Semantic Biological Modeling and Simulation

Tutorial at the Semantic Trilogy, 7th of July 2013, Montreal, Canada

Michel Dumontier * Dagmar Waltemath

Motivation
The systems biology life cycle involves developing models, analyzing these models by means of simulations, evaluating how the simulation results reflect observations in the experiments, and then refining the model. All steps in this cycle are now supported by minimum information checklists, standard formats and ontologies to enable exchange among tools and work groups. SBML encodes a model’s structure in terms of reactions, SED-ML encodes simulation setups, and NuML encodes simulation results. A wide range of biomedical ontologies are being used to annotate models, e.g. Gene Ontology, ChEBI, or KEGG, while the Systems Biology Ontology (SBO) is used to specify mathematical aspects, and the Kinetic Simulation Algorithm Ontology (KiSAO) provides detailed lists concerning algorithms used to simulate kinetic models of biological systems. In order to undertake effective studies in computational systems biology, one must not only be aware of these different ontologies and standards, but also understand how to make use of them in existing toolchains.

Objective
In this tutorial we will provide an overview of computational systems biology from the perspective of building and simulating biological systems. For each step of the workflow, we will describe ontologies and standards and provide examples of how these can be taken advantage of with respect to model search, validation, simulation, comparison and visualization. Throughout the tutorial we will use open online software.

Audience
The tutorial is aimed at researchers (modelers, computer scientists and tools developers alike) who wish to learn about the use of bio-ontologies in modeling and simulation of biological systems (including computational biology, medicine, physiology and neuroscience) .

Schedule
tba

Requirements
laptop with internet access

Literature
tba