Matthias König, Leandro Watanabe, Chris Myers

This repository provides guidelines and rules for the encoding of dynamic flux balance analysis (DFBA) models in SBML. The latest guidelines and rules are available from this repository at latest schema.

As part of this project DFBA implementations based on these guidelines have been implemented in iBioSim and sbmlutils.

This repository contains the following content

• ./docs/: documentation, presentation, tutorial
• ./schema/: guidelines for encoding DFBA in SBML
• ./models/: examples models with simulation results, cytoscape visualizations, jupyter notebooks
• ./README.md: this document

Detailed instructions on how to run the example models are provided below.

This effort builds on existing standards, i.e., SBML, SED-ML, and the COMBINE archive.

If you use these schema and guidelines and/or the provided examples, or want to reference the information within,
please cite corresponding manuscript and this repository via its DOI

The latest manuscript is available from https://www.overleaf.com/6382003zbbpfy#/21488847/.

• Source Code: LGPLv3
• Documentation: CC BY-SA 4.0

Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054).

The development of iBioSim is supported by the National Science Foundation under Grants CCF-1218095 and CCF-1748200. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Model examples encoded in the proposed dynamic FBA scheme in the ./models/ folder. Example models contain

• SBML model(s) according to guidelines and rules
• SED-ML file encoding example simulation experiments
• Simulation results for iBioSim and sbmlutils
• Jupyter notebooks
• Cytoscape visualization

The model examples are provided as COMBINE archives for exchange.

Example jupyter notebooks reproducing the results are available for the individual DFBA models. Installation instructions and the entry point is available at ./models/index.ipynb

• ./models/toy_wholecell/toy_wholecell.ipynb
• ./models/toy_atp/toy_atp.ipynb
• ./models/diauxic_growth/diauxic_growth.ipynb
• ./models/ecoli/ecoli.ipynb

To use iBioSim, you can follow the instructions available here.

The numerical identity of the results was checked with results available in the following notebook
./models/compare.ipynb