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yaml2sbml

yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML - Published in JOSS (2021)

https://github.com/yaml2sbml-dev/yaml2sbml

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

ode ode-model petab sbml yaml
Last synced: 6 months ago · JSON representation

Repository

Tool to convert an ODE model specified in the YAML format to SBML.

Basic Info
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 7
  • Open Issues: 8
  • Releases: 6
Topics
ode ode-model petab sbml yaml
Created about 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

yaml2sbml logo

CI codecov Documentation Status Codacy Badge PyPI DOI

Table of contents

About

yaml2sbml is a small package in Python to convert an ODE model specified in a YAML file into SBML for ODE simulation and into PEtab for parameter fitting. yaml2sbml offers:

  • a translator of ODE models specified in YAML into SBML/PEtab via a Python and a command-line interface;
  • a format validator for the input YAML; and
  • a model editor, which provides a simplified interface to generate, import and export YAML models.

Installation

yaml2sbml can be installed from PyPI with

shell pip install yaml2sbml For more info see the docs.

Getting Started

Basic Syntax

Python

A YAML model can be translated to SBML/PEtab in Python via ```python import yaml2sbml

SBML conversion

yaml2sbml.yaml2sbml(yamldir, sbmldir)

PEtab conversion

yaml2sbml.yaml2petab(yamldir, outputdir, sbml_name) ```

Command-Line Interface

and in the command-line via ```shell

SBML conversion

yaml2sbml

PEtab conversion

yaml2petab ```

Format Validation

Format validation is possible in Python via yaml2sbml.validate_yaml and in the command-line via yaml2sbml_validate.

How to cite

yaml2sbml is published in the Journal of Open Source Software.

When using yaml2sbml in your project, please cite

  • Vanhoefer J., Matos, M. R. A., Pathirana, D., Schälte, Y. and Hasenauer, J. (2021). yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML. Journal of Open Source Software, 6(61), 3215, https://doi.org/10.21105/joss.03215

@article{Vanhoefer2021, doi = {10.21105/joss.03215}, url = {https://doi.org/10.21105/joss.03215}, year = {2021}, publisher = {The Open Journal}, volume = {6}, number = {61}, pages = {3215}, author = {Jakob Vanhoefer and Marta R. A. Matos and Dilan Pathirana and Yannik Schälte and Jan Hasenauer}, title = {yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML}, journal = {Journal of Open Source Software} }

Contact

If you have a question regarding the tool: Please drop us an issue or a mail, we are happy to help.

JOSS Publication

yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML
Published
May 27, 2021
DOI
Volume 6, Issue 61, Page 3215
Authors
Jakob Vanhoefer ORCID
Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Marta R. a. Matos ORCID
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
Dilan Pathirana ORCID
Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
Yannik Schälte ORCID
Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany, Department of Mathematics, Technical University Munich, Garching, Germany
Jan Hasenauer ORCID
Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany, Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany, Department of Mathematics, Technical University Munich, Garching, Germany
Editor
Kelly Rowland ORCID
Tags
SBML Ordinary Differential Equation YAML
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GitHub Events

Total
  • Issue comment event: 3
Last Year
  • Issue comment event: 3

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 237
  • Total Committers: 6
  • Avg Commits per committer: 39.5
  • Development Distribution Score (DDS): 0.641
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jakob Vanhoefer j****r@u****e 85
Jakob Vanhoefer 3****r 84
martamatos m****s@g****m 32
yannikschaelte y****e@g****m 23
Dilan Pathirana 5****h 12
The Codacy Badger b****r@c****m 1
Committer Domains (Top 20 + Academic)
codacy.com: 1 uni-bonn.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 42
  • Total pull requests: 61
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Total issue authors: 9
  • Total pull request authors: 6
  • Average comments per issue: 2.93
  • Average comments per pull request: 1.69
  • Merged pull requests: 52
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jvanhoefer (23)
  • yannikschaelte (11)
  • aidinbii (2)
  • martamatos (1)
  • elbaraim (1)
  • NicholasCowie (1)
  • AoifeHughes (1)
  • marouenbg (1)
Pull Request Authors
  • jvanhoefer (36)
  • yannikschaelte (12)
  • dilpath (8)
  • martamatos (3)
  • C-Peiter (1)
  • alex-treebeard (1)
Top Labels
Issue Labels
fixed but not released (6) question (3) enhancement (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 35 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 6
  • Total maintainers: 1
pypi.org: yaml2sbml

A small package to convert ODEs specified in a YAML file to SBML/PEtab

  • Versions: 6
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 35 Last month
Rankings
Dependent packages count: 4.7%
Forks count: 13.3%
Stargazers count: 16.0%
Average: 16.6%
Dependent repos count: 21.7%
Downloads: 27.1%
Maintainers (1)
jvanhoefer
Last synced: 6 months ago

Dependencies

.github/workflows/ci.yml actions
  • actions/cache v1 composite
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • codecov/codecov-action v1 composite
.github/workflows/deploy.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
setup.py pypi