Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

Abstract Biological Pathway Exchange (BioPAX) is a standard language to represent
biological pathways at the molecular and cellular level and to facilitate the exchange of …

BioNetGen is an open-source software package for rule-based modeling of complex
biochemical systems. Version 2.2 of the software introduces numerous new features for both …

Background Quantitative models of biochemical and cellular systems are used to answer a
variety of questions in the biological sciences. The number of published quantitative models …

Many organisms exhibit visually striking spotted or striped pigmentation patterns.
Developmental models predict that such spatial patterns can form when a local autocatalytic …

Motivation: This article presents libRoadRunner, an extensible, high-performance, cross-
platform, open-source software library for the simulation and analysis of models expressed …

Structural properties of molecules are of primary concern in many fields. This report provides
a comprehensive overview on techniques that have been developed in the fields of …

Abstract SABIO-RK (http://sabiork. h-its. org/) is a manually curated database containing data
about biochemical reactions and their reaction kinetics. The data are primarily extracted from …

Context Under irradiation, a biological system undergoes a cascade of chemical reactions
that can lead to an alteration of its normal operation. There are different types of radiation …

Systems biology is an emerging discipline that combines high-content, multiplexed
measurements with informatic and computational modeling methods to better understand …