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

Collaborative genome-scale reconstruction endeavors of metabolic networks would not be
possible without a common, standardized formal representation of these systems. The ability …

Background Recent advances in experimental and computational technologies have fueled
the development of many sophisticated bioinformatics programs. The correctness of such …

For many expensive deterministic computer simulators, the outputs do not have replication
error and the desired metamodel (or statistical emulator) is an interpolator of the observed …

Background Bioinformatics software quality assurance is essential in genomic medicine.
Systematic verification and validation of bioinformatics software is difficult because it is often …

A fundamental problem for software testing is the oracle problem, which means that in many
practical situations, it is extremely expensive, if not impossible, to verify the test result given …

Objective: Like all scientific research, computational neuroscience research must be
reproducible. Big data science, including simulation research, cannot depend exclusively on …

The possibility to replicate and reproduce published research results is one of the biggest
challenges in all areas of science. In computational neuroscience, there are thousands of …

We describe how the use of the Python language improved the user interface of the program
STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled …

This book presents the latest research in computational biology and bioinformatics, with a
thematic focus on gene regulation. It is designed to be self-contained and comprehensive …