https://github.com/stelmo/differentiablemetabolism.jl

Differentiable constraint-based metabolic models
https://github.com/stelmo/differentiablemetabolism.jl

Last synced: 12 days ago
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Differentiable constraint-based metabolic models

• Host: GitHub
• URL: https://github.com/stelmo/differentiablemetabolism.jl
• Owner: stelmo
• License: apache-2.0
• Created: 2022-02-24T12:42:19.000Z (almost 3 years ago)
• Default Branch: master
• Last Pushed: 2024-12-06T10:37:53.000Z (17 days ago)
• Last Synced: 2024-12-06T11:27:52.584Z (17 days ago)
• Language: Julia
• Homepage:
• Size: 1.26 MB
• Stars: 11
• Watchers: 3
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# DifferentiableMetabolism.jl

| Build status | Documentation |

|:---:|:---:|

| ![CI status](https://github.com/stelmo/DifferentiableMetabolism.jl/workflows/CI/badge.svg) [![codecov](https://codecov.io/gh/stelmo/DifferentiableMetabolism.jl/branch/master/graph/badge.svg?token=A2ui7exGIH)](https://codecov.io/gh/stelmo/DifferentiableMetabolism.jl) | [![Documentation](https://img.shields.io/badge/documentation-8e44ad)](https://stelmo.github.io/DifferentiableMetabolism.jl/dev) |

This package extends [COBREXA.jl](https://github.com/LCSB-BioCore/COBREXA.jl)

with the ability to differentiate an optimal solution of a constraint-based

metabolic model with respect to parameters. 

Note, only non-degenerate (unique) solutions can be differentiated for the

derivatives to have a concrete interpretation. You need to ensure that your

solution is non-degenerate, otherwise you will only compute sub-gradients.

Builtin functionality (pruning) can help with this.

To use this package, [download and install Julia](https://julialang.org/downloads/), and add 

the following packages using the built in package manager:

```julia

] add COBREXA, DifferentiableMetabolism

```

Any optimization solver that is compatible with [JuMP](https://jump.dev/)

can be used, provided it can solve the optimization problems you are interested

in (LPs and QPs), and it returns the dual variables through the JuMP interface.

In the tests we use [Tulip.jl](https://github.com/ds4dm/Tulip.jl) for LPs, and

[Clarabel.jl](https://github.com/oxfordcontrol/Clarabel.jl) for QPs. Other

solvers, like Gurobi, work well, but they require a license (usually free for

academic use).

You can test the installation through:

```julia

] test DifferentiableMetabolism

```

For more information, please see the documentation.

This package is maintained and open for extensions. Feel free to discuss changes

and ideas via issues and pull requests.

#### Acknowledgements

`DifferentiableMetabolism.jl` was developed at Institute for Quantitative and

Theoretical Biology at Heinrich Heine University Düsseldorf

([qtb.hhu.de](https://www.qtb.hhu.de/en/)), and at the Luxembourg Centre for

Systems Biomedicine of the University of Luxembourg

([uni.lu/lcsb](https://www.uni.lu/lcsb)).