Jonathan R. Karr

The paper updates and corrects SED-ML files for 1055 models in BioModels to improve reproducibility and verification across simulation engines.

RBAtools provides a programming API for Resource Balance Analysis, enabling custom workflows and model manipulation for non-expert users.

This paper introduces SSA-FBA, a computational framework for simulating single-cell metabolism using genome-scale models and gene expression data, demonstrating its application to Mycoplasma pneumoniae.

runBioSimulations provides a web platform to execute diverse computational models, enabling easier access to simulation tools and promoting reproducibility in modeling.

The paper evaluates the reusability and composability of manually-built RAS-RAF-MEK-ERK signaling pathway maps from three databases to improve disease model assembly.

Datanator is a database that integrates molecular data for modeling cellular behavior, providing tools to access and analyze diverse biochemical data across organisms and environments.

The paper proposes a plan for developing human whole-cell models through technology, standards, and interdisciplinary collaboration.