isrene

Isotopologue reaction networks in Python

https://github.com/dweindl/isrene

Science Score: 57.0%

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Repository

Isotopologue reaction networks in Python

Basic Info

Host: GitHub
Owner: dweindl
License: bsd-3-clause
Language: Python
Default Branch: main
Size: 90.8 KB

Statistics

Stars: 1
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Created over 2 years ago · Last pushed 8 months ago

Metadata Files

Readme License Citation

Overview

isrene (pronounced "is-reen") is a Python package for creating dynamic models of metabolic isotopologue reaction networks.

Features

Writing up the equations for a dynamic model of metabolic stable isotope labeling experiments can be tedious and error-prone. isrene aims to make this process easier by providing a Python interface for:

specifying metabolic reaction networks in terms of reaction patterns (rule-based models) describing stoichiometry, reversibility, kinetics, and atom mappings
specifying isotopic tracers
conveniently specifying observation functions for mass spectrometry measurements
exporting the rule-based model to SBML-multi
generating the full species/reaction network from the rule-based formulation and exporting it to core-SBML

Installation

isrene is not yet available on PyPI. To install, clone this repository and run pip install . from the root directory.

Getting Started

Check out the examples at examples/ to get started.

Documentation

So far, only example notebooks and in-source documentation are available.

Development status

Note that isrene has not been thoroughly tested and is still under development. Use with caution. In particular, there is insufficient error checking, and certain assumptions are made on the uniqueness of identifiers and combinations thereof.

If you are interested in a collaboration to apply or extend this package, please contact the author.

Owner

Name: Daniel Weindl
Login: dweindl
Kind: user
Company: @ICB-DCM @ICBmunich

Website: https://backup.helmholtz-munich.de/icb/institute/staff/staff/ma/5122/Dr.-Weindl/index.html
Twitter: dweindl
Repositories: 3
Profile: https://github.com/dweindl

PostDoc at Helmholtz Munich ORCID 0000-0001-9963-6057

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: isrene
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Daniel
    family-names: Weindl
    email: sci@danielweindl.de
    orcid: 'https://orcid.org/0000-0001-9963-6057'
repository-code: 'https://github.com/dweindl/isrene/'
abstract: ' Isotopologue reaction networks in Python'
license: BSD-3-Clause

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