Constraint-based modeling is a framework to model reaction fluxes in genome-scale metabolic network models. Genome scale models have uses in fundamental and applied questions relevant to biotechnology, microbiology and biomedicine. Constraint-based modeling provides a scalable framework to analyze large-scale models and to associate genome potential and metabolic reactions.
Currently, libraries to simulate these models are available in general-purpose languages such as Matlab (COBRA Toolbox), Python (cobrapy), 2013 with last release 2023), Julia (COBREXA, 2025) or R (Sybil, 2013, unmaintained). There are also methods for model development and curation in Matlab (RAVEN toolbox), Python (CarveMe 2018, last release 2023) or Java (Merlin, KBase). However, currently there lacks an up-to-date R implementation of methods for model development and curation.
In this project, we propose the (re)development of an R based framework for developing and simulating constraint-based models. We propose to expand the Sybil library for model simulation with the functionalities for model reconstruction and analysis available in the widely used RAVEN toolbox in Matlab. The outcome will facilitate constraint based modelling to experimental scientists, thereby contributing to bridge the gap between data users and data generators. It will also be more FAIR by being usable with non-proprietary software, and align with software best practices as collected by the ELIXIR Tools Platform. We will work towards increased reproducibility by also considering implementation of FROG analysis in R. Moreover, as a tool developed by the ELIXIR Systems Biology Community for the wider community, the long-term maintenance burden is spread across a wider membership.
Maria Suarez Diez, Sébastien Moretti, Rahuman S Malik Sherif
We use an organization document to share all useful links (coordination spreadsheets), share detailed tasks, keep notes, and coordinate.
The interim project repository is hosted at GitHub.
The schedule is quite flexible. There is no requirement to join the whole week. 1 daily stand-up will be run to coordinate with online participants and the Australian outpost.
The main requirement is R. Knowledge of constraint based modelling is a plus.