Modelling the structure and dynamics of biological pathways

There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system's dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems

Tools for visualization and analysis of molecular networks, pathways, and -omics data

Jose M Villaveces, Prasanna Koti, Bianca H Habermann Max Planck Institute of Biochemistry, Research Group Computational Biology, Martinsried, Germany Abstract: Biological pathways have become the standard way to represent the coordinated reactions and actions of a series of molecules in a cell. A series of interconnected pathways is referred to as a biological network, which denotes a more holistic view on the entanglement of cellular reactions. Biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization. Here, we review a set of pathway and network visualization and analysis methods and take a look at potential future developments in the field. Keywords: biological networks, reactions, proteins, genes, signaling, protein-protein interactions, organism

Tools for visualization and analysis of molecular networks, pathways, and -omics data

Jose M Villaveces, Prasanna Koti, Bianca H Habermann Max Planck Institute of Biochemistry, Research Group Computational Biology, Martinsried, Germany Abstract: Biological pathways have become the standard way to represent the coordinated reactions and actions of a series of molecules in a cell. A series of interconnected pathways is referred to as a biological network, which denotes a more holistic view on the entanglement of cellular reactions. Biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization. Here, we review a set of pathway and network visualization and analysis methods and take a look at potential future developments in the field. Keywords: biological networks, reactions, proteins, genes, signaling, protein-protein interactions, organism

Anatomy of BioJS, an open source community for the life sciences

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects