sbmodelr - a tool to replicate a COPASI/SBML model into a set of replicas

Summary

This is a python-based command line utility (sbmodelr) that reads a systems biology model to create a new model that is composed of several connected units that are copies of the base model. These units may be organized as an arbitrarily connected network, a 2D rectangular grid, or a 3D cuboid array. Each unit contains a complete copy of the original model with all its species, reactions, compartments, events, and global quantities. sbmodlr can read models encoded in COPASI or SBML formats.

Connections between units in the new model can be:

• species being transported between units
• species acting as inhibitors/activators of the synthesis of other species (to make gene regulatory networks)
• diffusive coupling of explicit ODEs ("rate rules" in SBML)
• coupling of explicit ODEs through chemical synapse terms, appropriate for models representing membrane potentials

An additional unit can be added — called medium — which only contains the transported species, but is connected to all other units.

It is also possible to add randomness to parameter values, such that each unit becomes slightly different from each other.

Practical uses of sbmodelr include:

• using a cell model to create a model of a tissue or organoid,
• use a gene transcription model to create a gene regulatory network
• use a neuron model (e.g. the Hodgkin-Huxley) to create a network of neurons

The output of this program is a new model file with the more complex model. It is expected that the user may still have to tune parts of the resulting model in a regular modeling tool, such as COPASI, VCell, etc., where the model will be used for simulations. (sbmodelr only creates models, it does not carry out simulations.)

Usage

See User Manual for complete description of how to use sbmodelr. Detailed examples are provided in the examples folder.

Installation

The package works with python 3.8+ and requires the package copasi-basico (freely available on pypi).

You can install sbmodelr directly from pypi:

pip install sbmodelr

You can also install it directly from this repository:

pip install git+https://github.com/copasi/sbmodelr.git

or optionally for development with:

    git clone https://github.com/copasi/sbmodelr
    pip install -e ./sbmodelr

Credits

This program is inspired by MEG [1], a utility included in the old Gepasi simulator. The COPASI GUI and the BasiCO python API [2] both contain some functionality similar to that provided here, however they are limited to replicating compartments (with all their species and reactions) and connecting them by transport of species, but do not operate on global quantities, and can't add chemical synapse connections or regulatory interactions.

Thanks to Frank Bergmann for making BasiCO and the whole COPASI team for that simulator, which is ultimately the backend that is working behind sbmodelr.

References

1. Mendes P, Kell DB (2001) MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems. Bioinformatics 17:288–289
2. Bergmann FT (2023) BASICO: A simplified Python interface to COPASI. Journal of Open Source Software 8:5553

Funding

This package was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number GM137787 as part of the National Resource for Mechanistic Modeling of Cellular Systems. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

License

The software sbmodelr is Copyright © 2024 Pedro Mendes, Center for Cell Analysis and Modeling, UConn Health. It is provided under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge.