Publications

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

RunBioSimulations is an extensible, standards-driven web application for executing models across a broad range of modeling frameworks, simulation algorithms, and model formats and visualizing and sharing their results.

Bilal Shaikh, Gnaneswara Marupilla, Mike Wilson, Michael L Blinov, Ion I Moraru, Jonathan R Karr

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

SED-ML Validator: tool for debugging simulation experiments

More sophisticated models are needed to address problems in bioscience, synthetic biology, and precision medicine. To help facilitate …

Bilal Shaikh, A. Freiburger, Matthias Konig, Frank T. Bergmann, D. Nickerson, H. Sauro, M. Blinov, Lucian P. Smith, I. Moraru, Jonathan R. Karr

SED-ML Validator: tool for debugging simulation experiments

Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior

To facilitate biochemical research, we developed Datanator, an integrated database and set of tools for finding clouds of multiple types of molecular data about specific molecules and reactions in specific organisms and environments, as well as data about chemically-similar molecules and reactions in phylogenetically-similar organisms in similar environments.

Yosef D Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh, Jonathan R Karr