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

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. I am actively involved in the development of open community standards in Systems Biology.

Skills

biochemistry, modeling, metabolic control analysis, software development, Python, C++, CMAKE, SWIG, DevOps, systems biology, standards development, software interoperability, constraint-based modelling, kinetic modelling.

Contact details
Please contact me via email or Twitter (@Brett_Olivier).

Recent activities

  • 2019-01-23 presentation: “You want to store your data in … what? For how long? For how much!” at the DTL-SURF Focus meeting: Data storage beyond your project’s lifetime.
  • 2019-01-24 workshop: First Meeting VU RDM Support Network

Publications
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 have served on the editorial boards of two community standards: Systems Biology Markup Language (SBML) and Simulation Experiment Description Markup Language (SED-ML). I co-coordinate the specification of the SBML Level 3 Flux Balance Constraints Package (FBC) working group and develop libSBML as part of the SBML Team.

Software Projects
Software development projects:

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


PubMed publications (last 20)

  1. Neal, ML, König, M, Nickerson, D, Mısırlı, G, Kalbasi, R, Dräger, A et al.. Harmonizing semantic annotations for computational models in biology. Brief. Bioinformatics. 2019;20 (2):540-550. doi: 10.1093/bib/bby087. PubMed PMID:30462164 PubMed Central PMC6433895.
  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 PubMed Central PMC6167040.
  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 PubMed Central PMC6167036.
  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 PubMed Central PMC6167032.
  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;83 (21):. 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.
Search PubMed

Supervision and related

NameCo-supervisor(s)TitleTypeYear
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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