186 citations · 310 across the 31 of their papers we have counts for
32 papers
Use of Interactive Simulations in Fundamentals of Biochemistry, a LibreText Online Educational Resource, to Promote Understanding of Dynamic Reactions
Henry V. Jakubowski, Henry Agnew, Bartholomew E. Jardine +1
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to…
MakeSBML: A tool for converting between Antimony and SBML
Bartholomew E. Jardine, Lucian P. Smith, Herbert M. Sauro
We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repo…
SBcoyote: An Extensible Python-Based Reaction Editor and Viewer
Jin Xu, Gary Geng, Nhan D. Nguyen +3
SBcoyote is an open-source cross-platform biochemical reaction viewer and editor released under the liberal MIT license. It is written in Python and uses wxPython to implement the…
Adapting Modeling and Simulation Credibility Standards to Computational Systems Biology
Lillian T. Tatka, Lucian P. Smith, Joseph L. Hellerstein +1
Computational models are increasingly used in high-impact decision making in science, engineering, and medicine. The National Aeronautics and Space Administration (NASA) uses compu…
SBMLDiagrams: A python package to process and visualize SBML layout and render
Jin Xu, Jessie Jiang, Herbert M. Sauro
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render…
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu +68
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, becau…