Today, environmental pollution is a serious problem, and bioremediation can play an
important role in cleaning contaminated sites. Remediation strategies, such as chemical and …

Understanding complex systems often requires a bottom-up analysis towards a systems
biology approach. The need to investigate a system, not only as individual components but …

Abstract BioModels Database (http://www. ebi. ac. uk/biomodels/), part of the international
initiative BioModels. net, provides access to published, peer-reviewed, quantitative models …

Background Recent advances with high-throughput methods in life-science research have
increased the need for automatized data analysis and visual exploration techniques …

Most of the published quantitative models in biology are lost for the community because they
are either not made available or they are insufficiently characterized to allow them to be …

One element of classical systems analysis treats a system as a black or grey box, the inner
structure and behaviour of which can be analysed and modelled by varying an internal or …

Background Despite decades of new discoveries in biomedical research, the overwhelming
complexity of cells has been a significant barrier to a fundamental understanding of how …

BioNetGen allows a user to create a computational model that characterizes the dynamics of
a signal transduction system, and that accounts comprehensively and precisely for specified …

Formalized rules for protein-protein interactions have recently been introduced to represent
the binding and enzymatic activities of proteins in cellular signaling. Rules encode an …

Abstract Systems Biology has taken advantage of computational tools and high-throughput
experimental data to model several biological processes. These include signaling, gene …