Search Results for author: Jonathan R. Karr

Found 6 papers, 2 papers with code

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

no code implementations13 Mar 2022 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 Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matúš Kalaš, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurelien 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 S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr

To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators. org), a central registry of the capabilities of simulation tools and consistent Python, command-line, and containerized interfaces to each version of each tool.

SED-ML Validator: tool for debugging simulation experiments

2 code implementations1 Jun 2021 Bilal Shaikh, Andrew Philip Freiburger, Matthias König, Frank T. Bergmann, David P. Nickerson, Herbert M. Sauro, Michael L. Blinov, Lucian P. Smith, Ion I. Moraru, Jonathan R. Karr

To help modelers debug their simulations and to push the community to use SED-ML consistently, we developed a tool for validating SED-ML files.

Centralizing data to unlock whole-cell models

no code implementations22 May 2021 Yin Hoon Chew, Jonathan R. Karr

Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive.

Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology

no code implementations9 Apr 2021 Michael L. Blinov, John H. Gennari, Jonathan R. Karr, Ion I. Moraru, David P. Nickerson, Herbert M. Sauro

Toward improving the reproducibility of computational systems research, we identified several resources that investigators can leverage to make their research more accessible, executable, and comprehensible by others.

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

no code implementations11 May 2020 Arthur P. Goldberg, David R. Jefferson, John A. P. Sekar, Jonathan R. Karr

To enable fast, accurate, and scalable simulations of biochemistry, we present an exact parallel algorithm for SSA that partitions a biochemical network into many SSA processes that simulate in parallel.

BpForms: a toolkit for concretely describing modified DNA, RNA and proteins

2 code implementations24 Mar 2019 Paul F. Lang, Yassmine Chebaro, Jonathan R. Karr

We anticipate BpForms will be a valuable tool for communicating data about modified DNA, RNA, and proteins, as well as integrating data about epigenetic, post-transcriptional, and post-translational modification.

Biomolecules

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