About me

Current interests
Biochemist and Software Developer specializing in Systems Biology with experience in both fundamental theoretical research (metabolic regulation analysis, control analysis, constraint based modelling) and software design and development.

My current research includes developing and applying constraint based modelling techniques to the analysis of microbial communities and multiple environments. This involves both the development of theory (going from one to many organisms) but also software tools for large scale optimization. I am also actively involved in the development of standards in Systems Biology

Skill areas
biochemistry, modeling, metabolic control analysis, Python, software development, systems biology, standards, interoperability

Current position
Vrije Universiteit Amsterdam, Systems Bioinformatics, W&N building, room M-214, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
For a more detailed list of activities and CV see below or contact me by email, view my personal blog and try Twitter (@Brett_Olivier).

For a quick overview please try search Google Scholar and PubMed directly.

Standards Development
I am actively involved in the development of standards in systems biology and currently serve as an elected editor on the editorial boards of two community standards, the Systems Biology Markup Language (SBML) and Simulation Experiment Description Markup Language (SED-ML). I also co-ordinate the development of the SBML Level 3 Flux Balance Constraints Package (FBC) and working group responsible for developing a standard encoding format for genome-scale, constraint-based models.

Software Projects
Software projects that I am (or have been) involved with include: CBMPy (lead developer 2010-present), FAME (co-developer 2012-present), MEMESA Tools (co-developer 2012-present), StochPy, PySundials, PySCeS (lead developer 2001-present), JWS Online (lead developer 2001-2005).

Social profiles
OrchidID: 0000-0002-5293-5321
Twitter: @Brett_Olivier
LinkedIn: profile
ResearchGate: profile
FigShare: profile
SourceForge: profile
GitHub: profile
ResearcherID: A-2800-2008





  • 2012-11-19: Participated in the SED-ML development workshop, Rostock, Germany (talk)
  • 2012-11-07: Presented CBMPy Constraint based modelling workshop Heidelberg, Germany. (teaching)
  • Olivier B.G. (2012) Towards truly integrated modelling in Systems Biology, NISB symposium 2012, IJmuiden, Netherlands (poster)
  • Olivier B.G. (2012) Genome Scale Models: a data management problem? Systems Biology Data Management Foundry, Vienna, Austria (talk)
  • Olivier B.G. (2012) Towards truly integrated modelling in Systems Biology: Developing Software and Standards. HARMONY 2012: The Hackathon on Resources for Modeling in Biology, Maastricht, Netherlands (poster)
  • Olivier B.G. (2012) Pathway and Cells: Systems Biology Modelling with Python. EuroScipy 2012, Brussels, Belgium (talk)
  • Olivier B.G. & Bruggeman F.J (2012) To be fast or be flexible? International Study Group on Systems Biology 2012, Ameland, Netherlands (talk)




  • T. Maarleveld (2015) PhD co-supervisor
  • M. Hanemeijer (2015) PhD advisor
  • H. Hettling (2014) Viable Models of Energy Metabolism. PhD thesis commitee.


  • C. van Boxtel (2014) Re-engineering OptKnock in Python. advisor, MSc internship.
  • K. Schaarschuch (2014) Modeling the Warburg Effect in Keratinocytes. daily co-supervisor, MSc internship.


  • J. de Jonker (2012) Predicting drug synergy for combating (multidrug-resistant) Mycobacterium tuberculosis using a metabolomics approach. daily co-supervisor, Bachelor internship

Membership (committees, editorial boards, other)

  • Elected to the SED-ML editorial board (2015 - 2017)
  • Elected to the SBML editorial board (2014 - 2016)
  • Member of the BioSB Research School preparatory committee. (2014 - 2015)
  • Member of the NCSB Stimulus 2013 Data Integration Committee
    Regular reviewer for Bioinformatics, PLOS Computational Biology, Febs Journal, Royal Society Interface, BMC Systems Biology, IET Systems Biology.

Brief CV


  • 1992-1995 BSc (Biochemistry, Genetics), Stellenbosch University, South Africa
  • 1996 BSc Hons cum laude, Biochemistry, Stellenbosch University, South Africa
  • 1997-1999 MSc cum laude, Biochemistry, Stellenbosch University, South Africa
  • 2000-2005 PhD Biochemistry, Stellenbosch University, South Africa
  • 2005-2008 PostDoc, PySCeS, Stellenbosch University, South Africa
  • 2009-2010 Researcher, MEMESA, VU University Amsterdam, The Netherlands
  • 2011 Scientific Staff Member, Constraint Based Modelling, Center for Mathematics and Informatics (CWI), Amsterdam, The Netherlands
  • 2011- 2014 Bioinformatician, Community Constraint Based Modelling, VU University Amsterdam, The Netherlands
  • 2014 - Scientific software developer, BE-Basic project: Metatoolkit, VU University Amsterdam, The Netherlands


  • 1999-2003 Technical Officer Biochemistry Department, Stellenbosch University, 3/8 fte position providing IT user support (Windows, Novel) as well as network server (web, mail, firewall) setup and administration (Linux)

© Brett G. Olivier, Amsterdam, The Netherlands, 2015.
Site last updated: 2015-05-26.