92 citations · 130 across the 9 of their papers we have counts for
10 papers
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…
SED-ML Validator: tool for debugging simulation experiments
Bilal Shaikh, Andrew Philip Freiburger, Matthias König +7
Summary: More sophisticated models are needed to address problems in bioscience, synthetic biology, and precision medicine. To help facilitate the collaboration needed for such mod…
Centralizing data to unlock whole-cell models
Yin Hoon Chew, Jonathan R. Karr
Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive. One of the biggest challenges to whole-cell models is assembl…
Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology
Michael L. Blinov, John H. Gennari, Jonathan R. Karr +3
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in…
Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology
Lucia Marucci, Matteo Barberis, Jonathan Karr +11
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematica…
Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks
Arthur P. Goldberg, David R. Jefferson, John A. P. Sekar +1
Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulati…