Brett G. Olivier / Data Steward / Research Software Engineer


Brett G. Olivier

Data Steward – AIMMS,
Data steward – Faculty of Science (BETA),
Consultant VUO RDS program.

ORCID iD iconhttps://orcid.org/0000-0002-5293-5321

 

Vrije Universiteit Amsterdam

Room: 01W09, O|2 Lab Building, Amsterdam, The Netherlands
Contact: VU Research Portal

Current interests

Data steward, Research Software Engineer and Systems Biologist. By training a Biochemist my research includes metabolic networks, microbial ecosystems, metabolic regulation analysis, control analysis, kinetic and constraint-based modelling. To support this a large part of my career has been as a research software engineer, designing and developing modelling and simulation software.

I am currently Data Steward for the AIMMS Institute and the Faculty of Science and IT consultant for the VUO Research Data Support program. In addition I am actively involved in the development, specification and support of the open community, model encoding standards such as SBML, where I am an editor, specification author, FBC package co-ordinator and library developer (as part of the libSBML team).

Specialities

computational systems biology, Python programming, research software engineering, data stewardship, standards development

Contact details

Please contact me via the VU Research Portal. 

Some recent activities

  • 2020-03-12 conference: Chaired the FBC work group session at HARMONY 2020 (EMBL/EBI Cambridge)
  • 2019-07-18 presentation: “10 years of flux” as moderator of the SBML FBC breakout session at COMBINE 2019 (Heidelberg)
  • 2019-06-25 conference: “iRODS User Group Meeting 2019” (Utrecht)
  • 2019-06-14 presentation: “Bottom-up data management: iRODS, Yoda and AIMMS” at the DTL programmers meeting (Utrecht)

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
Larger software development projects that I have either designed and developed, worked on or co-supervised

LinkOut Profiles
Here are some online resources that are apparently me:


PubMed publications (last 20)

  1. Keating, SM, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C et al.. SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol. 2020;16 (8):e9110. doi: 10.15252/msb.20199110. PubMed PMID:32845085 .
  2. Lieven, C, Beber, ME, Olivier, BG, Bergmann, FT, Ataman, M, Babaei, P et al.. Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020;38 (4):504. doi: 10.1038/s41587-020-0477-4. PubMed PMID:32265554 PubMed Central PMC7138757.
  3. Lieven, C, Beber, ME, Olivier, BG, Bergmann, FT, Ataman, M, Babaei, P et al.. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020;38 (3):272-276. doi: 10.1038/s41587-020-0446-y. PubMed PMID:32123384 PubMed Central PMC7082222.
  4. Mendoza, SN, Olivier, BG, Molenaar, D, Teusink, B. A systematic assessment of current genome-scale metabolic reconstruction tools. Genome Biol. 2019;20 (1):158. doi: 10.1186/s13059-019-1769-1. PubMed PMID:31391098 PubMed Central PMC6685185.
  5. Hucka, M, Bergmann, FT, Chaouiya, C, Dräger, A, Hoops, S, Keating, SM et al.. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J Integr Bioinform. 2019;16 (2):. doi: 10.1515/jib-2019-0021. PubMed PMID:31219795 PubMed Central PMC6798823.
  6. Neal, ML, König, M, Nickerson, D, Mısırlı, G, Kalbasi, R, Dräger, A et al.. Harmonizing semantic annotations for computational models in biology. Brief Bioinform. 2019;20 (2):540-550. doi: 10.1093/bib/bby087. PubMed PMID:30462164 PubMed Central PMC6433895.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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 .
  15. 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.
  16. 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 .
  17. 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.
  18. 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 .
  19. 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.
  20. 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.
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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