James C. Schaff

According to our database, James C. Schaff authored at least 21 papers between 1998 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

SBML level 3 package: spatial processes, version 1, release 1.

James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith

J. Integr. Bioinform., March, 2023

2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

Nucleic Acids Res., 2022

2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.

Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang

J. Integr. Bioinform., 2019

2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson

J. Integr. Bioinform., 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson

J. Integr. Bioinform., 2018

2016

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.

James C. Schaff, Fei Gao, Li Ye, Igor L. Novak, Boris M. Slepchenko

PLoS Comput. Biol., 2016

Rule-based modeling with Virtual Cell.

James C. Schaff, Dan Vasilescu, Ion I. Moraru, Leslie M. Loew, Michael L. Blinov

Bioinform., 2016

2015

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson

J. Integr. Bioinform., 2015

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson

J. Integr. Bioinform., 2015

WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration.

Anthony Santella, Raúl Catena, Ismar Kovacevic, Pavak K. Shah, Zidong Yu, Javier Marquina-Solis, Abhishek Kumar, Yicong Wu, James C. Schaff, Daniel Colón-Ramos, Hari Shroff, William Mohler, Zhirong Bao

BMC Bioinform., 2015

2014

Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling.

Michael L. Blinov, James C. Schaff, Oliver Ruebenacker, Xintao Wei, Dan Vasilescu, Fei Gao, Frank Morgan, Li Ye, Anuradha Lakshminarayana, Ion I. Moraru, Leslie M. Loew

Bioinform., 2014

2011

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.

Sherry-Ann Brown, Ion I. Moraru, James C. Schaff, Leslie M. Loew

J. Comput. Neurosci., 2011

2010

Modeling without Borders: Creating and Annotating VCell Models Using the Web.

Michael L. Blinov, Oliver Ruebenacker, James C. Schaff, Ion I. Moraru

Proceedings of the Bioinformatics Research and Applications, 6th International Symposium, 2010

2007

Diffusion on a curved surface coupled to diffusion in the volume: Application to cell biology.

Igor L. Novak, Fei Gao, Yung-Sze Choi, Diana Resasco, James C. Schaff, Boris M. Slepchenko

J. Comput. Phys., 2007

Kinetic Modeling Using BioPAX Ontology.

Oliver Ruebenacker, Ion I. Moraru, James C. Schaff, Michael L. Blinov

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007

2006

Think simulation - think experiment: the virtual cell paradigm.

Ion I. Moraru, James C. Schaff, Leslie M. Loew

Proceedings of the Winter Simulation Conference WSC 2006, 2006

2003

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang

Bioinform., 2003

1999

The Virtual Cell.

James C. Schaff, Leslie M. Loew

Proceedings of the 4th Pacific Symposium on Biocomputing, 1999

A Distributed Architecture for a General Cellular Modeling and Simulation Framework.

James C. Schaff

Proceedings of the 12th IEEE Symposium on Computer-Based Medical Systems (CBMS '99). 18-20 June 1999, 1999

Ultrasound Image Deconvolution Using Adaptive Inverse Filtering.

M. A. Sapia, Leslie M. Loew, M. D. Fox, James C. Schaff

Proceedings of the 12th IEEE Symposium on Computer-Based Medical Systems (CBMS '99). 18-20 June 1999, 1999

1998

Virtual Cell: A General Framework for Simulating and Visualizing Cellular Physiology.

Dong-Guk Shin, Lei Liu, Leslie M. Loew, James C. Schaff

Proceedings of the Visual Database Systems 4 (VDB4), 1998