingNeurons_resonator No Algebraic or Rate rule
BIOMD0000000134 Izhikevich2004_SpikingNeurons_SpikeLatency No Algebraic or Rate rule
BIOMD0000000135 Izhikevich2004_SpikingNeurons_subthresholdOscillations No Algebraic or Rate rule
BIOMD0000000136 Izhikevich2004_SpikingNeurons_thresholdVariability No Algebraic or Rate rule
BIOMD0000000137 Sedaghat2002_InsulinSignalling_noFeedback No Events
BIOMD0000000138 Tabak2007_dopamine No Algebraic or Rate rule
BIOMD0000000139 Hoffmann2002_KnockOut_IkBNFkB_Signaling No Algebraic or Rate rule
BIOMD0000000140 Hoffmann2002_WT_IkBNFkB_Signaling No Algebraic or Rate rule
BIOMD0000000141 Izhikevich2004_SpikingNeurons_Class1Excitable No Algebraic or Rate rule
BIOMD0000000142 Izhikevich2004_SpikingNeurons_Class2Excitable No Algebraic or Rate rule
BIOMD0000000143 Olsen2003_neutrophil_oscillatory_metabolism No var H202_p not found in test dataset
BIOMD0000000144 Calzone2007_CellCycle No Events
BIOMD0000000145 Wang2007_ATP_induced_Ca_Oscillation No An assignment rule for species DG contains another species in the model, this is not allowed for a non-spatial model in VCell
BIOMD0000000146 Hatakeyama2003_MAPK DONE 0.7336852515087224
BIOMD0000000147 ODea2007_IkappaB No More than one top-level feature
BIOMD0000000148 Komarova2003_BoneRemodeling No Events
BIOMD0000000149 Kim2007_Wnt_ERK_Crosstalk No Events
BIOMD0000000150 Morris2002_CellCycle_CDK2Cyclin DONE 6.469020716409943E-8
BIOMD0000000151 Singh2006_IL6_Signal_Transduction No Non-integer stoichiometry

Possible way of dealing with inside/outside (infer from GO information embedded within curated SBML document).

  • already have code that uses JDOM to extract GO term for each compartment ID (could be passed into or included within SBMLImporter).
  • would probably fix most of the 20 BioModels with this problem (see above table).
  • the following table is taken by parsing the 113 sbml models in the curated branch (and ignoring 2 "neuromuscular synapse" and "chloroplast stroma").

group GO ID GO Name
1 http://www.geneontology.org/#GO:0005576 extracellular region
1 http://www.geneontology.org/#GO:0005615 extracellular space
2 http://www.geneontology.org/#GO:0005623 cell
3 http://www.geneontology.org/#GO:0016020 membrane
3 http://www.geneontology.org/#GO:0005886 plasma membrane
4 http://www.geneontology.org/#GO:0009898 internal side of plasma membrane
5 http://www.geneontology.org/#GO:0005622 intracellular
5 http://www.geneontology.org/#GO:0005737 cytoplasm
5 http://www.geneontology.org/#GO:0005829 cytosol
6 http://www.geneontology.org/#GO:0005783 endoplasmic reticulum
6 http://www.geneontology.org/#GO:0005790 smooth endoplasmic reticulum
6 http://www.geneontology.org/#GO:0005634 nucleus
7 http://www.geneontology.org/#GO:0005768 endosome
7 http://www.geneontology.org/#GO:0020015 glycosome
8 http://www.geneontology.org/#GO:0005739 mitochondrion
9 http://www.geneontology.org/#GO:0005758 mitochondrial intermembrane space

List of models from the old Validation Test Suite that were successfully imported into the VCell ('roundtrip'-ed)

Though these tests are very basic and probably do not exercise much, they are good to test some default functionalities of SBML, and are used for preliminary testing of changes to the SBMLImporter/SBMLExporter to make sure the basic functionalities haven't been altered.

(Note: Only the first sheet of the Excel file is relevant information for these purposes).

Topic attachments
I Attachment Action Size Date Who Comment
Microsoft Excel Spreadsheetxls BiomodelsDBModels.xls manage 16.0 K 2007-09-16 - 20:52 AnuradhaLakshminarayana Subset of list of models from Biomodels.net that were imported into the Virtual Cell; with comparison of simulation results for between VCell and MathSBML. The spreadsheet shows PASS/FAIL for the comparison, reasons for failing, if any.
Microsoft Excel Spreadsheetxls ValidationTestReport_2.xls manage 54.5 K 2007-09-16 - 21:12 AnuradhaLakshminarayana Results of running the old SBML Validation Test suite on the VCell SBMLImporter/Exporter.
Topic revision: r53 - 2009-03-27 - 17:15:02 - AnuradhaLakshminarayana
 
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