Software

Software I have created or actively being part of its development, with links to their homepages, source code, and associated publications.

JWS Online

Description

JWS Online was created in 2000 as one of the first browser-based systems biology tools, for the construction, modification and simulation of kinetic models and the storage of curated models. It provides a web model builder adhering to the SBML specification with MIRIAM and SBO annotation, and supports time evolution, steady-state, metabolic-control analysis, and parameter scans.

References

• Olivier, B. G., & Snoep, J. L. (2004). Web-based kinetic modelling using JWS Online. Bioinformatics, 20, 2143-2144. https://doi.org/10.1093/bioinformatics/bth200
• Snoep, J. L., & Olivier, B. G. (2001). Java Web Simulation (JWS); A Web Based Database of Kinetic Models. https://doi.org/10.1023/a:1020350518131

PySCeS

Description

PySCeS was the first generic systems biology simulator implemented in Python, providing a flexible and user-extensible platform for computational modelling of cellular reaction networks. Originally developed to support metabolic control analysis, it remains actively used by the research community for kinetic modelling and simulation.

Links

• Homepage: https://pysces.github.io
• Source code: https://github.com/PySCeS/pysces

References

• Olivier, B. G., & Rohwer, J. (2005). Modelling cellular systems with PySCeS. Bioinformatics, 21, 692-693. https://doi.org/10.1093/bioinformatics/bti046
• Olivier, B., & Rohwer, J. (2025). The Python Simulator for Cellular Systems: PySCeS. Zenodo. https://doi.org/10.5281/zenodo.15356070

CBMPy

Description

CBMPy is a Python-based platform for constraint-based metabolic modelling and analysis, supporting end-point FBA, Flux Balance Constraints V3 (including quadratic objectives and non-stoichiometric user constraints), and full SBML Level 3 Version 2 interoperability.

Links

• Homepage: https://systemsbioinformatics.github.io/cbmpy/
• Source code: https://github.com/SystemsBioinformatics/cbmpy

References

• Olivier, B., Gottstein, W., Teusink, B., & Molenaar, D. (2023). CBMPy release 0.8.8 update 1. Zenodo. https://doi.org/10.5281/zenodo.10067017

MetaDraft

Description

MetaDraft is a GUI-based tool for the reconstruction of genome-scale metabolic networks, providing a flexible and extensible pipeline from annotated genomic data to metabolic models.

Links

• Homepage: https://systemsbioinformatics.github.io/cbmpy-metadraft/
• Source code: https://github.com/SystemsBioinformatics/cbmpy-metadraft

References

• Olivier, B. G., Mendoza, S., Molenaar, D., & Teusink, B. (2020). MetaDraft Release 0.9.5. Zenodo. https://doi.org/10.5281/zenodo.4291058

readYmeta

Description

readYmeta is a Go-implemented tool that creates reviewer friendly PDFs from Yoda metadata files. It also applies basic quality control checks that highlight DataCite compatability and data reusability. readYmeta is not publically available yet, contact me if you are interested testing a beta version.

Links

• Homepage: https://github.com/bgoli/
• Source code: Closed - contact me to discuss reuse.