| Name | mxlbricks JSON |
| Version |
0.6.0
JSON |
| download |
| home_page | None |
| Summary | A package to build metabolic models |
| upload_time | 2025-09-11 08:53:26 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.12 |
| license | None |
| keywords |
metabolic
modelling
ode
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<p align="center">
<img src="https://raw.githubusercontent.com/Computational-Biology-Aachen/mxl-bricks/refs/heads/main/docs/assets/logo.png" width="400px" alt='mxlbricks-logo'>
</p>
# MxlBricks
[](https://pypi.python.org/pypi/mxlbricks)
[![docs][docs-badge]][docs]
[](https://github.com/astral-sh/ruff)
[](https://github.com/PyCQA/bandit)
[](https://pepy.tech/projects/mxlbricks)
[docs-badge]: https://img.shields.io/badge/docs-main-green.svg?style=flat-square
[docs]: https://computational-biology-aachen.github.io/mxl-bricks/
MxlBricks is a Python package to build mechanistic models composed of pre-defined reactions (bricks). This facilitates re-use and interoperability between different models by sharing common parts.
## Installation
You can install mxlpy using pip: `pip install mxlbricks`.
If you want access to the sundials solver suite via the [assimulo](https://jmodelica.org/assimulo/) package, we recommend setting up a virtual environment via [pixi](https://pixi.sh/) or [mamba / conda](https://mamba.readthedocs.io/en/latest/) using the [conda-forge](https://conda-forge.org/) channel.
```bash
pixi init
pixi add python assimulo
pixi add --pypi mxlbricks
```
## Development setup
Install pixi [as described in the docs](https://pixi.sh/latest/#installation).
Run
```bash
pixi instal
```
## Models
| Name | Description |
| -------------------- | --------------------------------------------------------------------------- |
| Ebenhöh 2011 | PSII & two-state quencher & ATP synthase |
| Ebenhöh 2014 | PETC & state transitions & ATP synthase from Ebenhoeh 2011 |
| Matuszyńska 2016 NPQ | 2011 + PSII & four-state quencher |
| Matuszyńska 2016 PhD | ? |
| Matuszyńska 2019 | Merges PETC (Ebenhöh 2014), NPQ (Matuszynska 2016) and CBB (Poolman 2000) |
| Saadat 2021 | 2019 + Mehler (Valero ?) & Thioredoxin & extendend PSI states & consumption |
| van Aalst 2023 | Saadat 2021 & Yokota 1985 & Witzel 2010 |
## References
| Name | Description |
| ------------ | ----------------------------------------------------- |
| Poolman 2000 | CBB cycle, based on Pettersson & Ryde-Pettersson 1988 |
| Yokota 1985 | Photorespiration |
| Valero ? | |
## Tool family 🏠
`MxlPy` is part of a larger family of tools that are designed with a similar set of abstractions. Check them out!
- [MxlPy](https://github.com/Computational-Biology-Aachen/MxlPy) is a Python package for mechanistic learning (Mxl)
- [MxlWeb](https://github.com/Computational-Biology-Aachen/mxl-web) brings simulation of mechanistic models to the browser!
Raw data
{
"_id": null,
"home_page": null,
"name": "mxlbricks",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.12",
"maintainer_email": "Marvin van Aalst <marvin.vanaalst@gmail.com>",
"keywords": "metabolic, modelling, ode",
"author": null,
"author_email": "Marvin van Aalst <marvin.vanaalst@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/88/e9/a1a68918c0a626cdaf1886b8f60e321a1c28644a602957a5737e73d4c068/mxlbricks-0.6.0.tar.gz",
"platform": null,
"description": "<p align=\"center\">\n <img src=\"https://raw.githubusercontent.com/Computational-Biology-Aachen/mxl-bricks/refs/heads/main/docs/assets/logo.png\" width=\"400px\" alt='mxlbricks-logo'>\n</p>\n\n# MxlBricks\n\n[](https://pypi.python.org/pypi/mxlbricks)\n[![docs][docs-badge]][docs]\n\n[](https://github.com/astral-sh/ruff)\n[](https://github.com/PyCQA/bandit)\n[](https://pepy.tech/projects/mxlbricks)\n\n[docs-badge]: https://img.shields.io/badge/docs-main-green.svg?style=flat-square\n[docs]: https://computational-biology-aachen.github.io/mxl-bricks/\n\nMxlBricks is a Python package to build mechanistic models composed of pre-defined reactions (bricks). This facilitates re-use and interoperability between different models by sharing common parts.\n\n## Installation\n\n\nYou can install mxlpy using pip: `pip install mxlbricks`.\n\n\nIf you want access to the sundials solver suite via the [assimulo](https://jmodelica.org/assimulo/) package, we recommend setting up a virtual environment via [pixi](https://pixi.sh/) or [mamba / conda](https://mamba.readthedocs.io/en/latest/) using the [conda-forge](https://conda-forge.org/) channel.\n\n```bash\npixi init\npixi add python assimulo\npixi add --pypi mxlbricks\n```\n\n\n## Development setup\n\nInstall pixi [as described in the docs](https://pixi.sh/latest/#installation).\n\nRun\n\n```bash\npixi instal\n```\n\n\n## Models\n\n| Name | Description |\n| -------------------- | --------------------------------------------------------------------------- |\n| Ebenh\u00f6h 2011 | PSII & two-state quencher & ATP synthase |\n| Ebenh\u00f6h 2014 | PETC & state transitions & ATP synthase from Ebenhoeh 2011 |\n| Matuszy\u0144ska 2016 NPQ | 2011 + PSII & four-state quencher |\n| Matuszy\u0144ska 2016 PhD | ? |\n| Matuszy\u0144ska 2019 | Merges PETC (Ebenh\u00f6h 2014), NPQ (Matuszynska 2016) and CBB (Poolman 2000) |\n| Saadat 2021 | 2019 + Mehler (Valero ?) & Thioredoxin & extendend PSI states & consumption |\n| van Aalst 2023 | Saadat 2021 & Yokota 1985 & Witzel 2010 |\n\n\n## References\n\n| Name | Description |\n| ------------ | ----------------------------------------------------- |\n| Poolman 2000 | CBB cycle, based on Pettersson & Ryde-Pettersson 1988 |\n| Yokota 1985 | Photorespiration |\n| Valero ? | |\n\n## Tool family \ud83c\udfe0\n\n`MxlPy` is part of a larger family of tools that are designed with a similar set of abstractions. Check them out!\n\n- [MxlPy](https://github.com/Computational-Biology-Aachen/MxlPy) is a Python package for mechanistic learning (Mxl)\n- [MxlWeb](https://github.com/Computational-Biology-Aachen/mxl-web) brings simulation of mechanistic models to the browser!\n",
"bugtrack_url": null,
"license": null,
"summary": "A package to build metabolic models",
"version": "0.6.0",
"project_urls": null,
"split_keywords": [
"metabolic",
" modelling",
" ode"
],
"urls": [
{
"comment_text": null,
"digests": {
"blake2b_256": "03e650a1bc327110c197f68f38e85751c7008e000e3b82941ad31fa0f5ac54d5",
"md5": "0ba50ab406c8f13069c99d532fae21b9",
"sha256": "11bb32dd989c0b4dcea94d3d0bce7623ad573b5a6454f388efc8aca32549a8b9"
},
"downloads": -1,
"filename": "mxlbricks-0.6.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "0ba50ab406c8f13069c99d532fae21b9",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.12",
"size": 107812,
"upload_time": "2025-09-11T08:53:24",
"upload_time_iso_8601": "2025-09-11T08:53:24.062042Z",
"url": "https://files.pythonhosted.org/packages/03/e6/50a1bc327110c197f68f38e85751c7008e000e3b82941ad31fa0f5ac54d5/mxlbricks-0.6.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": null,
"digests": {
"blake2b_256": "88e9a1a68918c0a626cdaf1886b8f60e321a1c28644a602957a5737e73d4c068",
"md5": "2757bf09450aa1c27df33672795a4b20",
"sha256": "18dc37b18a5c8bfdb2ce45c61d48d34bb9b543cbcdb333c965675c8a6e08ed43"
},
"downloads": -1,
"filename": "mxlbricks-0.6.0.tar.gz",
"has_sig": false,
"md5_digest": "2757bf09450aa1c27df33672795a4b20",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.12",
"size": 711575,
"upload_time": "2025-09-11T08:53:26",
"upload_time_iso_8601": "2025-09-11T08:53:26.462545Z",
"url": "https://files.pythonhosted.org/packages/88/e9/a1a68918c0a626cdaf1886b8f60e321a1c28644a602957a5737e73d4c068/mxlbricks-0.6.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-09-11 08:53:26",
"github": false,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"lcname": "mxlbricks"
}
