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).

Publications
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

News

  • 2017-04-18: New: uploaded my notes on setting up various development environments and compiling libSBML

2015

2015-05-26: Invited to give a presentation on SBML and constraint-based modelling at “Biomedical Engineering” group meeting (Eindhoven)

2015-05-21: Presented a talk on SBML and constraint-based modelling at “BioSB 2015” (Lunteren)

2015-05-20: On judging panel for "Best Application" showcase at “BioSB 2015” (Lunteren)

2015-04-23: SED-ML editorial board meeting “HARMONY 2015” (Wittenberg, Germany)
2015-04-19/22: SBML editorial board meeting “HARMONY 2015” (Wittenberg, Germany)

2015-04-16: Presented practical session on constraint-based modelling with FAME at the International Conference on Metabolic Engineering in Bacteria 2015 (Amsterdam)

2015-04-01: Presented a talk on MetaToolkit at the annual “Annual BE-BASIC Symposium” (Noordwijkerhout)

2015-03-11: Presented a talk on CBM modelling and software at the “NBV conference: Biotech@Work” (Ede)

2015-02-03: Day moderator, lectures and practicals presented on constraint-based modelling with FAME at the SB@NL Training Course: Data Integration in the Life Sciences course (Leiden)

2015-01-01: Elected as SED-ML editor (2015 - 2017)

2014

2014-12-03: The PySCeS Constraint Based Modelling package - CBMPy 0.7.0 released

2014-12-02: The Python Simulator for Cellular Systems - PySCeS 0.9.1 released

2014-11-04: Presented a talk on the use of standards in modelling micobial ecosystems at the Understanding Microbial Communities workshop (Cambridge, UK)

2014-10-06: Lectures and practicals given on constraint-based modelling with FAME at the ERASysAPP Course on Stoichiometric and Kinetic Modeling of Biochemical Networks course (Larnaca, Cyprus)

2014-09-19: Presented new work at the BE-BASIC Flagship 8 meeting (invited). (Wageningen)

2014-07-09: Invited speaker/participant ”Setting the Standards for analysing and integrating big data workshop (Berlin)

2014-05-19: Presented a talk at the “NORA workshop on Mathematical Modelling” (Brussels)

2014-05-15: Took part in the EraSysApp workshop “Networking Research Centers” (Berlin)

2014-05-05: Invited visit to Ursula Kummer‘s group (Heidelberg) to work on CBM modelling, standards and encoding the latest FBC models with Frank Bergmann.

2014-04-21: Chaired FBC session and presented status report at HARMONY 2014 at the MIB (Manchester).

2014-04-08: Presented CBMPy at the NBIC 2014 Application Showcase abstract.

2014-03-05: Gave a computer practical on Constraint Based Modelling with FAME at the SysBio2014 course in (Innsbruck)

2014-01-01: Elected as SBML editor (2014 - 2016)

2013

2013-11-15: Together with Mark Hanemaaijer co-presented a mini-workshop on Constraint Based Modelling, VU, Amsterdam (teaching)

2013-09-17: presented Standards at genome scale: introducing the SBML3 FBC package and chaired the SBML Flux Balance Constraints session at COMBINE 2013 (talk)

2013-09-02: Encoding Genome Scale models with SBML Level 3 FBC (Figshare) at ICSB 2013 (poster)

2013-06-11: Presented at a Systems Biology course, Riga, Latvia (teaching)

2013-06-03: PySCeS the Python Simulator for Cellular Systems 0.9.0 released!

2013-04-17: Genome Scale Models: standards, software and interoperability at NBIC2013 (talk)

2013-03-13: CBMPy software project has a new home.

2013-02-13: SBML L3 Flux Balance Constraints specification officially accepted

2012

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)

Publications

Google Scholar

PubMed

Researcher ID (ISI)

Supervision

Ph.D.

T. Maarleveld (2015) PhD co-supervisor

M. Hanemeijer (2015) PhD advisor

H. Hettling (2014) Viable Models of Energy Metabolism. PhD thesis commitee.

M.Sc.

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.

B.Sc.

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

Academic

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

Non-academic

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, 2017.
Site last updated: 2017-04-18.