The CellML model repository¶
The CellML project is a project which aims to collect and standardize models in an XML markup language. A complete list of all the models available at this site can be fount at https://models.physiomeproject.org/workspace.
For the purpose of this tutorail we have written a small utility script which allows for automatically downloading and generating gotran ode files from a cellml model
import utils
Create an instance of a CellML class which will scrape the cellml model repository and collect all the available models
cellml = utils.CellML()
List all models in the CellML repository
cellml.list_models()
['severi_fantini_charawi_difrancesco_2012',
'A 0D model of the Heart',
'A Bifurcation Analysis of Two Coupled Calcium Oscillators, Bindschadler and Sneyd 2001',
'A computational human ventricular electrophysiological model',
'A computational model of the human left-ventricular epicardial myocyte, Iyer, Mazhari, Winslow, 2004',
'A mathematical model of rat distal convoluted tubule. I. Cotransporter function in early DCT.',
'A mathematical model of the outer medullary collecting duct of the rat, A.M. Weinstein, 2000',
'A model for pacemaking in substantia nigra neurons (A simple model based on a spherical geometry)',
'A Model of Cardiac Electrical Activity Incorporating Ionic Pumps and Concentration Changes, DiFrancesco, Noble, 1985',
'A model of intracellular pH control',
'A Primer on Modular Mass Action Modelling with CellML',
'A review of cardiac cellular electrophysiology models',
'A Simplified Local Control Model of Calcium-Induced Calcium Release in Cardiac Ventricular Myocytes, Hinch, Greenstein, Tanskanen, Xu, Winslow, 2004',
'A single compartment model of pacemaking in dissasociated Substantia nigra neurons with hyperbolic tetrahedral geometry',
'A Thermodynamic Model of the Cardiac Sarcoplasmic/Endoplasmic Ca(2+) (SERCA) Pump, Kenneth Tran, Nicolas P. Smith, Denis S. Loiselle, and Edmund J. Crampin, 2009',
'ABI Comfort Simulator',
'Acid-Base Physiology',
'Activation of spaK',
'Activation of spaR',
'Activation of the Liver Glycogen Phosphorylase by Ca2+ Oscillations: a Theoretical Study',
'Adrian, Chandler, Hodgkin, 1970',
'Aguda, B, 1999',
'Aguda, Tang, 1999',
'Al Abed, Guo, Lovell, Dokos, 2013 (Generic Cardiac Ionic Models)',
'Albert, Haanstra, Hannaert, Van Roy, Opperdoes, Bakker and Michels, 2005',
'Albrecht, Colegrove, Friel, 2002',
'Albrecht, Colegrove, Hongpaisan, Pivovarova, Andrews, Friel, 2001',
'Alexander and Wahl 2010',
'Aliev & Panfilov (1996)',
'An encoding of the human ORd model by Steve Neiderer',
'An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements',
'An integrative dynamic model of brain energy metabolism using in vivo neurochemical measurements, Mathieu Cloutier, Fiachra B. Bolger, John P. Lowry and Peter Wellstead, 2009',
"Andre's Hodgkin Huxley model",
'Anion Exchanger',
'Annotation for a Symmetric Stomach Surface',
'Annotation for Human Stomach Surface',
'Aon, Cortassa, 2002',
'Approximating Sine Waves',
'Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation ',
'Aslanidi 2009',
'Aslanidi Atrial Model 2009',
'Aslanidi_etal_2010',
'Asthagiri, Lauffenburger, 2001',
'Atrial fibroblast model',
'Bacillus Chassis',
'Bagci 2006',
'Bagci 2008',
'Bakker, Mensonides, Teusink, Vanhoek, Michels, Westerhoff, 2000',
'Bakker, Michels, Opperdoes, Westerhoff, 1997',
'Barberis, Klipp, Vanoni, Alberghina, 2007',
'Bartolucci_Passini_Severi_2020',
'Basket Catheter Emulator',
'Baylor, Hollingworth, Chandler, 2002',
'Beard, 2005',
'Beeler, Reuter, 1977',
'Beeler, Reuter, 1977 uncertainty example',
'Benson 2008',
'Bental, 2006',
'Bernus, Wilders, Zemlin, Verschelde, Panfilov, 2002',
'Bertram, Arnot, Zamponi, 2002',
'Bertram, Pedersen, Luciani and Sherman 2006',
'Bertram, Previte, Sherman, Kinard, Satin, 2000',
'Bertram, Rhoads and Cimbora 2008',
'Bertram, Satin, Pedersen, Luciani, Sherman, 2007',
'Bertram, Satin, Zhang, Smolen, Sherman, 2004',
'Bertram, Sherman, 2004',
'Bertram, Smolen, Sherman, Mears, Atwater, Martin, Soria, 1995',
'Best Practice 1.0 and 1.1 Model Diagrams',
'BG Mica models',
'Bhalla, Iyengar, 1999',
'Bifurcation analysis of the regulatory modules of the mammalian G1/S transition',
'Bindschadler, Sneyd, 2001',
'Bingzheng, Zhenye, Liansong, 1990',
'Biophysical Characteristics of the Pig Kidney Na/Glucose Cotransporter SGLT2 Reveal a Common Mechanism for SGLT1 and SGLT2, Mackenzie, Loo, Panayotova-Heiermann and Wright, 1996',
'Blood HbO2 and HbCO2 Dissociation Curves',
'Body flatmap',
'Bond Graph Circulation',
'Bondarenko, Szigeti, Bett, Kim, Rasmusson, 2004',
'BondGraph Basic',
'Bonhoeffer, Rembiszewski, Ortiz, Nixon, 2000',
'Borghans 1997',
'Bornheimer et al. 2004',
'Boyett, Zhang, Garny, Holden, 2001',
'Brightman, Fell, 2000',
'Brown, Choe, Shanahan, Czeisler, 1997',
'Bueno, 2007',
'Bugbuster Promoter 1',
'Bugbuster Promoter 2',
'Bugbuster Standard Virtual Biological Machine',
'Bugenhagen 2010',
'Butera, Rinzel, Smith II 1999',
'Butera, Rinzel, Smith, 1999',
'Calzone, Thieffry, Tyson, Novak, 2007',
'Campbell, Chandra, 2006',
'Cardiovascular Circulation',
'Cardiovascular Circulation DVad',
'Cardiovascular Circulation IVad',
'Cardiovascular Circulation Systemic',
'Cardiovascular Circulation Westkessel',
'Cardiovascular Circulation Windkessel',
'Carro, Rodriguez, Laguna, Pueyo (2011)',
'Cartwright, Husain, 1986',
'Cell viability models for tissue exposed to thermal ablation temperatures.',
'CellML 2.0 testing',
'CFTR',
'Chang, Fujita, 1999',
'Chang, Fujita, 2001',
'Chang, Fujita, B, 1999',
'Chassagnole, Rais, Quentin, Fell, Mazat, 2001',
'Chauhan, Legewie, Westermark, Lorenzen and Herzel, 2008',
'Chay, 1997',
'Chay, Lee, Fan, 1995',
'Chen, Calzone, Csikasznagy, Cross, Novak, Tyson, 2004',
'Chen, Csikasz-Nagy, Gyorffy, Val, Novak, Tyson, 2000',
'Chen, Popel, 2006',
'Chen, Popel, 2007',
'Cheng, Brown, Loeb, 2000',
'Ciliberto, Novak, Tyson, 2003',
'Ciliberto, Petrus, Tyson, Sible, 2003',
'Ciliberto, Tyson, 2000',
'Clancy, Rudy, 2001',
'Clancy, Rudy, 2002',
'Cloutier 2009',
'Cloutier Wellstead 2009',
'CMISS active contraction models',
'Colegrove, Albrecht, Friel, 2000',
'Combine Archive Example',
'Computational analysis of the human sinus node action potential: model development and effects of mutations',
'Conradie, Bruggeman, Ciliberto, Csikasz-Nagy, Novak, Westerhoff and Snoep, 2010',
'Cooling, Hunter, Crampin, 2007',
'Cooling, Hunter, Crampin, 2009',
'Cooling, Hunter, Crampin, Cellml, 2008',
'Core Domains Principled Model Example',
'Corrias, Buist, 2007',
'Corrias, Buist, 2008',
'Cortassa et al (2006) ECME model',
'Cortassa, Aon, Marban, Winslow, Orourke, 2003',
'Cortassa, Aon, Winslow, Orourke, 2004',
'Costa, Holmes, Mcculloch, 2001',
'Courtemanche, Ramirez, Nattel, 1998',
'Covering a Broad Dynamic Range: Information Processing at the Erythropoietin Receptor ',
'Cronwright, Rohwer, Prior, 2002',
'Csilkasz-Nagy 2006',
'Cui, Kaandorp, 2006',
'Cui, Kaandorp, 2008',
'Cui, Kaandorp, Lloyd, 2008',
'Curien, Ravanel, Dumas, 2003',
'Dash, Bassingthwaighte, 2004',
'David Cumin PhD Model',
'Davies isAP 2012',
'Dawson, Lea, Irvine, 2003',
'Decker 2009',
'Deforming Heart',
'Degradation of Bugbuster RNA 1',
'Degradation of Bugbuster RNA 2',
'Degradation of ElectrEcoBlu RNA 1',
'Degradation of ElectrEcoBlu RNA 2',
'Degradation of GFP',
'Degradation of IC',
'Degradation of PhzM',
'Degradation of PhzS',
'Degradation of PYO',
'Degradation of spaK',
'Degradation of spaKactive ',
'Degradation of spaR',
'Degradation of spaRactive',
'Degradation of TF',
'Degradation of TFS',
'Delta-Notch Intercellular Signalling',
'Demir, Clark, Giles, 1999',
'Demir, Clark, Giles, Murphey, 1994',
'Demiray, 1981',
'Dempsher, Gann, Phair, 1984',
'Depaor, Timmons, 1986',
'Dependence of the period on the rate of protein degradation in minimal models for circadian oscillations ',
'Dephosphorylation of spaKactive',
'Dephosphorylation of spaRactive',
'Deterministic Nonperiodic Flow',
'Devries, Sherman, 2000',
'Devries, Sherman, 2001',
'Deyoung, Keizer, 1992',
'Diabetes',
'Diffusion',
'Difrancesco, Noble, 1985',
'difrancesco_noble_1985',
'Dijkstra, Neal, Beever and France, 1992',
'Dixit, Perelson, 2004',
'Dokos, Celler, Lovell, 1996',
'Dokos, Celler, Lovell, B, 1996',
'Dougherty, Wright, Yew, 2005',
'Drouhard, Roberge, 1987',
'Dumaine, Towbin, Brugada, Vatta, Nesterenko, Nesterenko, Brugada, Brugada, Antzelevitch, 1999',
'Dupont Berridge Goldbeter 1991',
'Dupont Goldbeter 1992',
'Dynamics of amino acid metabolism of primary human liver cells in 3D bioreactors',
'Earm, Noble, 1990',
'Ebihara, Johnson, 1980',
'EColi Chassis',
'Edwards, 2008',
'Edwards, 2010',
'Egli, Bertram, Sellix, Freeman, 2004',
'ElectrEcoBlu Promoter 1',
'ElectrEcoBlu Promoter 2',
'ElectrEcoBlu Standard Virtual Biological Machine',
'Elowitz, Leibler, 2000',
'EMBC 2013 Tutorial - Noble 1962 reproducibility',
'Enciso, Sontag, 2004',
'Endresen, 1996',
'Epithelial Transport',
'Eskandari, Wright, Loo 2005',
'Espinosa, 1998',
'Evans, Errington, Shelly, Feeney, Chapman, Godfrey, Smith, Chappell, 2004',
'Example bond graph models',
'Faber, Rudy, 2000',
'Faber, Rudy, 2000 and Tong, Ghouri, Taggart, 2014',
'Fall, Keizer, 2001',
'Fallon, Lauffenburger, 2000',
'Farhy, Bowers, Veldhuis, 2007',
'Faville, Pullan, Sanders, Koh, Lloyd, Smith, 2009',
'Faville, Pullan, Sanders, Smith, 2008',
'Feedback control of T-cell receptor activation',
'Fenton, Karma, 1998',
'Fenton, Karma, 2006',
'FieldML example - a simple mesh',
'Fink, Noble, Virag, Varro, Giles, 2008',
'Fink, Slepchenko, Loew, 1999',
'Fink, Slepchenko, Moraru, Watras, Schaff, Loew, 2000',
'Fitzhugh, 1961',
'Flynn, Green, Pedley, Boxer, Dearling, Watson, Boden, Begent, 2002',
'Fohlmeister, Miller, 1997',
'Formation of IC',
'Formation of PYO',
'Formation of TFS',
'Fox, Mcharg, Gilmour, 2002',
'Fridlyand, Tamarina, Philipson, 2003',
'Friel, 1995',
'Fujita, Toyoshima, Uda, Ozaki, Kubota and Kuroda 2010',
'Gall, Susa, 1999',
'Gardner, Dolnik, Collins, 1998',
'Garmendia-Torres, Goldbeter and Jacquet 2007',
'Garny, Kohl, Hunter, Boyett, Noble, 2003',
'Gasser, Ogden, Holzapfel, 2006',
'Gattoni 2016',
'Generic cat bladder scaffold',
'Generic human colon scaffold',
'Generic human heart scaffold',
'Generic human lung scaffold',
'Generic mouse colon scaffold',
'Generic mouse lung scaffold',
'Generic pig colon scaffold',
'Generic pig heart scaffold',
'Generic rat bladder scaffold',
'Generic rat heart scaffold',
'Generic rat stomach scaffold',
'Gerard and Goldbeter 2009',
'get-library',
'Gilbert, Heiner, Rosser, Fulton, Gu, Trybilo, 2007',
'Glucose Transport Model (Thorsen)',
'Glucose Uptake in Enterocyte',
'GLUT',
'Goforth, Bertram, Khan, Zhang, Sherman, Satin, 2002',
'Goldbeter 2006',
'Goldbeter Dupont Berridge 1990',
'Goldbeter, 1991',
'Goldbeter, 1995',
'Goldbeter, Gonze and Pourquie 2007',
'Goldbeter, Pourquie, 2008',
'Gonzalezheydrich, Steingard, Kohane, 1994',
'Goodwin, 1965',
'Grandi et al. 2011 Atrial Action Potential and Ca2+ Model',
'Grandi, Pasqualini and Bers, 2010',
'Grange 2001',
'Greenstein, Wu, Po, Tomaselli, Winslow, 2000',
'Gross and Hopfer, 1998',
'Gross and Hopfer, 1999',
'Grossman, Feinberg, Kuznetsov, Dimitrov, Paul, 1998',
'Guccione, Mcculloch, Waldman, 1991',
'Gupta, Aslakson, Gurbaxani, Vernon, 2007',
'Gupta, Maurya, Stephens, Dennis and Subramaniam, 2009',
'Guyton, Aldosterone, 2008',
'Guyton, Angiotensin, 2008',
'Guyton, Antidiuretic, Hormone, 2008',
'Guyton, Atrial, Natriuretic, Peptide, 2008',
'Guyton, Autonomics, 2008',
'Guyton, Capillary, Dynamics, 2008',
'Guyton, Circulatory, Dynamics, 2008',
'Guyton, Electrolytes, 2008',
'Guyton, Full cardiovascular circulation model',
'Guyton, Heart Hypertrophy or Deterioration, 2008',
'Guyton, Heart, Rate, And, Stroke, Volume, 2008',
'Guyton, Kidney, 2008',
'Guyton, Muscle, Blood, Flow, Control, 2008',
'Guyton, Muscle, Oxygen, Delivery, 2008',
'Guyton, Non, Muscle, Blood, Flow, Control, 2008',
'Guyton, Non, Muscle, Oxygen, Delivery, 2008',
'Guyton, Pulmonary, Fluid, Dynamics, 2008',
'Guyton, Pulmonary, Oxygen, Uptake, 2008',
'Guyton, Red, Cells, And, Viscosity, 2008',
'Guyton, Stress, Relaxation, 2008',
'Guyton, Thirst, Drinking, And, Salt, Appetite, 2008',
'Guyton, Volume, Receptors, 2008',
'H+-ATPase (proton pump)',
'Hai and Murphy 1988',
'Halloy, Bernard, Loussouarn, Goldbeter, 2002',
'Han 2019 - Solving a century-old conundrum underlying cardiac force-length relations',
'Harrington, 2009',
'Hatakeyama, Kimura, Naka, Kawasaki, Yumoto, Ichikawa, Kim, Saito, Saeki, Shirouzu, Yokoyama, Konagaya, 2003',
'Hatzimanikatis, Lee, Bailey, 1999',
'Haugh, 2004',
'Heart Model',
'Heinze, Keener, Midgley, 1998',
'Heldt 2002',
'Herz, Bonhoeffer, Anderson, May, Nowak, 1996',
'Heyd, Drew, 2003',
'HH Sodium Current model for estimation task',
'Hilgemann, Noble, 1987',
'Hill, 1972 - a model of feto-maternal oxygen exchange',
'Hinch, Greenstein, Tanskanen, Xu, Winslow, 2004',
'Hodgkin, Huxley, 1952',
'Hoefnagel, Starrenburg, Martens, Hugenholtz, Kleerebezem, Vanswam, Bongers, Westerhoff, Snoep, 2002',
'Holmes 2006',
'Hornberg, Binder, Bruggeman, Schoeberl, Heinrich, Westerhoff, 2005',
'Houart, Dupont and Goldbeter 1999',
'Huang, Ferrell, 1996',
'Human atrial cell models for investigating TBX5/PITX2 insufficiency-induced atrial fibrillation',
'Human Left Ventricle',
'Human Stomach Scaffold',
'Hund, Rudy, 2004',
'Hunt, Tilunaite, Bass, Soeller, Roderick, Rajagopal, Crampin',
'Hunter, Mcculloch, Terkeurs, 1998',
'Hunter, Mcnaughton, Noble, 1975',
'Hunter, Smaill, Hunter, 1995',
'Hynne, Dano, Sorensen, 2001',
'Iancu 2007',
'Iber, Maini, 2002',
'Ikeda BMadonna QKDB',
'Improvement of metabolic performance of primary hepatocytes in hyperoxic cultures by vitamin C in a novel small-scale bioreactor ',
'Inada 2009',
'Incorporation of sarcolemmal calcium transporters into the Shorten et al. (2007) model of skeletal muscle',
'Inner medullary lactate production and accumulation: a vasa recta model, S. Randall Thomas, 2000',
'Interaction of glycolysis and mitochondrial respiration in metabolic oscillations of pancreatic islets, Richard Bertram, Leslie S. Satin, Morten Gram Pedersen, Dan S. Luciani, and Arthur Sherman, 2007',
'Intercellular calcium waves mediated by diffusion of inositol trisphosphate: a two-dimensional model. J. Sneyd, B.T. Wetton, A.C. Charles and M.J. Sanderson, 1995',
'International, Si, Units, 2006',
'Interpolation field over mesh with uncertain nodal values',
'Interstitial Cell of Cajal Network Imaging Data',
'Iribe, Kohl, Noble, 2006',
'Irvine, Jafri, Winslow, 1999',
'Itskov, Ehret, Mavrilas, 2006',
'Iyer, Hajjar, Armoundas, 2007',
'Iyer, Mazhari, Winslow, 2004',
'Izakov, Katsnelson, Blyakhman, Markhasin, Shkylar, 1991',
'Jafri, Rice, Winslow, 1998',
'Jelic, Cupic, Kolaranic, 2005',
'Joseph, Zavros, Merchant, Kirschner, 2003',
'Kapela, A. Bezerianos, A. and Tsoukias, N. M. 2008',
'Karagiannis, Popel, 2004',
'Karagiannis, Popel, 2006',
'Katsnelson, Nikitina, Chemla, Solovyova, Coirault, Lecarpentier, Markhasin, 2004',
'Keener, 2001',
'Keizer, Levine, 1996',
'Kesmir, Deboer, 1999',
'Kholodenko, Demin, Moehren, Hoek, 1999',
'Kinetics of the Reverse Mode of the Na+/Glucose Cotransporter, Eskandari, Wright, Loo, 2005',
'Kirschner, Panetta, 1998',
'Kirschner, Webb, 1996',
'Kneller, Ramirez, Chartier, Courtemanche, Nattel, 2002',
'Koivumäki, Korhonen, Tavi 2011 Atrial AP model',
'Koivumaki,2009',
'Komarova 2005',
'Komarova, Smith, Dixon, Sims and Wahl, 2003',
'Komarova, Wodarz, 2003',
'Kongas, Vanbeek, 2001',
'Korzeniewski, Zoladz, 2001',
'Kroll, 2000',
'Kurata, Hisatome, Imanishi, Shibamoto, 2002',
'Kyrylov, Severyanova, Vieira, 2005',
'Lambeth, Kushmerick, 2002',
'Land et al. 2012',
'Landesberg, Sideman, 1994',
'Large Scale Left Ventricular Shape Atlas Using Automated Model Fitting to Contours',
'Latency correlates with period in a model for signal-induced Ca2+ oscillations based on Ca2+induced Ca2+ release',
'Lebeau, Robson, Mckinnon, Donald, Sneyd, 1997',
'Lebeau, Yule, Groblewski, Sneyd, 1999',
'Leloup, Goldbeter, 1998',
'Leloup, Goldbeter, 2003',
'Leloup, Goldbeter, 2004',
'Leloup, Gonze, Goldbeter, 1999',
'Lemaire, Tobin, Greller, Cho, Suva, 2004',
'Lemon, Gibson, Bennett, 2003',
'Lenbury, Pacheenburawana, 1991',
'Lenbury, Pornsawad, 2005',
'Lenbury, Ruktamatakul, Amornsamarnkul, 2001',
'Li, Bertram and Rinzel, 1996',
'Li, Kuang, Mason, 2006',
'Li, Rinzel, 1994',
'Li, Smith, 2009',
'Lindblad, Murphey, Clark, Giles, 1996',
'Linear 2nd order nonhomogeneous ODE with constant coefficients',
'Liu, Hu, Peng, Liu, 1999',
'Livshitz, Rudy, 2007',
'Lockwood, Ewy, Hermann, Holford, 2006',
'Loewe-Lutz-Fabbri-Severi human sinus node cellular electrophysiology model',
'Lokta, Volterra',
'Lovell, Cloherty, Celler, Dokos, 2004',
'Luo, Rudy, 1991',
'Luo, Rudy, 1994',
'luo_rudy_1991',
'Macgregor, Leng, 2005',
'Mackenzie, Loo, Panayotova-Heiermann and Wright, 1996',
'Magnus, Keizer, 1997',
'Magnus, Keizer, 1998',
'Mahajan, Shiferaw, Sato, Baher, Olcese, Xie, Yang, Chen, Restrepo, Karma, Garfinkel, Qu, Weiss, 2008',
'Maldonado, Borchers, Findeisen and Allgower, 2006',
'Maleckar, Greenstein, Trayanova, Giles, 2009',
'Maltsev 2009',
'Maly, Wiley, Lauffenburger, 2004',
'Malys et al. 2010',
'Marcano, Yang, Nieves-Gonzalez, Clausen, Moore 2009',
'Margaridamartins, Mendes, Coreiro, Pocesfreire, 2001',
'Marhl, Haberichter, Brumen, Heinrich, 2000',
'Marhl, Schuster, Brumen, Heinrich, 1997',
'Martinov, Vitvitsky, Mosharov, Banerjee, Ataullakhanov, 2000',
'Marwan, 2003',
'Matsuoka, Sarai, Kuratomi, Ono, Noma, 2003',
'Maurya et al. 2005',
'Mazhari, Greenstein, Winslow, Marban, Nuss, 2001',
'Mcallister, Noble, Tsien, 1975',
'McIntyre, Richardson, Grill, 2001',
'Mckenzie, Sneyd, 1998',
'Mclean, Su, Vandenbogert, 2003',
'Mears 1997',
'Mechanism of doxorubicin cardiotoxicity evaluated by integrating multiple molecular effects into a biophysical model',
'Metabolic Component Library',
'Michailova 2005',
'Michailova, Mcculloch, 2001',
'Miftakhov, Abdusheva, Christensen, 1999',
'Mijailovich, Butler, Fredburg, 2000',
'Mikane, Araki, Kohno, Nakayama, Suzuki, Shimuzi, Matsubara, Hirakawa, Takaki, Suga, 1997',
'Minimal haemodynamic system model including ventricular interaction and valve dynamics, Bram W Smith, J Geoffrey Chase, Roger I Nokes, Geoffrey M Shaw, Graeme Wake, 2004',
'Mitchell, Schaeffer, 2003',
'Mitochondria regulate the amplitude of simple and complex calcium oscillations',
'Mittler, Sulzer, Neumann, Perelson, 1998',
'Mlcek, Neumann, Kittnar, Novak, 2001',
'Model of a rabbit Purkinje cell',
'Model of skeletal muscle cramp and its reversal',
'Models for the OpenCOR and PMR tutorial by Peter Hunter',
'Modular Analysis of Signal Transduction Networks',
'Mohr, Taylor, Newell, 2008',
'Moore, Li, 2004',
'Morris and Lecar 1981',
'Mosekilde, Lading, Yanchuk, Maistrenko, 2001',
'Moss, Kazmierczak, Kirley, Harris, 2009',
'mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: A population-based simulation study',
'Muller, Obeyesekere, Mills, Ram, 2008',
'My Beeler Model',
'Myocardial contractility and regional work throughout the cardiac cycle using FEM and MRI',
'Na+/Glucose Transporter',
'Na+/H+ Exchanger',
'Na+/HCO3- Cotransporter',
'Na+/K+-ATPase (sodium-potassium pump)',
'Nagano and Gerritsen, 2001',
'Nagerl, Novo, Mody, Vergara, 2000',
'Nash, Panfilov, 2004',
'Nazaret, Heiske, Thurley and Mazat, 2009',
'Nelson, Murray, Perelson, 2000',
'Nelson, Perelson 1995',
'Neumann, Lam, Dahari, Gretch, Wiley, Layden, Perelson, 1998',
'Neurovascular Coupling',
'Nevo, Golding, Neumann, Schwartz, Akselrod, 2004',
'Ni et al. 2017 Human atrial model',
'Niederer 2013 PlosOne',
'Niederer, Hunter, Smith, 2006',
'Niederer, Smith, 2007',
'Noble 1962 model for Physiome article',
'Noble, 1962',
'Noble, 2000',
'Noble, Difrancesco, Denyer, 1989',
'Noble, Noble, 1984',
'Noble, Noble, 2001',
'Noble, Noble, Bett, Earm, Ho, So, 1991',
'Noble, Varghese, Kohl, Noble, 1998',
'Noble1998',
'Noble_Noble_1984',
'Nonlinearities make a difference: comparison of two common Hill-type models with real muscle, Siebert, Rode, Herzog, Till, Blickhan, 2008',
'Novak, Csikasznagy, Gyorffy, Chen, Tyson, 1998',
'Novak, Pataki, Ciliberto, Tyson, 2001',
'Novak, Tyson, 1993',
'Novak, Tyson, 1997',
'Novak, Tyson, 2004',
'Nowak, Bangham, 1996',
'NVC',
'Nygren, Fiset, Firek, Clark, Lindblad, Clark, Giles, 1998',
"O'Hara-Rudy-CiPA-v1.0 (2017)",
'Obeyesekere, Zimmerman, Tecarro, Auchmuty, 1999',
'Olsen, Hauser, Kummer, 2003',
'On the encoding and decoding of calcium signals in hepatocytes',
'One-pool model for Ca2+ oscillations involving Ca2+ and inositol 1,4,5-trisphosphate as co-agonists for Ca2+ release',
'Oomens, Maenhout, Vanoijen, Drost, Baaijens, 2003',
'OpenCOR',
'OpenCOR issue 231',
'OpenCOR issue 458',
'OpenCOR issue demonstration - initial_value',
'Optimal velocity and safety of discontinuous conduction through the heterogeneous Purkinje-ventricular junction, Oleg V. Aslanidi, Philip Stewart, Mark R. Boyett and Henggui Zhang, 2009',
'Ostby, Oyehaug, Einevoll, Nagelhus, Plahte, Zeuthen, Voipio, Lloyd, Ottersen, Omholt, 2008',
'Overgaard 2007',
'Oyehaug, Ostby, Lloyd, Omholt, Einevoll, 2011',
'Oyehaug, Ostby, Lloyd, Ottersen, Omholt, Einevoll, 2009',
'paci_hyttinen_aaltosetala_severi_2013',
'Palecek, Horwitz, Lauffenburger, 1999',
'Pandit, Clark, Giles, Demir, 2001',
'Pandit, Giles, Demir, 2003',
'Panerai, 1980',
'Parent, Supplisson, Loo, Wright, 1992',
'Pasek, Simurda, Christe, 2006',
'Pasek, Simurda, Orchard, Christe, 2008',
'Passive epithelial cell transport models',
'Pedersen, Bertram, Sherman, 2005',
'Per Pixel Lighting',
'Perelson 1993',
'Perelson, Neumann, Markowitz, Leonard, Ho, 1996',
'Peterson and Riggs, 2010',
'pH control',
'pH Regulation',
'Phillips 2007',
'Phillips 2008',
'Pivonka, Zimak, Smith, Gardiner, Dunstan, Sims, Martin and Mundy, 2008',
'Plant, 1981',
'Playing with stimulus frequency and the ORd model',
'Poh, 2012',
'Potter, Greller, Cho, Nuttall, Stroup, Suva, Tobin, 2005',
'Potter, Zager, Barton, 2006',
'Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model',
'Priebe, Beuckelmann, 1998',
'Principled Model Base',
'Proctor, 2005',
'Proctor, 2007',
'Protein CDS for GFP',
'Protein CDS for PhzM',
'Protein CDS for PhzS',
'Protein CDS for spaK',
'Protein CDS for spaR',
'Protein CDS for TF ElectrEcoblu Device 1',
'Protein CDS for TF ElectrEcoblu Device 2',
'Prototype reset rules',
'Puglisi, Bers, 2001',
'Purvis, Butera, 2005',
'Purvis, Smith, Koizumi, Butera, 2007',
'Qu, Maclellan, Weiss, 2003',
'Ralser at el. 2007',
'Ramirez, Nattel, Courtemanche, 2000',
'Rangamani 2007',
'Raposo, Sobrinho and Ferreira, 2002',
'Rattananakul, Lenbury, Krishnamara, Wollkind, 2003',
'Razumova, Bukatina, Campbell, 1999',
'Razumova, Bukatina, Campbell, 2000',
'RBS for GFP',
'RBS for PhzM',
'RBS for PhzS',
'RBS for spaK',
'RBS for spaR',
'RBS for TF Electroblu Device 2',
'RBS for TF Electroblu Device 1',
'Reed, Nijhout, Sparks, Ulrich, 2004',
'Reidl, Borowski, Sensse, Starke, Zapotocky, Eiswirth, 2006',
'Renal Transport',
'Respiratory System',
'Revilla, Garcia-Ramos, 2003',
'Riccobene, Omann, Linderman, 1999',
'Rice, Jafri, Winslow, 2000',
'Rice, Wang, Bers, Detombe, 2008',
'Rice, Winslow, Hunter, 1999',
'Rice, Winslow, Jafri, 1999',
'Riemer, Sobie, Tung, 1998',
'Rivlin, Saunders, 1951',
'Rogers & McCulloch (1994)',
'Rogers, Mcculloch, 1994',
'Romond, Rustici, Gonze, Goldbeter, 1999',
'Rong, Perelson 2009',
'Roux, Noble, Noble, Marhl, 2006',
'Rubin, Shevtsova, Ermentrout, Smith and Rybak 2009',
'Sachse, Glanzel, Seemann, 2003',
'Sachse, Moreno, Abildskov, 2008',
'Saftenku, Williams, Sitsapesan, 2001',
'Sakmann, Spindler, Bryant, Linz, Noble, 2000',
'Salem, Saidel, Stanley, Cabrera, 2002',
'Sarai, Matsuoka, Kuratomi, Ono, Noma, 2003',
'Sarkar, Lauffenburger, 2003',
'Saucerman, Bers, 2008',
'Saucerman, Brunton, Michailova, Mcculloch, 2003',
'Saucerman, Mcculloch, 2004',
'Schenzle 1994',
'Schlosser, Selgrade, 2000',
'Schmid, Nash, Young, Hunter, 2006',
'Schneider, Shimayoshi, Amano, Matsuda, 2006',
'Schoeberl, Eichler-Jonsson, Gilles, Muller, 2002',
'Schuster, Beny, Meister, 2003',
'SED-ML example',
'Sedaghat, Sherman, Quon, 2002',
'Seemann, Sachse, Weib, Dossel, 2003',
'SEIR',
'semantic-annotation',
'Session Resource Workspace',
'Shannon, Wang, Puglisi, Weber, Bers, 2004',
'Shaw, Chase, Starfinger, Smith, Hann, Desaive, Ghuysen, 2007',
'Shaw, Rudy, 1997',
'Shi, Hose, 2009',
'Shiferaw, Watanabe, Garfinkel, Weiss, Karma, 2003',
'Shim 2006',
'Shorten, Ocallaghan, Davidson, Soboleva, 2007',
'Shorten, Robson, Mckinnon, Wall, 2000',
'Shorten, Wall, 2000',
'Shrestha, Hollot, Chipkin, Schmitt and Chait 2010',
'Siebert, Rode, Herzog, Till and Blickhan, 2008',
'Signalling Principled Model Example',
'Simple Growth Model ',
'Simple sine test model',
'Simulations of the effects of inositol 1,4,5=trisphosphate 3-kinase and S-phosphatase activities on Ca+ oscillations ',
'Sine-Approximations',
'Skouibine, Trayanova, Moore, 1999',
'Smith Chase 2004',
'Smith, 1980',
'Smith, Abdala, Koizumi, Rybak and Paton 2007',
'Smith, Crampin, 2004',
'Sneyd, Dufour, 2002',
'Sneyd, Tsaneva-Atanasova, Yule, Thompson, Shuttleworth, 2004',
'Sneyd, Tsanevaatanasova, Bruce, Straub, Giovannucci, Yule, 2003',
'Snyder, Palmer, Moore, 2000',
'Snyed, Wetton, Charles, Sanderson, 1995',
'Sobie, Dilly, Dossantoscruz, Lederer, Jafri, 2002',
'Soboleva, Vetharaniam, Nixon, Montenegro, Pearson, Sneyd, 2005',
'Some "test" models',
'Some test SED-ML to play with the nested proposal',
'SPARC MIS Data Model',
'Spiro, Parkinson, Othmer, 1997',
'Spronck, 2012',
'Sriram, Bernot, Kepes, 2007',
'Standard Virtual Parts Template Models v200906',
'Starbuck, Wiley, Lauffenburger, 1990',
'Steady state HMT',
'Stern, Song, Sham, Yang, Boheler, Rios, 1999',
'Stewart, Aslanidi, Noble, Noble, Boyett, Zhang, 2009',
'Sthilaire, Gronfier, Zeitzer, Klerman, 2007',
'Stilianakis, Dietz, Schenzle, 1997',
'Stomach Annotator for SPARC',
'Structural Test CellML 1.1 Models',
'Sulman et al. 2008',
'Surkis, Peskin, Tranchina, Leonard, 1998',
'Sveiczer, Csikasznagy, Gyorffy, Tyson, Novak, 2000',
'SVP Template Library',
'Swanson, True, Lin, Buhler, Vessella, Murray, 2001',
'Swat, Kel and Herzel 2004',
'Switching from Simple to Complex Oscillations in Calcium Signaling',
'Synchronized Scene Viewer',
'Tabak, Mascagni and Bertram 2010',
'Tabak, Toporikova, Freeman, Bertram, 2007',
'Takotsubo modelling, Land et al. 2014',
'Tentusscher, Noble, Noble, Panfilov, 2004',
'Tentusscher, Noble, Noble, Panfilov, 2006',
'Tentusscher, Panfilov, 2006',
'Terkildsen, Niederer, Crampin, Hunter, Smith, 2008',
'Test Area',
'Test cellml model(s) for LibOmexMeta',
'Test model for using data to control a variable value',
'Testing plugin annotation',
'Testing RDF linking across CellML, SED-ML, and SVG',
'Teusink, Passarge, Reijenga, Esgalhado, Vanderweijden, Schepper, Walsh, Bakker, Vandam, Westerhoff, Snoep, 2000',
'Tham 2008',
'The cardiac Na+ /K+ ATPase: An updated, thermodynamically consistent model',
'The Glucose-induced Switch Between Glycogen Phosphorylase and Glycogen Synthase in the Liver: Outlines of a Theoretical Approach',
'The inflection point hypothesis: The relationship between the temperature dependence of enzyme catalyzed reaction rates and microbial growth rates',
'Thomas, 2000',
'Thomsen, Neubig, 1989',
'Tolic, Mosekilde, Sturis, 2000',
'Tomida, Hirose, Takizawa, Shibasaki, Iino, 2003',
'Tong, Choi, Kharche, Holden, Zhang, Taggart, 2011',
'Tong, Tribe, Smith, Taggart, 2014',
'Topp, Promislow, Devries, Miura, Finegood, 2000',
'Tran 2010',
'Tran 2017 - Cross-bridge model of shortening heat',
'Tran, Smith, Loiselle, Crampin, 2009',
'Tutorial on Constructing a Systems Model from SVPs',
'Two compartment model of diazepam biotransformation in an organotypical culture of primary human hepatocytes',
'Tyson, 1991',
'Tyson, Hong, Thron, Novak, 1999',
'Ueda, Hagiwara, Kitano, 2001',
'Uncertain starting point parabola',
'Units',
'units import test',
'Vanbeek, 2007',
'Vancapelle, Durrer, 1980',
'Vanderpol, Vandermark, 1928',
'Vangoor, Lebeau, Krsmanovic, Sherman, Catt, Stojilkovic, 2000',
'Varela - Canine Atrial Cell Models',
'Vasalou and Henson 2010',
'Vaseghi, Baumeister, Rizzi, Reuss, 1999',
'Vempati, Karagiannis, Popel, 2007',
'Vendelin, Kongas, Saks, 2000',
'Vilar 2006',
'Vilar, Kueh, Barkai, Leibler, 2002',
'Vinnakota, Kemp and Kushmerick, 2006',
'Vinnakota, Rusk, Palmer, Shankland and Kushmerick, 2010',
'Virtual Bacterial Photography',
'Viswanathan, Shaw, Rudy, 1999',
'viswanathan_shaw_rudy_1999',
'Voigt, Heijman et al. 2013 human atrial AP model',
'Volume mesh of liver',
'VPH-MIP case study on CellML',
'Wanant, Quon, 2000',
'Wang, Cirit and Haugh 2009',
'Wang, Huang, Huang, 2006',
'Wang, Li, Kuang, 2007',
'Wang, Lin, Lin, Wu, 2008',
'Wang, Sobie, 2008',
'Warashina, Ogura, 2004',
'Warren, Tawhai, Crampin, 2009',
'Waugh, Sherratt, 2006',
'Waugh, Sherratt, 2007',
'Weak Acid Hydration',
'Webb, Sherratt, Fish, 2002',
"Wein, D'Amato, Perelson 1998",
'Weinstein 2000',
'Weinstein, 1995',
'Weinstein, 1998',
'Westermark, Lansner, 2003',
'Wierschem 2004',
'Wilkins, Sneyd, 1998',
'Winograd, Destexhe, Sanchezvives, 2008',
'Winslow, Rice, Jafri, Marban, Ororke, 1999',
'Wodarz, 2003',
'Wodarz, Hamer, 2007',
'Wodarz, Jansen, 2003',
'Wodarz, Nowak, 1999',
'Wodarz, Sierro, Klenerman, 2007',
'Wolf, Heinrich, 2000',
'Wolf, Passarge, Somsen, Snoep, Heinrich, Westerhoff, 2000',
'Wolf, Sohn, Heinrich, Kuriyama, 2001',
'Workflows for analysis of valvular and aortic disease',
'Workspace Annotations',
'Wu, Jeneson, Beard, 2006',
'Wu, Yang, Vinnakota, Beard, 2007',
'Yamaguchi, Takaki, Matsubara, Yasuhara, Suga, 1996',
'Yanagihara 1980',
'Yang, Clark, Bryan, Robertson, 2003',
'Yang, Tong, Mccarver, Hines, Beard, 2006',
'Yasumura, Suga, 1988',
'Yates, Stark, Klein, Antia, Callard, 2007',
'Yi, Fogelson, Keener, Peskin, 2003',
'Youm, Kim, Han, Kim, Joo, Leem, Goto, Noma, Earm, 2006',
'Zager, Schlosser, Tran, 2007',
'Zeng, Laurita, Rosenbaum, Rudy, 1995',
'Zhang, Holden, Kodama, Honjo, Lei, Varghese, Boyett, 2000',
'Zinc/JSON resources']
List only the models that contains the name tentusscher
cellml.list_models(name="tentusscher")
['Tentusscher, Noble, Noble, Panfilov, 2004',
'Tentusscher, Noble, Noble, Panfilov, 2006',
'Tentusscher, Panfilov, 2006']
List the cellml models that are stored locally
utils.list_cellml_models()
{'tentusscher_noble_noble_panfilov_2006': ['tentusscher_noble_noble_panfilov_2006_c.cellml']}
Download the model Tentusscher, Noble, Noble, Panfilov, 2006
cellml.download_model("Tentusscher, Noble, Noble, Panfilov, 2006", overwrite=True)
Download model Tentusscher, Noble, Noble, Panfilov, 2006 for https://models.physiomeproject.org/workspace/tentusscher_noble_noble_panfilov_2006 to /home/runner/work/heart_cells_in_action/heart_cells_in_action/models/cellml/tentusscher_noble_noble_panfilov_2006
List the cellml models that are stored locally again and see that we now have a new model available
utils.list_cellml_models()
{'tentusscher_noble_noble_panfilov_2006': ['tentusscher_noble_noble_panfilov_2006_c.cellml']}
List all the local gotran ode files
utils.list_ode_models()
['tentusscher_noble_noble_panfilov_2006_c.ode']
Generate a gotran ode file from the newly downloaded cellml model
utils.cellml2gotran('tentusscher_noble_noble_panfilov_2006', 'tentusscher_noble_noble_panfilov_2006_c.cellml')
List all the local gotran ode files again and see that it has been updated
utils.list_ode_models()
['tentusscher_noble_noble_panfilov_2006_c.ode']