Life science researchers use computational models to articulate and test hypotheses about
the behavior of biological systems. Semantic annotation is a critical component for …

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 …

The use of computational modeling to describe and analyze biological systems is at the
heart of systems biology. Model structures, simulation descriptions and numerical results …

Protein ubiquitylation is an important post-translational modification, regulating aspects of
virtually every biochemical pathway in eukaryotic cells. Hundreds of enzymes participate in …

There now exists a rich set of ontologies that provide detailed semantics for biological
entities of interest. However, there is not (nor should there be) a single source ontology that …

Background Systems biology is an approach to biology that emphasizes the structure and
dynamic behavior of biological systems and the interactions that occur within them. To …

It has become increasingly evident that the descriptions of many complex diseases are only
possible by taking into account multiple influences at different physiological scales. To do …

Abstract Background Mathematics and Phy sics-based simulation models have the potential
to help interpret and encapsulate biological phenomena in a computable and reproducible …

Motivation: The need for the automated computational design of genetic circuits is becoming
increasingly apparent with the advent of ever more complex and ambitious synthetic biology …

Motivation: Biological systems are complex and challenging to model and therefore model
reuse is highly desirable. To promote model reuse, models should include both information …