Search Results for author: Herbert M. Sauro

Found 13 papers, 4 papers with code

Design Patterns of Biological Cells

no code implementations11 Oct 2023 Steven S. Andrews, H. Steven Wiley, Herbert M. Sauro

Design patterns are generalized solutions to frequently recurring problems.

MakeSBML: A tool for converting between Antimony and SBML

no code implementations6 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.

SBcoyote: An Extensible Python-Based Reaction Editor and Viewer

1 code implementation17 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.

Adapting Modeling and Simulation Credibility Standards to Computational Systems Biology

no code implementations15 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.

Decision Making

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.

libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library

no code implementations26 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).

Vocal Bursts Intensity Prediction

SBbadger: Biochemical Reaction Networks with Definable Degree Distributions

no code implementations25 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.

Inference Optimization

The Practice of Ensuring Repeatable and Reproducible Computational Models

no code implementations7 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.

Dynamics and Sensitivity of Signaling Pathways

1 code implementation13 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.

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.

Real-Time Interactive Modeling and Simulation in Biological Physics and Active Matter with Mechanica

no code implementations6 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.

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.

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