no code implementations • 11 Oct 2023 • Steven S. Andrews, H. Steven Wiley, Herbert M. Sauro
Design patterns are generalized solutions to frequently recurring problems.
no code implementations • 6 Sep 2023 • Bartholomew E. Jardine, Lucian P. Smith, Herbert M. Sauro
MakeSBML is a client-based web application that translates models expressed in human-readable Antimony to the System Biology Markup Language (SBML) and vice-versa.
1 code implementation • 17 Feb 2023 • Jin Xu, Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes, Claire Samuels, Herbert M. Sauro
A unique feature of the tool is the extensive Python plugin API, where third-party developers can include new functionality.
no code implementations • 15 Jan 2023 • Lillian T. Tatka, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro
For this reason, institutes including NASA, the FDA, and the EMA have developed standards to promote and assess the credibility of computational models and simulations.
1 code implementation • 26 Apr 2022 • Jin Xu, Jessie Jiang, Herbert M. Sauro
One of the extensions for SBML is the SBML Layout and Render package.
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.
no code implementations • 26 Feb 2022 • Ciaran Welsh, Jin Xu, Lucian Smith, Matthias König, Kiri Choi, Herbert M. Sauro
Motivation: This paper presents libRoadRunner 2. 0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language SBML).
no code implementations • 25 Feb 2022 • Michael A. Kochen, H. Steven Wiley, Song Feng, Herbert M. Sauro
Motivation: An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks.
no code implementations • 7 Jul 2021 • Herbert M. Sauro
Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible.
1 code implementation • 13 Jun 2021 • Michael A. Kochen, Steven S. Andrews, H. Steven Wiley, Song Feng, Herbert M. Sauro
Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses.
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 • 6 May 2021 • Endre T. Somogyi, Jeffery Coulter, Fanbo Sun, Herbert M. Sauro, James A. Glazier
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated.
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.