Brett Olivier

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dr. Brett Olivier

 https://orcid.org/0000-0002-5293-5321

  • De Boelelaan 1108, O|2 building

    1081 HZ Amsterdam

    Netherlands

Personal profile

Personal information

Data Steward of the Faculty of Science and departments of A-LIFE, Chemistry & Pharmaceutical Sciences and AIMMS institute.

By training a Biochemist, my research includes metabolic networks, microbial ecosystems, metabolic regulation analysis, control analysis, kinetic and constraint-based modelling. In support of my research a large part of my career has been as a research software engineer, designing and developing modelling and simulation software.

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 libSBML developer.

Ancillary activities

No ancillary activities

Ancillary activities are updated daily

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  • SDG 3 - Good Health and Well-being
  • SDG 16 - Peace, Justice and Strong Institutions
  • SDG 17 - Partnerships for the Goals

Academic qualification

Biochemistry, PhD, Simulation and database software for computational systems biology: PySCeS and JWS Online, University of Stellenbosch

1 Jan 2000 → 31 Dec 2004

Award Date: 1 Jun 2005

Keywords

  • QD Chemistry
  • Biochemistry
  • Systems Biology
  • Standards
  • Simulation
  • Modelling
  • QA76 Computer software
  • Software Engineering
  • SBML
  • Python
  • Open Source Communities

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  • 42 Article
  • 2 Erratum / Corrigendum
  • 2 Review article
  • 1 Comment / Letter to the editor

  • SBML Level 3: an extensible format for the exchange and reuse of biological models

    Keating, S. M., Waltemath, D., König, M., Zhang, F., Dräger, A., Chaouiya, C., Bergmann, F. T., Finney, A., Gillespie, C. S., Helikar, T., Hoops, S., Malik-Sheriff, R. S., Moodie, S. L., Moraru, I. I., Myers, C. J., Naldi, A., Olivier, B. G., Sahle, S., Schaff, J. C. & Smith, L. P. & 121 others, Swat, M. J., Thieffry, D., Watanabe, L., Wilkinson, D. J., Blinov, M. L., Begley, K., Faeder, J. R., Gómez, H. F., Hamm, T. M., Inagaki, Y., Liebermeister, W., Lister, A. L., Lucio, D., Mjolsness, E., Proctor, C. J., Raman, K., Rodriguez, N., Shaffer, C. A., Shapiro, B. E., Stelling, J., Swainston, N., Tanimura, N., Wagner, J., Meier-Schellersheim, M., Sauro, H. M., Palsson, B., Bolouri, H., Kitano, H., Funahashi, A., Hermjakob, H., Doyle, J. C., Hucka, M., Adams, R. R., Allen, N. A., Angermann, B. R., Antoniotti, M., Bader, G. D., Červený, J., Courtot, M., Cox, C. D., Dalle Pezze, P., Demir, E., Denney, W. S., Dharuri, H., Dorier, J., Drasdo, D., Ebrahim, A., Eichner, J., Elf, J., Endler, L., Evelo, C. T., Flamm, C., Fleming, R. M. T., Fröhlich, M., Glont, M., Gonçalves, E., Golebiewski, M., Grabski, H., Gutteridge, A., Hachmeister, D., Harris, L. A., Heavner, B. D., Henkel, R., Hlavacek, W. S., Hu, B., Hyduke, D. R., de Jong, H., Juty, N., Karp, P. D., Karr, J. R., Kell, D. B., Keller, R., Kiselev, I., Klamt, S., Klipp, E., Knüpfer, C., Kolpakov, F., Krause, F., Kutmon, M., Laibe, C., Lawless, C., Li, L., Loew, L. M., Machne, R., Matsuoka, Y., Mendes, P., Mi, H., Mittag, F., Monteiro, P. T., Natarajan, K. N., Nielsen, P. M. F., Nguyen, T., Palmisano, A., Pettit, J. B., Pfau, T., Phair, R. D., Radivoyevitch, T., Rohwer, J. M., Ruebenacker, O. A., Saez-Rodriguez, J., Scharm, M., Schmidt, H., Schreiber, F., Schubert, M., Schulte, R., Sealfon, S. C., Smallbone, K., Soliman, S., Stefan, M. I., Sullivan, D. P., Takahashi, K., Teusink, B., Tolnay, D., Vazirabad, I., von Kamp, A., Wittig, U., Wrzodek, C., Wrzodek, F., Xenarios, I., Zhukova, A. & Zucker, J., 1 Aug 2020, In: Molecular Systems Biology. 16, 8, p. 1-21 21 p., e9110.

    Research output: Contribution to Journal › Review article › Academic › peer-review

    Open Access

  • SBML Level 3 Package: Flux Balance Constraints version 2

    Olivier, B. G. & Bergmann, F. T., 9 Mar 2018, In: Journal of Integrative Bioinformatics. 15, 1, p. 1-39 39 p.

    Research output: Contribution to Journal › Article › Academic › peer-review

    Open Access

  • A systematic assessment of current genome-scale metabolic reconstruction tools

    Mendoza, S. N., Olivier, B. G., Molenaar, D. & Teusink, B., 7 Aug 2019, In: Genome Biology. 20, 1, 158.

    Research output: Contribution to Journal › Article › Academic › peer-review

    Open Access

  • BioSimulators: a central registry of simulation engines and services for recommending specific tools

    Shaikh, B., Smith, L. P., Vasilescu, D., Marupilla, G., Wilson, M., Agmon, E., Agnew, H., Andrews, S. S., Anwar, A., Beber, M. E., Bergmann, F. T., Brooks, D., Brusch, L., Calzone, L., Choi, K., Cooper, J., Detloff, J., Drawert, B., Dumontier, M. & Ermentrout, G. B. & 55 others, Faeder, J. R., Freiburger, A. P., Fröhlich, F., Funahashi, A., Garny, A., Gennari, J. H., Gleeson, P., Goelzer, A., Haiman, Z., Hasenauer, J., Hellerstein, J. L., Hermjakob, H., Hoops, S., Ison, J. C., Jahn, D., Jakubowski, H. V., Jordan, R., Kalaš, M., König, M., Liebermeister, W., Sheriff, R. S. M., Mandal, S., McDougal, R., Medley, J. K., Mendes, P., Müller, R., Myers, C. J., Naldi, A., Nguyen, T. V. N., Nickerson, D. P., Olivier, B. G., Patoliya, D., Paulevé, L., Petzold, L. R., Priya, A., Rampadarath, A. K., Rohwer, J. M., Saglam, A. S., Singh, D., Sinha, A., Snoep, J., Sorby, H., Spangler, R., Starruß, J., Thomas, P. J., Van Niekerk, D., Weindl, D., Zhang, F., Zhukova, A., Goldberg, A. P., Schaff, J. C., Blinov, M. L., Sauro, H. M., Moraru, I. I. & Karr, J. R., 5 Jul 2022, In: Nucleic acids research. 50, W1, p. W108-W114 7 p.

    Research output: Contribution to Journal › Article › Academic › peer-review

    Open Access

  • Top 10 metrics for life science software good practices.

    Artaza, H., Chue Hong, N., Corpas, M., Corpuz, A., Hooft, R., Jimenez, R. C., Leskosek, B., Olivier, B. G., Stourac, J., Svobodova Varekova, R., van Parys, T. & Vaughan, D., 2016, In: F1000Research. 5, ELIXIR-2000.

    Research output: Contribution to Journal › Article › Academic › peer-review

    Open Access
View all 47 research outputs
View all 16 datasets / software