Workspaces

The list of model workspaces.

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
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
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
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, 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, 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
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, 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
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 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
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
Vasalou and Henson 2010
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
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, 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, 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 and Robertson 2005
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