Workspaces

The list of model workspaces.

Human Stomach Scaffold
Human whole-body scaffold
Human whole-body scaffold with embedded organs
Human whole-body with embedded organs using automatic workflow for inserting the organs
HUMERUS
Hund, Rudy, 2004
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
ICC_Lees_Green_2014
Ikeda BMadonna QKDB
Ikeda BMadonna QKDB
Improvement of metabolic performance of primary hepatocytes in hyperoxic cultures by vitamin C in a novel small-scale bioreactor
Imtiaz_IP3_2002
Inada 2009
Incorporation of sarcolemmal calcium transporters into the Shorten et al. (2007) model of skeletal muscle
Infraspinatus
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
Iyer, Mazhari, Winslow, 2004
Izakov, Katsnelson, Blyakhman, Markhasin, Shkylar, 1991
Jafri, Rice, Winslow, 1998
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
Kernik et al. 2019
Kesmir, Deboer, 1999
Kholodenko, Demin, Moehren, Hoek, 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
Lees_Green_2014
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, 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
Longus Capitis
Longus Colli Inferior
Lovell, Cloherty, Celler, Dokos, 2004
Lumbrical I
Lumbrical II
Lumbrical III
Lumbrical IV
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
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
METACARPAL_I
METACARPAL_II
Michailova 2005
Michailova, Mcculloch, 2001
MIDDLE_PHALANX_II
MIDDLE_PHALANX_III
MIDDLE_PHALANX_IV
MIDDLE_PHALANX_V
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 excitation-contraction in uterine myocytes from a pregnant rat
Model of Excitation-Contraction in a uterine SMC
Model of Human Jejunal Smooth Muscle Cell Electrophysiology
Model of skeletal muscle cramp and its reversal
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
Moore, Li, 2004
Morris and Lecar 1981
Mosekilde, Lading, Yanchuk, Maistrenko, 2001
Moss, Kazmierczak, Kirley, Harris, 2009
Moss, Kazmierczak, Kirley, Harris, 2009
mouse flatmap
Mouse whole-body scaffold with embedded organs
mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: A population-based simulation study
MSK Models
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, 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
Notch signaling pathway
Novak, Csikasznagy, Gyorffy, Chen, Tyson, 1998
Novak, Pataki, Ciliberto, Tyson, 2001
Novak, Tyson, 1993
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
Opponens digiti minimi
Opponens pollicis
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
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
paci_hyttinen_aaltosetala_severi_2013
Palecek, Horwitz, Lauffenburger, 1999
Palmar interossei I
Palmar interossei II
Palmar interossei III
Palmaris brevis
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
PATELLA
Pedersen, Bertram, Sherman, 2005
Per Pixel Lighting
Perelson 1993
Perelson, Neumann, Markowitz, Leonard, Ho, 1996
Peripheral airways matlab/CellML
Peterson and Riggs, 2010
pH control
pH Regulation
Phillips 2007
Phillips 2008
Phillips 2008
pig flatmap
Pig whole-body with embedded organs using automatic workflow for inserting the organs
PISIFORM
Pivonka, Zimak, Smith, Gardiner, Dunstan, Sims, Martin and Mundy, 2008
Plant, 1981
Playing with stimulus frequency and the ORd model
Poh, 2012
Popliteus
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
Pronator quadratus
Pronator teres
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, 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
rat flatmap
rat flatmap
rat flatmap
Rat whole body scaffold
Rat whole-body scaffold with embedded organs
Rat whole-body with embedded organs using automatic workflow for inserting the organs
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
Rectus femoris
Reed, Nijhout, Sparks, Ulrich, 2004
Reidl, Borowski, Sensse, Starke, Zapotocky, Eiswirth, 2006
Renal Transport
Reproducibility of the computational model of induced pluripotent stem-cell derived cardiomyocytes
Reproducibility study of Computational modelling of glucose uptake by SGLT1 and GLUT2 in the enterocyte
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
Sampson-Iyer-Marks-Kass-2010
Sarai, Matsuoka, Kuratomi, Ono, Noma, 2003
Sarkar, Lauffenburger, 2003
Sartorius
Saucerman, Bers, 2008
Saucerman, Brunton, Michailova, Mcculloch, 2003
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
SEIR
semantic-annotation
semantic-annotation
Semimembranosus
Semitendinosus
Session Resource Workspace
SFong_saucerman2003_physiome
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
Simon-Chica et al. (2021) Novel insights into the electrophysiology of murine cardiac macrophages
Simple Growth Model
Simple sine test model
Simulation of the effects of extracellular calcium changes leads to a novel computational model of human ventricular action potential with a revised calcium handling
Simulations of the effects of inositol 1,4,5=trisphosphate 3-kinase and S-phosphatase activities on Ca+ oscillations
Sine-Approximations
SinglePASMC
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
Sneyd_2016
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
Sternohyoideus
Stewart, Aslanidi, Noble, Noble, Boyett, Zhang, 2009
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
Subscapularis
Sulman et al. 2008
Supinator
Supraspinatus
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, Mascagni and Bertram 2010
Tabak, Toporikova, Freeman, Bertram, 2007
Takotsubo modelling, Land et al. 2014
Temporalis Left
Temporalis Right
Tentusscher, Noble, Noble, Panfilov, 2004
Tentusscher, Noble, Noble, Panfilov, 2004
Tentusscher, Noble, Noble, Panfilov, 2006
Tentusscher, Panfilov, 2006
Tentusscher, Panfilov, 2006
Teres major
Teres minor
Terkildsen, Niederer, Crampin, Hunter, Smith, 2008
Terkildsen, Niederer, Crampin, Hunter, Smith, 2008
Test
Test ApiNATOMY to flatmap connectivity
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 cardiac Na+ /K+ ATPase: An updated, thermodynamically consistent model
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
Thomas, 2000
Thomsen, Neubig, 1989
TIBIA
Tolic, Mosekilde, Sturis, 2000
Tomida, Hirose, Takizawa, Shibasaki, Iino, 2003
Tong, Choi, Kharche, Holden, Zhang, Taggart, 2011
Tong, Tribe, Smith, Taggart, 2014
Tong_2011_V1
Topp, Promislow, Devries, Miura, Finegood, 2000
Tran 2010
Tran 2017 - Cross-bridge model of shortening heat
Tran, Smith, Loiselle, Crampin, 2009
Triceps brachii
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
units_and_constants_for_BG
Vanbeek, 2007
Vancapelle, Durrer, 1980
Vanderpol, Vandermark, 1928
Vangoor, Lebeau, Krsmanovic, Sherman, Catt, Stojilkovic, 2000
Varela - Canine Atrial Cell Models
Vasalou and Henson 2010
Vasalou and Henson 2010
Vasalou and Henson 2010
Vaseghi, Baumeister, Rizzi, Reuss, 1999
Vastus Intermedius
Vastus lateralis
Vastus medialis
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
Wang, Sobie, 2008
Warashina, Ogura, 2004
Warren, Tawhai, Crampin, 2009
Waugh, Sherratt, 2006
Waugh, Sherratt, 2007
Weak Acid Hydration
Webb, Sherratt, Fish, 2002