Jonathan R. Karr

According to our database, Jonathan R. Karr authored at least 23 papers between 2008 and 2024.

Collaborative distances:

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

2024

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.

Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König

J. Integr. Bioinform., 2024

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

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, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, 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, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

CoRR, 2022

2021

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.

Bilal Shaikh, Gnaneswara Marupilla, Mike Wilson, Michael L. Blinov, Ion I. Moraru, Jonathan R. Karr

Nucleic Acids Res., 2021

Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior.

Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh, Jonathan R. Karr

Nucleic Acids Res., 2021

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.

Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König

J. Integr. Bioinform., 2021

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.

Andreas Dräger, Tomás Helikar, Matteo Barberis, Marc R. Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar

Bioinform., 2021

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling.

Alexander Mazein, Adrien Rougny, Jonathan R. Karr, Julio Saez-Rodriguez, Marek Ostaszewski, Reinhard Schneider

Briefings Bioinform., 2021

2020

DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python.

Arthur P. Goldberg, Jonathan R. Karr

J. Open Source Softw., 2020

Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks.

Arthur P. Goldberg, John A. P. Sekar, Jonathan R. Karr

CoRR, 2020

Structured spreadsheets with ObjTables enable data reuse and integration.

Jonathan R. Karr, Wolfram Liebermeister, Arthur P. Goldberg, John A. P. Sekar, Bilal Shaikh

CoRR, 2020

2016

Toward Community Standards and Software for Whole-Cell Modeling.

Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber

IEEE Trans. Biomed. Eng., 2016

Guidelines for Reproducibly Building and Simulating Systems Biology Models.

J. Kyle Medley, Arthur P. Goldberg, Jonathan R. Karr

IEEE Trans. Biomed. Eng., 2016

Toward Scalable Whole-Cell Modeling of Human Cells.

Arthur P. Goldberg, Yin Hoon Chew, Jonathan R. Karr

Proceedings of the 2016 annual ACM Conference on SIGSIM Principles of Advanced Discrete Simulation, 2016

2015

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, Simon Wilkinson, Brandon A. Allgood, Brian M. Bot, Bruce R. Hoff, Michael R. Kellen, Markus W. Covert, Gustavo A. Stolovitzky, Pablo Meyer

PLoS Comput. Biol., 2015

DREAMTools: a Python package for scoring collaborative challenges.

Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Mehmet Gönen, Steven M. Hill, Bruce R. Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Saez-Rodriguez

F1000Research, 2015

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium.

Denis Kazakiewicz, Jonathan R. Karr, Karol M. Langner, Dariusz Plewczynski

Comput. Biol. Chem., 2015

NetworkPainter: dynamic intracellular pathway animation in Cytobank.

Jonathan R. Karr, Harendra Guturu, Edward Y. Chen, Stuart L. Blair, Jonathan M. Irish, Nikesh Kotecha, Markus W. Covert

BMC Bioinform., 2015

Causal Inference in Biology Networks with Integrated Belief Propagation.

Rui Chang, Jonathan R. Karr, Eric E. Schadt

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2014

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.

Jonathan R. Karr, Nolan C. Phillips, Markus W. Covert

Database J. Biol. Databases Curation, 2014

2013

WholeCellKB: model organism databases for comprehensive whole-cell models.

Jonathan R. Karr, Jayodita C. Sanghvi, Derek N. Macklin, Abhishek Arora, Markus W. Covert

Nucleic Acids Res., 2013

WholeCellViz: data visualization for whole-cell models.

Ruby Lee, Jonathan R. Karr, Markus W. Covert

BMC Bioinform., 2013

2008

Integrating metabolic, transcriptional regulatory and signal transduction models in <i>Escherichia coli</i>.

Markus W. Covert, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr

Bioinform., 2008