no code implementations • 13 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.
2 code implementations • 1 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.
no code implementations • 22 May 2021 • Yin Hoon Chew, Jonathan R. Karr
Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive.
no code implementations • 9 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.
no code implementations • 11 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.
2 code implementations • 24 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