186 citations · 309 across the 8 of their papers we have counts for
8 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…
PEtab -- interoperable specification of parameter estimation problems in systems biology
Leonard Schmiester, Yannik Schälte, Frank T. Bergmann +26
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of p…
Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation
Christoph Zimmer, Frank T. Bergmann, Sven Sahle
Ordinary differential equations (ODE) are widely used for modeling in Systems Biology. As most commonly only some of the kinetic parameters are measurable or precisely known, param…
One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project
Frank T. Bergmann, Richard Adams, Stuart Moodie +15
Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily…
TinkerCell: Modular CAD Tool for Synthetic Biology
Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between c…