Brett G. Olivier / Data Steward / Research Software Engineer

Brett G. Olivier

Data Steward, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)
VU University Amsterdam

Room: 01W09, O|2 Lab Building, Amsterdam, The Netherlands
Tel: +31 20 59 87248
Email: b.g.olivier@vu_dot_nl

Current interests
Biochemist, Data Steward, Research Software Engineer with experience in both fundamental theoretical research: metabolic regulation analysis, control analysis, constraint based modelling and software design and development. Actively involved in the development of standards in Systems Biology including SBML, SBML3-FBC, SEDML

Skill areas
biochemistry, modeling, metabolic control analysis, Python, software development, systems biology, standards development, software interoperability, constraint-based modelling, kinetic modelling.

Contact details
For a more detailed list of activities and CV please see my personal website or contact me on Twitter (@Brett_Olivier).

See the PubMed listing at the end of this page or 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:

Social Profiles
Here are some web2 profiles (apparently all me):


PubMed publications

  1. Neal, ML, König, M, Nickerson, D, Misirli, G, Kalbasi, R, Dräger, A et al.. Harmonizing semantic annotations for computational models in biology. Brief. Bioinformatics. 2018; :. doi: 10.1093/bib/bby087. PubMed PMID:30462164 .
  2. Waltemath, D, Bergmann, FT, Chaouiya, C, Czauderna, T, Gleeson, P, Goble, C et al.. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci. 2018;13 :17. doi: 10.1186/s40793-018-0320-4. PubMed PMID:30117501 PubMed Central PMC6083578.
  3. Bergmann, FT, Cooper, J, König, M, Moraru, I, Nickerson, D, Le Novère, N et al.. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). J Integr Bioinform. 2018;15 (1):. doi: 10.1515/jib-2017-0086. PubMed PMID:29550789 .
  4. Olivier, BG, Bergmann, FT. SBML Level 3 Package: Flux Balance Constraints version 2. J Integr Bioinform. 2018;15 (1):. doi: 10.1515/jib-2017-0082. PubMed PMID:29522419 .
  5. Hucka, M, Bergmann, FT, Dräger, A, Hoops, S, Keating, SM, Le Novère, N et al.. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J Integr Bioinform. 2018;15 (1):. doi: 10.1515/jib-2017-0081. PubMed PMID:29522418 .
  6. Branco Dos Santos, F, Olivier, BG, Boele, J, Smessaert, V, De Rop, P, Krumpochova, P et al.. Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough. Appl. Environ. Microbiol. 2017; :. doi: 10.1128/AEM.01528-17. PubMed PMID:28842544 PubMed Central PMC5648915.
  7. Hanemaaijer, M, Olivier, BG, Röling, WF, Bruggeman, FJ, Teusink, B. Model-based quantification of metabolic interactions from dynamic microbial-community data. PLoS ONE. 2017;12 (3):e0173183. doi: 10.1371/journal.pone.0173183. PubMed PMID:28278266 PubMed Central PMC5344373.
  8. Artaza, H, Chue Hong, N, Corpas, M, Corpuz, A, Hooft, R, Jimenez, RC et al.. Top 10 metrics for life science software good practices. F1000Res. 2016;5 :. doi: 10.12688/f1000research.9206.1. PubMed PMID:27635232 PubMed Central PMC5007752.
  9. Levering, J, Fiedler, T, Sieg, A, van Grinsven, KW, Hering, S, Veith, N et al.. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets. J. Biotechnol. 2016;232 :25-37. doi: 10.1016/j.jbiotec.2016.01.035. PubMed PMID:26970054 .
  10. Gottstein, W, Olivier, BG, Bruggeman, FJ, Teusink, B. Constraint-based stoichiometric modelling from single organisms to microbial communities. J R Soc Interface. 2016;13 (124):. doi: 10.1098/rsif.2016.0627. PubMed PMID:28334697 PubMed Central PMC5134014.
  11. Olivier, BG, Swat, MJ, Moné, MJ. Modeling and Simulation Tools: From Systems Biology to Systems Medicine. Methods Mol. Biol. 2016;1386 :441-63. doi: 10.1007/978-1-4939-3283-2_19. PubMed PMID:26677194 .
  12. Hucka, M, Bergmann, FT, Dräger, A, Hoops, S, Keating, SM, Le Novère, N et al.. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J Integr Bioinform. 2015;12 (2):271. doi: 10.2390/biecoll-jib-2015-271. PubMed PMID:26528569 PubMed Central PMC5457286.
  13. Olivier, BG, Bergmann, FT. The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. J Integr Bioinform. 2015;12 (2):269. doi: 10.2390/biecoll-jib-2015-269. PubMed PMID:26528567 .
  14. Hanemaaijer, M, Röling, WF, Olivier, BG, Khandelwal, RA, Teusink, B, Bruggeman, FJ et al.. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure. Front Microbiol. 2015;6 :213. doi: 10.3389/fmicb.2015.00213. PubMed PMID:25852671 PubMed Central PMC4365725.
  15. Maarleveld, TR, Wortel, MT, Olivier, BG, Teusink, B, Bruggeman, FJ. Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models. PLoS Comput. Biol. 2015;11 (4):e1004166. doi: 10.1371/journal.pcbi.1004166. PubMed PMID:25849486 PubMed Central PMC4388735.
  16. Reimers, AC, Bruggeman, FJ, Olivier, BG, Stougie, L. Fast flux module detection using matroid theory. J. Comput. Biol. 2015;22 (5):414-24. doi: 10.1089/cmb.2014.0141. PubMed PMID:25565150 .
  17. Veith, N, Solheim, M, van Grinsven, KW, Olivier, BG, Levering, J, Grosseholz, R et al.. Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl. Environ. Microbiol. 2015;81 (5):1622-33. doi: 10.1128/AEM.03279-14. PubMed PMID:25527553 PubMed Central PMC4325170.
  18. Bergmann, FT, Adams, R, Moodie, S, Cooper, J, Glont, M, Golebiewski, M et al.. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics. 2014;15 :369. doi: 10.1186/s12859-014-0369-z. PubMed PMID:25494900 PubMed Central PMC4272562.
  19. Maarleveld, TR, Olivier, BG, Bruggeman, FJ. StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes. PLoS ONE. 2013;8 (11):e79345. doi: 10.1371/journal.pone.0079345. PubMed PMID:24260203 PubMed Central PMC3832486.
  20. Maarleveld, TR, Khandelwal, RA, Olivier, BG, Teusink, B, Bruggeman, FJ. Basic concepts and principles of stoichiometric modeling of metabolic networks. Biotechnol J. 2013;8 (9):997-1008. doi: 10.1002/biot.201200291. PubMed PMID:23893965 PubMed Central PMC4671265.
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Supervision and related

Thomas BraamBas TeusinkAccounting for enzyme costs in FBAMSc project2016
Nicolas HuberBas TeusinkVisualising genome scale networksMSc project2016-2017
Carl ChristensenDevelopment of an Integrated Metabolic Analysis ToolboxPhD thesis (examiner)2016
Marnette CoetzeeFeedforward activation in metabolic systemsMSc thesis (examiner)2016
Timo MaarleveldFrank Bruggeman
Bas Teusink
Fluxes and Feedback in Biochemical modelsPhD2015
Maarten ReitsemaBas TeusinkComparison of Gap Filling AlgorithmsMSc literature2015
Hanneke LaanBas TeusinkThe integration of the macromolecular synthesis machinery with genome-scale metabolic modelsMSc literature2015
Johannes HettlingViable Models of Energy MetabolismPhD thesis (committee)2013

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