Webinars | Brett Olivier




Scientific Researcher,
Vrije Universiteit Amsterdam,
Systems Bioinformatics,
The Netherlands.
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Dr. Brett Olivier trained as a Biochemist in the Triple-J Group at the University of Stellenbosch where he specialised in computational systems biology. Working on theoretical research (metabolic control analysis, kinetic and constraint-based modelling) as well as writing scientific software for its analysis. He developed the Python Simulator for Cellular Systems (PySCeS) and JWS Online, an interactive model repository (together with Jacky Snoep).
Moving to the Systems Bioinformatics group at the Vrije Universiteit Amsterdam his research includes the application of constraint-based modelling techniques to the analysis of microbial communities and the development of the CBMPy constraint-based modelling framework. He is actively involved in the development of community standards and their implementation in research software. Together with Frank Bergmann he leads the development of the FBC extension to SBML used for the standard encoding of constraint-based, genome-scale models and serves as an editor for the SBML and SED-ML standards.

Webinar Presentations

29th February 2016 (14:00 – 14:45 GMT) : “Models, standards and software in systems biology”

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Standards play an important role in our everyday life; they define how our appliances communicate with one another and the address format of our last email. While ubiquitous in experimental sciences, the application of standards to mathematical modelling in the life sciences is relatively new. With its integral use of computer modelling many of these standardisation efforts have taken root in the relatively new field of systems biology [1].

With the field now moving to big data and whole-cell modelling, standardisation becomes even more important. Where very large models will consist of many sub-models, themselves data, that need to be exchanged between researchers and groups and used in ways not originally envisioned by their authors. Beyond exchange, standards enable the development of interoperable simulation software which will allow ensembles of software, with a diverse range of functionality, to be combined together and enable a new in silico biology.

Key to this development is an iterative cycle that exists between model users, software developers and standards communities. Here I will mostly focus on a single, yet critical, step the implementation of standards in software. This I will do by considering two tools, the simulation software PySCeS and the constraint-based modelling framework, CBMPy. The later an integral part in the development of the SBML Level 3 FBC package, a standard format for encoding genome-scale, constraint-based models [2, 3, 4].

[1] http://ercim-news.ercim.eu/en104/special/modelling-using-standards-can-help-you

[2] http://pysces.sourceforge.net

[3] http://cbmpy.sourceforge.net

[4] http://sbml.org