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https://github.com/matthiaskoenig/dfba

Encoding Dynamic Flux Balance Analysis in SBML
https://github.com/matthiaskoenig/dfba

dfba sbml simulation

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Encoding Dynamic Flux Balance Analysis in SBML

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README 

        
# Dynamic Flux Balance Analysis in SBML

[![DOI](https://www.zenodo.org/badge/71236313.svg)](https://www.zenodo.org/badge/latestdoi/71236313)

[![GitHub version](https://badge.fury.io/gh/matthiaskoenig%2Fdfba.svg)](https://badge.fury.io/gh/matthiaskoenig%2Fdfba)

[![License (LGPL version 3)](https://img.shields.io/badge/license-LGPLv3.0-blue.svg?style=flat-square)](http://opensource.org/licenses/LGPL-3.0)



 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](./schema/DFBA_models_in_SBML.md). 



As part of this project DFBA implementations based on these guidelines have been implemented in 

[iBioSim](http://www.async.ece.utah.edu/ibiosim) and [sbmlutils](https://github.com/matthiaskoenig/sbmlutils/).

 



 

 



This repository contains the following content

* [`./docs/`](./docs/): documentation, presentation, tutorial

* [`./schema/`](./schema/): guidelines for encoding DFBA in SBML

* [`./models/`](./models/): examples models with simulation results, cytoscape visualizations, jupyter notebooks

* [`./README.md`](./README.md): this document



Detailed instructions on how to run the example models are provided [below](#running-example-models).



## Standardization

This effort builds on existing standards, i.e., [SBML](http://sbml.org), [SED-ML](http://sed-ml.org), and the [COMBINE archive](http://co.mbine.org/documents/archive).



 

 

 



##  How to cite

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



[![DOI](https://www.zenodo.org/badge/71236313.svg)](https://www.zenodo.org/badge/latestdoi/71236313)



The latest manuscript is available from

[https://www.overleaf.com/6382003zbbpfy#/21488847/](https://www.overleaf.com/6382003zbbpfy#/21488847/).



  

## License

* Source Code: [LGPLv3](http://opensource.org/licenses/LGPL-3.0)

* Documentation: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)



## Funding

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.



 



# Example models

Model examples encoded in the proposed dynamic FBA scheme in the [`./models/`](./models/) folder. 

Example models contain

* SBML model(s) according to guidelines and rules

* SED-ML file encoding example simulation experiments

* Simulation results for [iBioSim](http://www.async.ece.utah.edu/ibiosim) and [sbmlutils](https://github.com/matthiaskoenig/sbmlutils/)

* Jupyter notebooks

* Cytoscape visualization



The model examples are provided as COMBINE archives for exchange.



## sbmlutils 

 



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/index.ipynb)



* [`./models/toy_wholecell/toy_wholecell.ipynb`](./models/toy_wholecell/toy_wholecell.ipynb)

* [`./models/toy_atp/toy_atp.ipynb`](./models/toy_atp/toy_atp.ipynb)

* [`./models/diauxic_growth/diauxic_growth.ipynb`](./models/diauxic_growth/diauxic_growth.ipynb)

* [`./models/ecoli/ecoli.ipynb`](./models/ecoli/ecoli.ipynb)



## iBioSim




To use iBioSim, you can follow the instructions available [here](./models/iBioSim_Tutorial.md).



## Tool reproducibility

The numerical identity of the results was checked with results available in the

following notebook  

[`./models/compare.ipynb`](./models/compare.ipynb)