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Cardiac Physiome Society workshop: November 6-9, 2017 , Toronto

JSim Biomodels Page

This page allows users to run curated models from the Biomodels Database under JSim. To run these models online, you must have a Java plugin installed in your WWW browser. To run them in JSim on your own computer, download the model code and the JSim application. Either way, see Running JSim for instructions on how to use JSim. Since these models do not specify simulation time length or delta, these must be set by the user before running the model.

Notes:

Return to complete JSim model archives.

Currently available curated models

Terms of use

BIOMD0000000001: Edelstein1996 - EPSP ACh event

BIOMD0000000002: Edelstein1996 - EPSP ACh species

BIOMD0000000003: Goldbeter1991 - Min Mit Oscil

BIOMD0000000004: Goldbeter1991 - Min Mit Oscil, Expl Inact

BIOMD0000000005: Tyson1991 - Cell Cycle 6 var

BIOMD0000000006: Tyson1991 - Cell Cycle 2 var

BIOMD0000000007: Novak1997 - Cell Cycle

BIOMD0000000008: Gardner1998 - Cell Cycle Goldbeter

BIOMD0000000009: Huang1996 - Ultrasensitivity in MAPK cascade

BIOMD0000000010: Kholodenko2000 - Ultrasensitivity and negative feedback bring oscillations in MAPK cascade

BIOMD0000000011: Levchenko2000 MAPK noScaffold

BIOMD0000000012: Elowitz2000 - Repressilator

BIOMD0000000013: Poolman2004 CalvinCycle

BIOMD0000000014: Levchenko2000 MAPK Scaffold

BIOMD0000000015: Curto1998 - purine metabolism

BIOMD0000000016: Goldbeter1995 CircClock

BIOMD0000000017: Hoefnagel2002 PyruvateBranches

BIOMD0000000018: Morrison1989 FolateCycle

BIOMD0000000019: Schoeberl2002 - EGF MAPK

BIOMD0000000020: hodgkin-huxley squid-axon 1952

BIOMD0000000021: Leloup1999 CircClock

BIOMD0000000022: Ueda2001 CircClock

BIOMD0000000023: Rohwer2001 Sucrose

BIOMD0000000024: Scheper1999 CircClock

BIOMD0000000025: Smolen2002 CircClock

BIOMD0000000026: Markevich2004 MAPK orderedElementary

BIOMD0000000027: Markevich2004 MAPK orderedMM

BIOMD0000000028: Markevich2004 MAPK phosphoRandomElementary

BIOMD0000000029: Markevich2004 MAPK phosphoRandomMM

BIOMD0000000030: Markevich2004 MAPK AllRandomElementary

BIOMD0000000031: Markevich2004 MAPK orderedMM2kinases

BIOMD0000000032: Kofahl2004 PheromonePathway

BIOMD0000000033: Brown2004 NGF EGF signaling

BIOMD0000000034: Smolen2004 CircClock

BIOMD0000000035: Vilar2002 Oscillator

BIOMD0000000036: Tyson1999 CircClock

BIOMD0000000037: Marwan2003 - Genetics, regulatory hierarchy between genes

BIOMD0000000038: Rohwer2000 Phosphotransferase System

BIOMD0000000039: Marhl2000 CaOscillations

BIOMD0000000040: Field1974 Oregonator

BIOMD0000000041: Kongas2007 - Creatine Kinase in energy metabolic signaling in muscle

BIOMD0000000042: Nielsen1998 Glycolysis

BIOMD0000000043: Borghans1997 - Calcium Oscillation - Model 1

BIOMD0000000044: Borghans1997 - Calcium Oscillation - Model 2

BIOMD0000000045: Borghans1997 - Calcium Oscillation - Model 3

BIOMD0000000046: Olsen2003 peroxidase

BIOMD0000000047: Oxhamre2005 Ca oscillation

BIOMD0000000048: Kholodenko1999 - EGFR signaling

BIOMD0000000049: Sasagawa2005 MAPK

BIOMD0000000050: Martins2003 AmadoriDegradation

BIOMD0000000051: Chassagnole2002 Carbon Metabolism

BIOMD0000000052: Brands2002 - Monosaccharide-casein systems

BIOMD0000000053: Ferreira2003 CML generation2

BIOMD0000000054: Ataullahkhanov1996 Adenylate

BIOMD0000000055: Locke2005 - Circadian Clock

BIOMD0000000056: Chen2004 - Cell Cycle Regulation

BIOMD0000000057: Sneyd2002 IP3 Receptor

BIOMD0000000058: Bindschadler2001 coupled Ca oscillators

BIOMD0000000059: Fridlyand2003 Calcium flux

BIOMD0000000060: Keizer1996 Ryanodine receptor adaptation

BIOMD0000000061: Hynne2001 Glycolysis

BIOMD0000000062: Bhartiya2003 Tryptophan operon

BIOMD0000000063: Galazzo1990 FermentationPathwayKinetics

BIOMD0000000064: Teusink2000 Glycolysis

BIOMD0000000065: Yildirim2003 Lac Operon

BIOMD0000000066: Chassagnole2001 Threonine Synthesis

BIOMD0000000067: Fung2005 Metabolic Oscillator

BIOMD0000000068: Curien2003 MetThr synthesis

BIOMD0000000069: Fuss2006 MitoticActivation

BIOMD0000000070: Holzhutter2004 Erythrocyte Metabolism

BIOMD0000000071: Bakker2001 Glycolysis

BIOMD0000000072: Yi2003 GproteinCycle

BIOMD0000000073: Leloup2003 CircClock DD

BIOMD0000000074: Leloup2003 CircClock DD REV-ERBalpha

BIOMD0000000075: Xu2003 - Phosphoinositide turnover

BIOMD0000000076: Cronwright2002 Glycerol Synthesis

BIOMD0000000077: Blum2000 LHsecretion 1

BIOMD0000000078: Leloup2003 CircClock LD

BIOMD0000000079: Goldbeter2006 weightCycling

BIOMD0000000080: Thomsen1989 AdenylateCyclase

BIOMD0000000081: Suh2004 KCNQ Regulation

BIOMD0000000082: Thomsen1988 AdenylateCyclase Inhibition

BIOMD0000000083: Leloup2003 CircClock LD REV-ERBalpha

BIOMD0000000084: Hornberg2005 ERKcascade

BIOMD0000000085: Maurya2005 GTPaseCycle reducedOrder

BIOMD0000000086: Bornheimer2004 GTPaseCycle

BIOMD0000000087: Proctor2006 telomere

BIOMD0000000088: Maeda2006 MyosinPhosphorylation

BIOMD0000000089: Locke2006 CircClock LL

BIOMD0000000090: Wolf2001 Respiratory Oscillations

BIOMD0000000091: Proctor2005 - Actions of chaperones and their role in ageing

BIOMD0000000092: Fuentes2005 ZymogenActivation

BIOMD0000000093: Yamada2003 JAK STAT pathway

BIOMD0000000094: Yamada2003 JAK STAT SOCS1 knockout

BIOMD0000000095: Zeilinger2006 PRR7-PRR9-Y

BIOMD0000000096: Zeilinger2006 PRR7-PRR9light-Y

BIOMD0000000097: Zeilinger2006 PRR7-PRR9light-Yprime

BIOMD0000000098: Goldbeter1990 CalciumSpike CICR

BIOMD0000000099: Laub1998 SpontaneousOscillations

BIOMD0000000100: Rozi2003 GlycogenPhosphorylase Activation

BIOMD0000000101: Vilar2006 TGFbeta

BIOMD0000000102: Legewie2006 apoptosis WT

BIOMD0000000103: Legewie2006 apoptosis NC

BIOMD0000000104: Klipp2002 MetabolicOptimization linearPathway(n=2)

BIOMD0000000105: Proctor2007 - Age related decline of proteolysis, ubiquitin-proteome system

BIOMD0000000106: Yang2007 ArachidonicAcid

BIOMD0000000107: Novak1993 M phase control

BIOMD0000000108: Kowald2006 SOD

BIOMD0000000109: Haberichter2007 cellcycle

BIOMD0000000110: Qu2003 CellCycle

BIOMD0000000111: Novak2001 FissionYeast CellCycle

BIOMD0000000112: Clarke2006 Smad signalling

BIOMD0000000113: Dupont1992 Ca dpt protein phospho

BIOMD0000000114: Somogyi1990 CaOscillations

BIOMD0000000115: Somogyi1990 CaOscillations SingleCaSpike

BIOMD0000000116: McClean2007 CrossTalk

BIOMD0000000117: Dupont1991 CaOscillation

BIOMD0000000118: Golomb2006 SomaticBursting

BIOMD0000000119: Golomb2006 SomaticBursting nonzero[Ca]

BIOMD0000000120: Chan2004 TCell receptor activation

BIOMD0000000121: Clancy2001 Kchannel

BIOMD0000000122: Fisher2006 Ca Oscillation dpdnt NFAT dynamics

BIOMD0000000123: Fisher2006 NFAT Activation

BIOMD0000000124: Wu2006 K+Channel

BIOMD0000000125: Komarova2005 TheoreticalFramework BasicArchitecture

BIOMD0000000126: Clancy2002 CardiacSodiumChannel WT

BIOMD0000000127: Izhikevich2003 SpikingNeuron

BIOMD0000000128: Bertram2006 Endothelin

BIOMD0000000129: Izhikevich2004 SpikingNeurons inhibitionInducedSpiking

BIOMD0000000130: Izhikevich2004 SpikingNeurons integrator

BIOMD0000000131: Izhikevich2004 SpikingNeurons reboundBurst

BIOMD0000000132: Izhikevich2004 SpikingNeurons reboundSpike

BIOMD0000000133: Izhikevich2004 SpikingNeurons resonator

BIOMD0000000134: Izhikevich2004 SpikingNeurons SpikeLatency

BIOMD0000000135: Izhikevich2004 SpikingNeurons subthresholdOscillations

BIOMD0000000136: Izhikevich2004 SpikingNeurons thresholdVariability

BIOMD0000000137: Sedaghat2002 InsulinSignalling noFeedback

BIOMD0000000138: Tabak2007 dopamine

BIOMD0000000139: Hoffmann2002 KnockOut IkBNFkB Signaling

BIOMD0000000140: Hoffmann2002 WT IkBNFkB Signaling

BIOMD0000000141: Izhikevich2004 SpikingNeurons Class1Excitable

BIOMD0000000142: Izhikevich2004 SpikingNeurons Class2Excitable

BIOMD0000000143: Olsen2003 neutrophil oscillatory metabolism

BIOMD0000000144: Calzone2007 CellCycle

BIOMD0000000145: Wang2007 - ATP induced intracellular Calcium Oscillation

BIOMD0000000146: Hatakeyama2003 MAPK

BIOMD0000000147: ODea2007 IkappaB

BIOMD0000000148: Komarova2003 BoneRemodeling

BIOMD0000000149: Kim2007 - Crosstalk between Wnt and ERK pathways

BIOMD0000000150: Morris2002 CellCycle CDK2Cyclin

BIOMD0000000151: Singh2006 IL6 Signal Transduction

BIOMD0000000152: Fernandez2006 ModelA

BIOMD0000000153: Fernandez2006 ModelB

BIOMD0000000154: Zatorsky2006 p53 Model3

BIOMD0000000155: Zatorsky2006 p53 Model6

BIOMD0000000156: Zatorsky2006 p53 Model5

BIOMD0000000157: Zatorsky2006 p53 Model4

BIOMD0000000158: Zatorsky2006 p53 Model2

BIOMD0000000159: Zatorsky2006 p53 Model1

BIOMD0000000160: Xie2007 CircClock

BIOMD0000000161: Eungdamrong2007 Ras Activation

BIOMD0000000162: Hernjak2005 Calcium Signaling

BIOMD0000000163: Zi2007 TGFbeta signaling

BIOMD0000000164: SmithAE2002 RanTransport

BIOMD0000000165: Saucerman2006 PKA

BIOMD0000000166: Zhu2007 TF modulated by Calcium

BIOMD0000000167: Mayya2005 STATmodule

BIOMD0000000168: Obeyesekere1999 CellCycle

BIOMD0000000169: Aguda1999 CellCycle

BIOMD0000000170: Weimann2004 CircadianOscillator

BIOMD0000000171: Leloup1998 CircClock LD

BIOMD0000000172: Pritchard2002 glycolysis

BIOMD0000000173: Schmierer 2008 Smad Tgfb

BIOMD0000000174: Del Conte Zerial2008 Rab5 Rab7 cut out switch

BIOMD0000000175: Birtwistle2007 ErbB Signalling

BIOMD0000000176: Conant2007 WGD glycolysis 2A3AB

BIOMD0000000177: Conant2007 glycolysis 2C

BIOMD0000000178: Lebeda2008 BoTN Paralysis 4stepModel

BIOMD0000000179: Kim2007 CellularMemory AsymmetricModel

BIOMD0000000180: Kim2007 CellularMemory SymmetricModel

BIOMD0000000181: Sriram2007 CellCycle

BIOMD0000000182: Neves2008 - Role of cell shape and size in controlling intracellular signalling

BIOMD0000000183: Stefan2008 - calmodulin allostery

BIOMD0000000184: Lavrentovich2008 Ca Oscillations

BIOMD0000000185: Locke2008 Circadian Clock

BIOMD0000000186: Ibrahim2008 - Mitotic Spindle Assembly Checkpoint - Dissociation variant

BIOMD0000000187: Ibrahim2008 - Mitotic Spindle Assembly Checkpoint - Convey variant

BIOMD0000000188: Proctor2008 - p53/Mdm2 circuit - p53 stabilisation by ATM

BIOMD0000000189: Proctor2008 - p53/Mdm2 circuit - p53 stablisation by p14ARF

BIOMD0000000190: Rodriguez-Caso2006 Polyamine Metabolism

BIOMD0000000191: Montañez2008 Arginine catabolism

BIOMD0000000192: Görlich2003 RanGTP gradient

BIOMD0000000193: Ibrahim2008 MCC assembly model KDM

BIOMD0000000194: Ibrahim2008 Cdc20 Sequestring Template Model

BIOMD0000000195: Tyson2001 Cell Cycle Regulation

BIOMD0000000196: Srividhya2006 CellCycle

BIOMD0000000197: Bartholome2007 MDCKII

BIOMD0000000198: Stone1996 NOsGC

BIOMD0000000199: Santolini2001 nNOS Mechanism Regulation

BIOMD0000000200: Bray1995 chemotaxis receptorlinkedcomplex

BIOMD0000000201: Goldbeter2008 Somite Segmentation Clock Notch Wnt FGF

BIOMD0000000202: ChenXF2008 CICR

BIOMD0000000203: Chickarmane2006 - Stem cell switch reversible

BIOMD0000000204: Chickarmane2006 - Stem cell switch irreversible

BIOMD0000000205: Ung2008 EGFR Endocytosis

BIOMD0000000206: Wolf2000 Glycolytic Oscillations

BIOMD0000000207: Romond1999 CellCycle

BIOMD0000000208: Deineko2003 CellCycle

BIOMD0000000209: Chickarmane2008 - Stem cell lineage determination

BIOMD0000000210: Chickarmane2008 - Stem cell lineage - NANOG GATA-6 switch

BIOMD0000000211: Albert2005 Glycolysis

BIOMD0000000212: Curien2009 Aspartate Metabolism

BIOMD0000000213: Nijhout2004 Folate Cycle

BIOMD0000000214: Akman2008 Circadian Clock Model2

BIOMD0000000215: Schulz2009 Th1 differentiation

BIOMD0000000216: Hong2009 CircadianClock

BIOMD0000000217: Bruggeman2005 AmmoniumAssimilation

BIOMD0000000218: Singh2006 TCA mtu model2

BIOMD0000000219: Singh2006 TCA mtu model1

BIOMD0000000220: Albeck2008 extrinsic apoptosis

BIOMD0000000221: Singh2006 TCA Ecoli acetate

BIOMD0000000222: Singh2006 TCA Ecoli glucose

BIOMD0000000223: Borisov2009 EGF Insulin Crosstalk

BIOMD0000000224: Meyer1991 CalciumSpike ICC

BIOMD0000000225: Westermark2003 Pancreatic GlycOsc basic

BIOMD0000000226: Radulescu2008 NFkB hierarchy M 14 25 28 Lipniacky

BIOMD0000000227: Radulescu2008 NFkB hierarchy M 39 65 90

BIOMD0000000228: Swat2004 Mammalian G1 S Transition

BIOMD0000000229: Ma2002 cAMP oscillations

BIOMD0000000230: Ihekwaba2004 NFkB Sensitivity

BIOMD0000000231: Valero2006 Adenine TernaryCycle

BIOMD0000000232: Nazaret2009 TCA RC ATP

BIOMD0000000233: Wilhelm2009 BistableReaction

BIOMD0000000234: Tham2008 - PDmodel, Tumour shrinkage by gemcitabine and carboplatin

BIOMD0000000235: Kuhn2009 EndoMesodermNetwork

BIOMD0000000236: Westermark2003 Pancreatic GlycOsc extended

BIOMD0000000237: Schaber2006 Pheromone Starvation Crosstalk

BIOMD0000000238: Overgaard2007 PDmodel IL21

BIOMD0000000239: Jiang2007 - GSIS system, Pancreatic Beta Cells

BIOMD0000000240: Veening2008 DegU Regulation

BIOMD0000000241: Shi1993 Caffeine pressor tolerance

BIOMD0000000242: Bai2003 G1phaseRegulation

BIOMD0000000243: Neumann2010 CD95Stimulation NFkB Apoptosis

BIOMD0000000244: Kotte2010 Ecoli Metabolic Adaption

BIOMD0000000245: Lei2001 Yeast Aerobic Metabolism

BIOMD0000000246: Vasalou2010 Pacemaker Neuron SCN

BIOMD0000000247: Ralser2007 Carbohydrate Rerouting ROS

BIOMD0000000248: Lai2007 O2 Transport Metabolism

BIOMD0000000249: Restif2006 Whooping Cough

BIOMD0000000250: Nakakuki2010 CellFateDecision Mechanistic

BIOMD0000000251: Nakakuki2010 CellFateDecision Core

BIOMD0000000252: Hunziker2010 p53 StressSpecificResponse

BIOMD0000000253: Teusink1998 Glycolysis TurboDesign

BIOMD0000000254: Bier2000 GlycolyticOscillation

BIOMD0000000255: Chen2009 - ErbB Signaling

BIOMD0000000256: Rehm2006 Caspase

BIOMD0000000257: Piedrafita2010 MR System

BIOMD0000000258: Ortega2006 bistability doublePhosphorylation

BIOMD0000000259: Tiago2010 FeMetabolism FeDeficient

BIOMD0000000260: Tiago2010 FeMetabolism FeAdequate

BIOMD0000000261: Tiago2010 FeMetabolism FeLoaded

BIOMD0000000262: Fujita2010 Akt Signalling EGF

BIOMD0000000263: Fujita2010 Akt Signalling NGF

BIOMD0000000264: Fujita2010 Akt Signalling EGFRinhib

BIOMD0000000265: Conradie2010 RPControl CellCycle

BIOMD0000000266: Voit2003 Trehalose Cycle

BIOMD0000000267: Lebeda2008 BoNT Paralysis 3stepModel

BIOMD0000000268: Reed2008 Glutathione Metabolism

BIOMD0000000269: Liu2010 Hormonal Crosstalk Arabidopsis

BIOMD0000000270: Schilling2009 - ERK distributive

BIOMD0000000271: Becker2010 EpoR CoreModel

BIOMD0000000272: Becker2010 EpoR AuxiliaryModel

BIOMD0000000273: Pokhilko2010 CircClock

BIOMD0000000274: Rattanakul2003 BoneFormationModel

BIOMD0000000275: Goldbeter2007 Somitogenesis Switch

BIOMD0000000276: Shrestha2010 HypoCalcemia PTHresponse

BIOMD0000000277: Shrestha2010 HyperCalcemia PTHresponse

BIOMD0000000278: Lemaire2004 - Role of RANK/RANKL/OPG pathway in bone remodelling process

BIOMD0000000279: Komarova2005 PTHaction OsteoclastOsteoblastCoupling

BIOMD0000000280: Morris1981 MuscleFibre Voltage reduced

BIOMD0000000281: Chance1960 Glycolysis Respiration

BIOMD0000000282: Chance1952 Catalase Mechanism

BIOMD0000000283: Chance1943 Peroxidase ES Kinetics

BIOMD0000000284: Hofmeyer1986 SeqFb Proc AA Synthesis

BIOMD0000000285: Tang2010 PolyGlutamate

BIOMD0000000286: Proctor2010 - a link between GSK3 and p53 in Alzheimer's Disease

BIOMD0000000287: Passos2010 DNAdamage CellularSenescence

BIOMD0000000288: Wang2009 - PI3K Ras Crosstalk

BIOMD0000000289: Alexander2010 Tcell Regulation Sys1

BIOMD0000000290: Alexander2010 Tcell Regulation Sys2

BIOMD0000000291: Nikolaev2005 AlbuminBilirubinAdsorption

BIOMD0000000292: Rovers1995 Photsynthetic Oscillations

BIOMD0000000293: Proctor2010 - UCHL1 Protein Aggregation

BIOMD0000000294: Restif2007 Vaccination Invasion

BIOMD0000000295: Akman2008 Circadian Clock Model1

BIOMD0000000296: Balagaddé2008 E coli Predator Prey

BIOMD0000000297: Ciliberto2003 Morphogenesis Checkpoint

BIOMD0000000298: Leloup1999 CircadianRhythms Drosophila

BIOMD0000000299: Leloup1999 CircadianRhythms Neurospora

BIOMD0000000300: Schmierer2010 FIH Ankyrins

BIOMD0000000301: Friedland2009 Ara RTC3 counter

BIOMD0000000302: Wang1996 Synaptic Inhibition Two Neuron

BIOMD0000000303: Liu2011 Complement System

BIOMD0000000304: Plant1981 BurstingNerveCells

BIOMD0000000305: Kolomeisky2003 MyosinV Processivity

BIOMD0000000306: Tyson2003 Activator Inhibitor

BIOMD0000000307: Tyson2003 Substrate Depletion Osc

BIOMD0000000308: Tyson2003 NegFB Oscillator

BIOMD0000000309: Tyson2003 NegFB Homeostasis

BIOMD0000000310: Tyson2003 Mutual Inhibition

BIOMD0000000311: Tyson2003 Mutual Activation

BIOMD0000000312: Tyson2003 Perfect Adaption

BIOMD0000000313: Raia2010 IL13 Signalling MedB1

BIOMD0000000314: Raia2011 IL13 L1236

BIOMD0000000315: Montagne2011 Oligator optimised

BIOMD0000000316: Shen-Orr2002 FeedForward AND gate

BIOMD0000000317: Shen-Orr2002 Single Input Module

BIOMD0000000318: Yao2008 Rb E2F Switch

BIOMD0000000319: Decroly1982 Enzymatic Oscillator

BIOMD0000000320: Grange2001 - PK interaction of L-dopa and benserazide

BIOMD0000000321: Grange2001 - L Dopa PK model

BIOMD0000000322: Kim2011 Oscillator SimpleI

BIOMD0000000323: Kim2011 Oscillator SimpleIII

BIOMD0000000324: Morris1981 MuscleFibre Voltage full

BIOMD0000000325: Palini2011 Minimal 2 Feedback Model

BIOMD0000000326: DellOrco2009 phototransduction

BIOMD0000000327: Whitcomb2004 Bicarbonate Pancreas

BIOMD0000000328: Bucher2011 Atorvastatin Metabolism

BIOMD0000000329: Kummer2000 - Oscillations in Calcium Signalling

BIOMD0000000330: Larsen2004 CalciumSpiking

BIOMD0000000331: Larsen2004 CalciumSpiking EnzymeBinding

BIOMD0000000332: Bungay2006 Plasma

BIOMD0000000333: Bungay2006 FollicularFluid

BIOMD0000000334: Bungay2003 Thrombin Generation

BIOMD0000000335: Hockin2002 BloodCoagulation

BIOMD0000000336: Jones1994 BloodCoagulation

BIOMD0000000337: Pfeiffer2001 ATP-ProducingPathways CooperationCompetition

BIOMD0000000338: Wajima2009 BloodCoagulation aPTTtest

BIOMD0000000339: Wajima2009 BloodCoagulation PTtest

BIOMD0000000340: Wajima2009 BloodCoagulation warfarin heparin

BIOMD0000000341: Topp2000 BetaCellMass Diabetes

BIOMD0000000342: Zi2011 TGF-beta Pathway

BIOMD0000000343: Brannmark2010 InsulinSignalling Mifamodel

BIOMD0000000344: Proctor2011 ProteinHomeostasis NormalCondition

BIOMD0000000345: Koschorreck2008 InsulinClearance

BIOMD0000000346: FitzHugh1961 NerveMembrane

BIOMD0000000347: Bachmann2011 JAK2-STAT5 FeedbackControl

BIOMD0000000348: Fridlyand2010 GlucoseSensitivity A

BIOMD0000000349: Fridlyand2010 GlucoseSensitivity B

BIOMD0000000350: Troein2011 ClockCircuit OstreococcusTauri

BIOMD0000000351: Vernoux2011 AuxinSignaling AuxinSingleStepInput

BIOMD0000000352: Vernoux2011 AuxinSignaling AuxinFluctuating

BIOMD0000000353: Nag2011 ChloroplasticStarchDegradation

BIOMD0000000354: Abell2011 CalciumSignaling WithoutAdaptation

BIOMD0000000355: Abell2011 CalciumSignaling WithAdaptation

BIOMD0000000356: Nyman2011 M3Hierarachical InsulinGlucosedynamics

BIOMD0000000357: Lee2010 ThrombinActivation OneForm reduced

BIOMD0000000358: Stortelder1997 - Thrombin Generation Amidolytic Activity

BIOMD0000000359: Panteleev2002 TFPImechanism schmema3

BIOMD0000000360: Panteleev2002 TFPImechanism schmema2

BIOMD0000000361: Panteleev2002 TFPImechanism schmema1

BIOMD0000000362: Butenas2004 BloodCoagulation

BIOMD0000000363: Lee2010 ThrombinActivation OneForm minimal

BIOMD0000000364: Lee2010 ThrombinActivation OneForm

BIOMD0000000365: Hockin1999 BloodCoagulation VaInactivation

BIOMD0000000366: Orfao2008 ThrombinGeneration AmidolyticActivity

BIOMD0000000367: Muller2008 treshold minimal

BIOMD0000000368: Beltrami1995 ThrombinGeneration C

BIOMD0000000369: Beltrami1995 ThrombinGeneration D

BIOMD0000000370: Vinod2011 MitoticExit

BIOMD0000000371: DeVries2000 PancreaticBetaCells InsulinSecretion

BIOMD0000000372: Tolic2000 InsulinGlucoseFeedback

BIOMD0000000373: Bertram2004 PancreaticBetaCell modelB

BIOMD0000000374: Bertram1995 PancreaticBetaCell CRAC

BIOMD0000000375: Mears1997 CRAC PancreaticBetaCells

BIOMD0000000376: Bertram2007 IsletCell Oscillations

BIOMD0000000377: Bertram2000 PancreaticBetaCells Oscillations

BIOMD0000000378: Chay1997 CalciumConcentration

BIOMD0000000379: DallaMan2007 MealModel GlucoseInsulinSystem

BIOMD0000000380: Smallbone2011 TrehaloseBiosynthesis

BIOMD0000000381: Maree2006 DuCa Type1DiabetesModel

BIOMD0000000382: Sturis1991 InsulinGlucoseModel UltradianOscillation

BIOMD0000000383: Arnold2011 Farquhar1980 RuBisCO-CalvinCycle

BIOMD0000000384: Arnold2011 Medlyn2002 RuBisCO-CalvinCycle

BIOMD0000000385: Arnold2011 Schultz2003 RuBisCO-CalvinCycle

BIOMD0000000386: Arnold2011 Sharkey2007 RuBisCO-CalvinCycle

BIOMD0000000387: Arnold2011 Damour2007 RuBisCO-CalvinCycle

BIOMD0000000388: Arnold2011 Zhu2009 CalvinCycle

BIOMD0000000389: Arnold2011 Hahn1986 CalvinCycle Starch Sucrose

BIOMD0000000390: Arnold2011 Giersch1990 CalvinCycle

BIOMD0000000391: Arnold2011 Poolman2000 CalvinCycle Starch

BIOMD0000000392: Arnold2011 Laisk2006 CalvinCycle Starch Sucrose

BIOMD0000000393: Arnold2011 Zhu2007 CalvinCycle Starch Sucrose Photorespiration

BIOMD0000000394: Sivakumar2011 - EGF Receptor Signaling Pathway

BIOMD0000000395: Sivakumar2011 - Hedgehog Signaling Pathway

BIOMD0000000396: Sivakumar2011 - Notch Signaling Pathway

BIOMD0000000397: Sivakumar2011 WntSignalingPathway

BIOMD0000000398: Sivakumar2011 NeuralStemCellDifferentiation Crosstalk

BIOMD0000000399: Jenkinson2011 EGF MAPK

BIOMD0000000400: Cooling2007 IP3transients CardiacMyocyte

BIOMD0000000401: Ayati2010 BoneRemodelingDynamics NormalCondition

BIOMD0000000402: Ayati2010 BoneRemodelingDynamics WithTumour

BIOMD0000000403: Ayati2010 BoneRemodelingDynamics WithTumour+DrugTreatment

BIOMD0000000404: Bray1993 chemotaxis

BIOMD0000000405: Cookson2011 EnzymaticQueueingCoupling

BIOMD0000000406: Moriya2011 CellCycle FissionYeast

BIOMD0000000407: Schliemann2011 TNF ProAntiApoptosis

BIOMD0000000408: Hettling2011 CreatineKinase

BIOMD0000000409: Queralt2006 MitoticExit Cdc55DownregulationBySeparase

BIOMD0000000410: Wegner2012 TGFbetaSignalling FeedbackLoops

BIOMD0000000411: Heiland2012 CircadianClock C.reinhardtii

BIOMD0000000412: Pokhilko2012 CircClock RepressilatorFeedbackloop

BIOMD0000000413: Band2012 DII-Venus FullModel

BIOMD0000000414: Band2012 DII-Venus ReducedModel

BIOMD0000000415: Mellor2012 LipooxygenasePathway

BIOMD0000000416: Muraro2011 Cytokinin-Auxin CrossRegulation

BIOMD0000000417: Ratushny2012 NF

BIOMD0000000418: Ratushny2012 SPF

BIOMD0000000419: Ratushny2012 SPF I

BIOMD0000000420: Ratushny2012 ASSURE I

BIOMD0000000421: Ratushny2012 ASSURE II

BIOMD0000000422: Middleton2012 GibberellinSignalling

BIOMD0000000423: Nyman2012 InsulinSignalling

BIOMD0000000424: Faratian2009 - Role of PTEN in Trastuzumab resistance

BIOMD0000000425: Tan2012 - Antibiotic Treatment, Inoculum Effect

BIOMD0000000426: Mosca2012 - Central Carbon Metabolism Regulated by AKT

BIOMD0000000427: Bianconi2012 - EGFR and IGF1R pathway in lung cancer

BIOMD0000000428: Achcar2012 - Glycolysis in bloodstream form T. brucei

BIOMD0000000429: Schaber2012 - Hog pathway in yeast

BIOMD0000000430: Sarma2012 - Interaction topologies of MAPK cascade (M4 K2 USEQ)

BIOMD0000000431: Sarma2012 - Interaction topologies of MAPK cascade (M4 K2 PSEQ)

BIOMD0000000432: Sarma2012 - Interaction topologies of MAPK cascade (M4 K2 QSS USEQ)

BIOMD0000000433: Sarma2012 - Interaction topologies of MAPK cascade (M4 K2 QSS PSEQ)

BIOMD0000000434: McAuley2012 - Whole-body Cholesterol Metabolism

BIOMD0000000435: deBack2012 - Lineage Specification in Pancreas Development

BIOMD0000000436: Gupta2009 - Eicosanoid Metabolism

BIOMD0000000437: Tseng2012 - Circadian clock of N.crassa

BIOMD0000000438: Saeidi2012 - Quorum sensing device that produces GFP

BIOMD0000000439: Smith2009 - RGS mediated GTP hydrolysis

BIOMD0000000440: Sarma2012 - Oscillations in MAPK cascade (S1)

BIOMD0000000441: Sarma2012 - Oscillations in MAPK cascade (S2)

BIOMD0000000442: Sarma2012 - Oscillations in MAPK cascade (S2), inclusion of external signalling module

BIOMD0000000443: Sarma2012 - Oscillations in MAPK cascade (S1n)

BIOMD0000000444: Sarma2012 - Oscillations in MAPK cascade (S2n)

BIOMD0000000445: Pokhilko2013 - TOC1 signalling in Arabidopsis circadian clock

BIOMD0000000446: Erguler2013 - Unfolded protein stress response

BIOMD0000000447: Venkatraman2012 - Interplay between PLS and TSP1 in TGF-β1 activation

BIOMD0000000448: Brännmark2013 - Insulin signalling in human adipocytes (normal condition)

BIOMD0000000449: Brännmark2013 - Insulin signalling in human adipocytes (diabetic condition)

BIOMD0000000450: Reyes-Palomares2012 - a combined model hepatic polyamine and sulfur aminoacid metabolism - version2

BIOMD0000000451: Carbo2013 - Cytokine driven CD4+ T Cell differentiation and phenotype plasticity

BIOMD0000000452: Bidkhori2012 - normal EGFR signalling

BIOMD0000000453: Bidkhori2012 - EGFR signalling in NSCLC

BIOMD0000000454: Smallbone2013 - Metabolic Control Analysis - Example 1

BIOMD0000000455: Smallbone2013 - Metabolic Control Analysis - Example 2

BIOMD0000000456: Smallbone2013 - Metabolic Control Analysis - Example 3

BIOMD0000000457: Firczuk2013 - Eukaryotic mRNA translation machinery

BIOMD0000000458: Smallbone2013 - Serine biosynthesis

BIOMD0000000459: Liebal2012 - B.subtilis post-transcriptional instability model

BIOMD0000000460: Liebal2012 - B.subtilis sigB proteolysis model

BIOMD0000000461: Liebal2012 - B.subtilis transcription inhibition model

BIOMD0000000462: Proctor2012 - Role of Amyloid-beta dimers in aggregation formation

BIOMD0000000463: Heldt2012 - Influenza Virus Replication

BIOMD0000000464: Koo2013 - Shear stress induced calcium influx and eNOS activation - Model 1

BIOMD0000000465: Koo2013 - Shear stress induced AKT and eNOS phosphorylation - Model 2

BIOMD0000000466: Koo2013 - Shear stress induced eNOS expression - Model 3

BIOMD0000000467: Koo2013 - Shear stress induced NO production - Model 4

BIOMD0000000468: Koo2013 - Integrated shear stress induced NO production model

BIOMD0000000469: Smallbone2013 - E.coli metabolic model with linlog rate law

BIOMD0000000470: Smallbone2013 - E.coli metabolic model with modular rate law

BIOMD0000000471: Smallbone2013 - Yeast metabolic model with linlog rate law

BIOMD0000000472: Smallbone2013 - Yeast metabolic model with modular rate law

BIOMD0000000473: Smallbone2013 - Yeast metabolic model with modular rate law, merged with Pritchard 2002

BIOMD0000000474: Smith2013 - Regulation of Insulin Signalling by Oxidative Stress

BIOMD0000000475: Amara2013 - PCNA ubiquitylation in the activation of PRR pathway

BIOMD0000000476: Adams2012 - Locke2006 Circadian Rhythm model refined with Input Signal Light Function

BIOMD0000000477: Mol2013 - Immune Signal Transduction in Leishmaniasis

BIOMD0000000478: Besozzi2012 - Oscillatory regimes in the Ras/cAMP/PKA pathway in S.cerevisiae

BIOMD0000000479: Croft2013 - GPCR-RGS interaction that compartmentalizes RGS activity

BIOMD0000000480: Carbo2013 - Mucosal Immune Response during H.pylori Infection

BIOMD0000000481: Stötzel2012 - Bovine estrous cycle, synchronization with prostaglandin F2α

BIOMD0000000482: Noguchi2013 - Insulin dependent glucose metabolism

BIOMD0000000483: Cao2008 - Network of a toggle switch

BIOMD0000000484: Cao2013 - Application of ABSIS method in birth-death process

BIOMD0000000485: Cao2013 - Application of ABSIS method in the bistable Schlögl model

BIOMD0000000486: Cao2013 - Application of ABSIS method in the reversible isomerization model

BIOMD0000000487: Cao2013 - Application of ABSIS in the the enzymatic futile cycle

BIOMD0000000488: Proctor2013 - Effect of Aβ immunisation in Alzheimer's disease

BIOMD0000000489: Sharp2013 - Lipopolysaccharide induced NFkB activation

BIOMD0000000490: Demin2013 - PKPD behaviour - 5-Lipoxygenase inhibitors

BIOMD0000000491: Pathak2013 - MAPK activation in response to various abiotic stresses

BIOMD0000000492: Pathak2013 - MAPK activation in response to various biotic stresses

BIOMD0000000493: Schittler2010 - Cell fate of progenitor cells, osteoblasts or chondrocytes

BIOMD0000000494: Roblitz2013 - Menstrual Cycle following GnRH analogue administration

BIOMD0000000495: Sen2013 - Phospholipid Synthesis in P.knowlesi

BIOMD0000000496: Stanford2013 - Kinetic model of yeast metabolic network (standard)

BIOMD0000000497: Stanford2013 - Kinetic model of yeast metabolic network (regulation)

BIOMD0000000498: Mitchell2013 - Liver Iron Metabolism

BIOMD0000000499: Vizan2013 - TGF pathway long term signaling

BIOMD0000000500: Begitt2014 - STAT1 cooperative DNA binding - single GAS polymer model

BIOMD0000000501: Begitt2014 - STAT1 cooperative DNA binding - double GAS polymer model

BIOMD0000000502: Messiha2013 - Pentose phosphate pathway model

BIOMD0000000503: Messiha2013 - combined glycolysis and pentose phosphate pathway model

BIOMD0000000504: Proctor2013 - Cartilage breakdown, interventions to reduce collagen release

BIOMD0000000505: vanEunen2013 - Network dynamics of fatty acid β-oxidation (steady-state model)

BIOMD0000000506: vanEunen2013 - Network dynamics of fatty acid β-oxidation (time-course model)

BIOMD0000000507: Gardner2000 - genetic toggle switch in E.coli

BIOMD0000000508: Barrack2014 - Calcium/cell cycle coupling - Cyclin D dependent ATP release

BIOMD0000000509: Barrack2014 - Calcium/cell cycle coupling - Rs dependent ATP release

BIOMD0000000510: Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL C (with glucosomal ribokinase)

BIOMD0000000511: Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL D (with ATP:ADP antiporter)

BIOMD0000000512: Benson2014 - FAAH inhibitors for the treatment of osteoarthritic pain

BIOMD0000000513: Kerkhoven2013 - Glycolysis in T.brucei - MODEL A

BIOMD0000000514: Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL B

BIOMD0000000515: Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL C in fructose medium (with glucosomal ribokinase)

BIOMD0000000516: Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL D in fructose medium (with ATP:ADP antiporter)

BIOMD0000000517: Smallbone2013 - Colon Crypt cycle - Version 3

BIOMD0000000518: Smallbone2013 - Colon Crypt cycle - Version 2

BIOMD0000000519: Smallbone2013 - Colon Crypt cycle - Version 1

BIOMD0000000520: Smallbone2013 - Colon Crypt cycle - Version 0

BIOMD0000000521: Ribba2012 - Low-grade gliomas, tumour growth inhibition model

BIOMD0000000522: Muraro2014 - Vascular patterning in Arabidopsis roots

BIOMD0000000523: Kallenberger2014 - CD95L induced apoptosis initiated by caspase-8, CD95 HeLa cells (cis/trans variant)

BIOMD0000000524: Kallenberger2014 - CD95L induced apoptosis initiated by caspase-8, wild-type HeLa cells (cis/trans variant)

BIOMD0000000525: Kallenberger2014 - CD95L induced apoptosis initiated by caspase-8, CD95 HeLa cells (cis/trans-cis/trans variant)

BIOMD0000000526: Kallenberger2014 - CD95L induced apoptosis initiated by caspase-8, wild-type HeLa cells (cis/trans-cis/trans variant)

BIOMD0000000527: Kaiser2014 - Salmonella persistence after ciprofloxacin treatment

BIOMD0000000528: Fribourg2014 - Dynamics of viral antagonism and innate immune response (H1N1 influenza A virus - Cal/09)

BIOMD0000000529: Fribourg2014 - Dynamics of viral antagonism and innate immune response (H1N1 influenza A virus - NC/99)

BIOMD0000000530: Schmitz2014 - RNA triplex formation

BIOMD0000000531: Crespo2012 - Kinetics of Amyloid Fibril Formation

BIOMD0000000532: Vazquez2014 - Chemical inhibition from amyloid protein aggregation kinetics

BIOMD0000000533: Steckmann2012 - Amyloid beta-protein fibrillogenesis (kinetics of secondary structure conversion)

BIOMD0000000534: Dwivedi2014 - Healthy Volunteer IL6 Model

BIOMD0000000535: Dwivedi2014 - Crohns IL6 Disease model - Anti-IL6 Antibody

BIOMD0000000536: Dwivedi2014 - Crohns IL6 Disease model - sgp130 activity

BIOMD0000000537: Dwivedi2014 - Crohns IL6 Disease model - Anti-IL6R Antibody

BIOMD0000000538: Clarke2000 - One-hit model of cell death in neuronal degenerations

BIOMD0000000539: François2005 - Mixed Feedback Loop (two-gene network)

BIOMD0000000540: Yugi2014 - Insulin induced signalling (PFKL phosphorylation) - model 1

BIOMD0000000541: Yugi2014 - Insulin induced signalling (PFKL phosphorylation) - model 2

BIOMD0000000542: Yuraszeck2010 - Vulnerabilities in the Tau Network in Tau Pathophysiology

BIOMD0000000543: Qi2013 - IL-6 and IFN crosstalk model (non-competitive)

BIOMD0000000544: Qi2013 - IL-6 and IFN crosstalk model

BIOMD0000000545: Ouyang2014 - photomorphogenic UV-B signalling network

BIOMD0000000546: Miao2010 - Innate and adaptive immune responses to primary Influenza A Virus infection

BIOMD0000000547: Talemi2014 - Arsenic toxicity and detoxification mechanisms in yeast

BIOMD0000000548: Sneppen2009 - Modeling proteasome dynamics in Parkinson's disease

BIOMD0000000549: Baker2013 - Cytokine Mediated Inflammation in Rheumatoid Arthritis - Age Dependant

BIOMD0000000550: Baker2013 - Cytokine Mediated Inflammation in Rheumatoid Arthritis

BIOMD0000000551: Das2010 - Effect of a gamma-secretase inhibitor on Amyloid-beta dynamics

BIOMD0000000552: Ehrenstein2000 - Positive-Feedback model for the loss of acetylcholine in Alzheimer's disease

BIOMD0000000553: Ehrenstein1997 - The choline-leakage hypothesis in Alzheimer's disease

BIOMD0000000554: Cloutier2009 - Brain Energy Metabolism

BIOMD0000000555: Auer2010 - Correlation between lag time and aggregation rate in protein aggregation

BIOMD0000000556: Ortega2013 - Interplay between secretases determines biphasic amyloid-beta level

BIOMD0000000557: Reiterer2013 - pseudophosphatase STYX role in ERK signalling

BIOMD0000000558: Cloutier2012 - Feedback motif for Parkinson's disease

BIOMD0000000559: Ouzounoglou2014 - Modeling of alpha-synuclein effects on neuronal homeostasis

BIOMD0000000560: Hui2014 - Age-related changes in articular cartilage

BIOMD0000000561: Martins2013 - True and apparent inhibition of amyloid fribril formation

BIOMD0000000562: Chaouiya2013 - EGF and TNFalpha mediated signalling pathway

BIOMD0000000563: Pritchard2014 - plant-microbe interaction

BIOMD0000000564: Gould2013 - Temperature Sensitive Circadian Clock

BIOMD0000000565: Machado2014 - Curcumin production pathway in Escherichia coli

BIOMD0000000566: Morris2008 - Fitting protein aggregation data via F-W 2-step mechanism

BIOMD0000000567: Morris2009 - α-Synuclein aggregation variable temperature and pH

BIOMD0000000568: Mueller2015 - Hepatocyte proliferation, T160 phosphorylation of CDK2

BIOMD0000000569: Dutta-Roy2015 - Opening of the multiple AMPA receptor conductance states

BIOMD0000000570: Aubert2002 - Coupling between Brain electrical activity, Metabolism and Hemodynamics

BIOMD0000000571: Nishio2008 - Design of the phosphotransferase system for enhanced glucose uptake in E. coli.

BIOMD0000000572: Costa2014 - Computational Model of L. lactis Metabolism

BIOMD0000000573: Aguilera 2014 - HIV latency. Interaction between HIV proteins and immune response

BIOMD0000000574: Lai2014 - Hemiconcerted MWC model of intact calmodulin with two targets

BIOMD0000000575: Sass2009 - Approach to an α-synuclein-based BST model of Parkinson's disease

Model development and archiving support at physiome.org provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.