Metadata-Version: 2.1
Name: pasmopy
Version: 0.0.7
Summary: Patient-Specific Modeling in Python
Home-page: https://github.com/pasmopy/pasmopy
Author: Hiroaki Imoto
Author-email: himoto@protein.osaka-u.ac.jp
Maintainer: Hiroaki Imoto
Maintainer-email: himoto@protein.osaka-u.ac.jp
License: Apache 2.0
Download-URL: https://github.com/pasmopy/pasmopy/releases
Project-URL: Documentation, https://pasmopy.readthedocs.io/en/latest/
Project-URL: Source Code, https://github.com/pasmopy/pasmopy
Project-URL: Bug Tracker, https://github.com/pasmopy/pasmopy/issues
Keywords: systems,biology,cancer,stratification,personalized,modeling,simulation,precision,oncology
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: biomass (>=0.5.2)
Requires-Dist: numpy (>=1.17)
Requires-Dist: pandas (>=0.23)
Requires-Dist: seaborn (>=0.11)
Requires-Dist: scipy (>=1.6)
Requires-Dist: tqdm (>=4.50.2)
Requires-Dist: typing-extensions
Provides-Extra: dev
Requires-Dist: black (==21.9b0) ; extra == 'dev'
Requires-Dist: flake8 (==4.0.1) ; extra == 'dev'
Requires-Dist: isort (==5.9.3) ; extra == 'dev'
Requires-Dist: pre-commit ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Provides-Extra: docs
Requires-Dist: importlib-metadata ; extra == 'docs'
Requires-Dist: setuptools ; extra == 'docs'
Requires-Dist: setuptools-scm ; extra == 'docs'
Requires-Dist: sphinx (>=1.7) ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme (>=0.3) ; extra == 'docs'
Requires-Dist: sphinx-autodoc-typehints (>=1.10) ; extra == 'docs'
Requires-Dist: sphinxcontrib-bibtex (>=2.2) ; extra == 'docs'

# Pasmopy – Patient-Specific Modeling in Python

![overview](https://raw.githubusercontent.com/pasmopy/pasmopy/master/docs/_static/img/overview.png)

[![PyPI version](https://img.shields.io/pypi/v/pasmopy.svg?logo=PyPI&logoColor=white)](https://pypi.python.org/pypi/pasmopy)
[![Actions Status](https://github.com/pasmopy/pasmopy/workflows/Tests/badge.svg)](https://github.com/pasmopy/pasmopy/actions)
[![Documentation Status](https://img.shields.io/readthedocs/pasmopy/latest.svg?logo=read%20the%20docs&logoColor=white&&label=Docs&version=latest)](https://pasmopy.readthedocs.io/en/latest/?badge=latest)
[![License](https://img.shields.io/badge/License-Apache%202.0-green.svg?logo=apache)](https://opensource.org/licenses/Apache-2.0)
[![Downloads](https://pepy.tech/badge/pasmopy)](https://pepy.tech/project/pasmopy)
[![PyPI pyversions](https://img.shields.io/pypi/pyversions/pasmopy.svg?logo=Python&logoColor=white)](https://pypi.python.org/pypi/pasmopy)
[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/pasmopy/pasmopy.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/pasmopy/pasmopy/context:python)
[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/pasmopy/pasmopy/master.svg)](https://results.pre-commit.ci/latest/github/pasmopy/pasmopy/master)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)

**Pasmopy** is a scalable toolkit to identify prognostic factors for cancers based on intracellular signaling dynamics generated from personalized kinetic models. It is compatible with [biomass](https://github.com/biomass-dev/biomass) and offers the following features:

- Construction of mechanistic models from text
- Personalization of the model using transcriptome data
- Prediction of patient outcome based on _in silico_ signaling dynamics
- Sensitivity analysis for prediction of potential drug targets

## Documentation

The documentation is hosted on readthedocs.io: https://pasmopy.readthedocs.io

## Installation

The latest stable release (and required dependencies) can be installed from [PyPI](https://pypi.python.org/pypi/pasmopy):

```
$ pip install pasmopy
```

Pasmopy requires Python 3.7+ to run.

## Example

### Building mathematical models of biochemical systems from text

This example shows you how to build a simple Michaelis-Menten two-step enzyme catalysis model with Pasmopy.

> E + S ⇄ ES → E + P

_An enzyme, E, binding to a substrate, S, to form a complex, ES, which in turn releases a product, P, regenerating the original enzyme._

1. Prepare a text file describing the biochemical reactions (e.g., `michaelis_menten.txt`)

   ```
   E binds S --> ES | kf=0.003, kr=0.001 | E=100, S=50
   ES dissociates to E and P | kf=0.002, kr=0

   @obs Substrate: u[S]
   @obs E_free: u[E]
   @obs E_total: u[E] + u[ES]
   @obs Product: u[P]
   @obs Complex: u[ES]

   @sim tspan: [0, 100]
   ```

1. Convert the text into an executable model

   ```shell
   $ python
   ```

   ```python
   >>> from pasmopy import Text2Model
   >>> description = Text2Model("michaelis_menten.txt")
   >>> description.convert()
   ```

1. Run simulation

   ```python
   >>> from pasmopy import Model, run_simulation
   >>> import michaelis_menten
   >>> model = Model(michaelis_menten.__package__).create()
   >>> run_simulation(model)
   ```

   ![michaelis_menten](https://raw.githubusercontent.com/pasmopy/pasmopy/master/docs/_static/img/michaelis_menten_sim.png)

For more examples, please refer to the [Documentation](https://pasmopy.readthedocs.io/en/latest/).

### Personalized signaling models for cancer patient stratification

Using Pasmopy, we built a mechanistic model of ErbB receptor signaling network, trained with protein quantification data obtained from cultured cell lines, and performed _in silico_ simulation of the pathway activities on 377 breast cancer patients using The Cancer Genome Atlas (TCGA) transcriptome datasets. All the codes for model construction, patient-specific simulations, and model-based stratification can be found here: https://github.com/pasmopy/breast_cancer.

## Author

[Hiroaki Imoto](https://github.com/himoto)

## License

[Apache License 2.0](https://github.com/pasmopy/pasmopy/blob/master/LICENSE)


