semvec/pypi-packages huggingface dataset:
SBMLKinetics 1.1.1
Analyze SBML kinetics.
License: MIT License
Requires Python: >=3.8

[![Coverage](https://codecov.io/gh/ModelEngineering/SBMLKinetics/branch/master/graph/badge.svg)](https://codecov.io/gh/ModelEngineering/SBMLKinetics)

# SBMLKinetics

SBMLKinetics is a Python package to evaluate and classify kinetics in SBML models. 
There are many possible kinetics like the zeroth order, mass action, Michaelis-Menten, 
Hill kinetics and others. This work characterizes the kinetics in the BioModels 
Database as an example to improve modeling best practices. Our tool can analyze any data sets 
with SBML files as input. Users can also use this tool to compare different data sets. For 
instance, we compare the distribution of kinetics for the signaling and metabolic networks and 
find the substantial differences between two types of networks. 

## Citing
If you are using any of the 
code, please cite the article (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05380-3) and the PYPI web page (https://pypi.org/project/SBMLKinetics/).

## For users
### Installation

``pip install SBMLKinetics``

## A Classification Example

Here is a classification example generated by SBMLKinetics:

<img src="https://raw.githubusercontent.com/SunnyXu/SBMLKinetics/master/docs/Figures/Fig2_signalling_vs_metabolic.png" width="900" height="330">

Please see more examples in the documentation.

### Documentation
Please see the documentation at https://sunnyxu.github.io/SBMLKinetics/ for details.


## For developers
### Setup environment
- Install [spyder3](http://www.psych.mcgill.ca/labs/mogillab/anaconda2/lib/python2.7/site-packages/spyder/doc/installation.html)
- Clone the ``SBMLKinetics`` repository using ``git clone https://github.com/SunnyXu/SBMLKinetics``
- Create a virtual environment for the project.
  - ``cd SBMLKinetics``
  - ``python -m venv kv``
  - ``source kv/Scripts/activate``
(Use "\\" in windows.)
  - ``pip install -r requirements.txt``
  - ``deactivate``

To verify the setup:
- Return to the ``SBMLKinetics`` directory.
- ``source kv/Scripts/activate``
(Use "\\" in windows.)
- ``export PYTHONPATH=`pwd` ``
- ``python tests/test_simple_sbml.py``. The
tests should run without error.
(Use "\\" in windows.)

### Running Codes
- ``cd SBMLKinetics``
- ``source kv/bin/activate``
(Use "\\" in windows.)
When you're done, use ``deactivate``.

### Documentation
- ``examples/tutorial.py`` has code illustrating usage
- ``SBMLKinetics/common/*.py`` has codes for the 
SmpleSBML (``simple_sbml.py``),
Reaction (``reaction.py``),
and KineticLaw (``kinetic_law.py``).
SBMLDiagrams 1.4.2
Visualize, edit and write SBML files.
License: MIT License
Requires Python: >=3.8

# SBMLDiagrams
[![Coverage](https://codecov.io/gh/sunnyXu/SBMLDiagrams/branch/main/graph/badge.svg)](https://codecov.io/gh/sunnyXu/SBMLDiagrams)

[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT) [![PyPI version](https://badge.fury.io/py/SBMLDiagrams.svg)](https://badge.fury.io/py/SBMLDiagrams) [![PyPI download month](https://img.shields.io/pypi/dm/ansicolortags.svg)](https://pypi.python.org/pypi/SBMLDiagrams/) ![Funding](https://img.shields.io/badge/Funding-NIH%20(EB028887)-blue)

## Introduction

SBMLDiagrams is a Python package to visualize networks embedded in SBML Level 3 models. If the SBML layout and render extension are used, the package will use this data to display the network. SBMLDiagrams can export PNG, JPG, PDF files. SBMLDiagrams can be used to add SBML layout and render to an existing valid SBML model which can subsequently be exported.

We also have an interface of SBMLDiagrams to NetworkX to exploit the variety of layout algorithms. 

***Note that please make sure to save a copy of your SBML file before importing into SBMLDiagrams.***

## Citing
If you are using any of the code, please cite the article (https://doi.org/10.1093/bioinformatics/btac730) and the PYPI web page (https://pypi.org/project/SBMLDiagrams/). 

## Installation

``pip install SBMLDiagrams``

## A Figure Example

Here is a figure example visualized by SBMLDiagrams below. Users could use another GUI tool SBcoyote (https://github.com/sys-bio/SBcoyote; https://doi.org/10.1016/j.biosystems.2023.105001) together with SBMLDiagrams to adjust positions, i.e., bezier curves of reactions.

<img src="https://raw.githubusercontent.com/SunnyXu/SBMLDiagrams/main/docs/Figures/Introduction/Jana_WolfGlycolysis-corrected.png" width="350" height="500">


Its animation is also available at https://youtu.be/6VgjzrXLLoc. 
Please see more figure examples in the documentation.

## Documentation
Please see the documentation at https://sys-bio.github.io/SBMLDiagrams/ for details.