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

The weighted ensemble (WE) methodology orchestrates quasi-independent parallel
simulations run with intermittent communication that can enhance sampling of rare events …

G protein-coupled receptors (GPCRs) are classically characterized as cell-surface receptors
transmitting extracellular signals into cells. Here we show that central components of a …

Automatic differentiation (AD), a technique for constructing new programs which compute
the derivative of an original program, has become ubiquitous throughout scientific …

Quantitative properties of stochastic systems are usually specified in logics that allow one to
compare the measure of executions satisfying certain temporal properties with thresholds …

As the amount of biological data in the public domain grows, so does the range of modeling
and analysis techniques employed in systems biology. In recent years, a number 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 …

The re-use of previously validated designs is critical to the evolution of synthetic biology from
a research discipline to an engineering practice. Here we describe the Synthetic Biology …

The advances in genetics and biochemistry that have taken place over the last 10 years led
to significant advances in experimental and clinical immunology. In turn, this has led to the …

Mathematical equations are fundamental to modeling biological networks, but as networks
get large and revisions frequent, it becomes difficult to manage equations directly or to …