A package to build metabolic models

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for ebenhoeh from gravatar.com ebenhoeh Avatar for jmass from gravatar.com jmass Avatar for marvin.vanaalst from gravatar.com marvin.vanaalst Avatar for matuszynska from gravatar.com matuszynska Avatar for qtb from gravatar.com qtb

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: GNU General Public License v3 or later (GPLv3+) (GPL-3.0-or-later)
  • Author: Marvin van Aalst
  • Maintainer: Marvin van Aalst
  • Tags modelling , ode , metabolic
  • Requires: Python >=3.7.1, <3.11
Classifiers
Report project as malware

Project description

modelbase

pipeline status coverage report Documentation Status PyPi Code style: black Checked with mypy Downloads

modelbase is a python package to help you build and analyze dynamic mathematical models of biological systems. It has originally been designed for the simulation of metabolic systems, but can be used for virtually any processes, in which some substances get converted into others.

modelbase incorporates an easy construction method to define 'reactions'. A rate law and the stoichiometry need to be specified, and the system of differential equations is assembled automatically.

modelbase allows 'algebraic modules', which are useful to implement rapid equilibrium or quasi steady-state approximations. In the simplest instance, they allow easy incorporation of conserved quantities.

modelbase also allows a simple construction of isotope-specific models. This class contains a constructor method that automatically construct all isotope specific versions of a particular reaction. Very cool - check it out!

Release notes

Versions 1.0 and 0.4.0 introduced changes not compatible with the previous official release 0.2.5. API changes are summarised in this notebook

Version 0.4.5 was the prior stable version

Version 0.2.5 is the official release for the submission of the mansucript "Building mathematical models of biological systems with modelbase, a Python package for semi-automatic ODE assembly and construction of isotope-specific models" to the Journal of Open Research Software.

See changelog.md for details on changes of earlier versions.

Installation

If you quickly want to test out modelbase, or do not require assimulo support, install modelbase via

pip install modelbase

To enable assimulo support, the easiest way is to install modelbase via conda. We also recommend using the conda-forge channels.

# recommended to avoid package clashes
conda config --add channels conda-forge

# Create a new environment (not necessary, but recommended)
conda create -n mb39 python=3.9
conda install -c conda-forge modelbase

License

GPL 3

Documentation

The official documentation is hosted on ReadTheDocs.

Issues and support

If you experience issues using the software please contact us through our issues page.

Contributing to modelbase

All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome. See our contribution guide for more information.

How to cite

If you use this software in your scientific work, please cite this article:

van Aalst, M., Ebenhöh, O. & Matuszyńska, A. Constructing and analysing dynamic models with modelbase v1.2.3: a software update. BMC Bioinformatics 22, 203 (2021)

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for ebenhoeh from gravatar.com ebenhoeh Avatar for jmass from gravatar.com jmass Avatar for marvin.vanaalst from gravatar.com marvin.vanaalst Avatar for matuszynska from gravatar.com matuszynska Avatar for qtb from gravatar.com qtb

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: GNU General Public License v3 or later (GPLv3+) (GPL-3.0-or-later)
  • Author: Marvin van Aalst
  • Maintainer: Marvin van Aalst
  • Tags modelling , ode , metabolic
  • Requires: Python >=3.7.1, <3.11
Classifiers

Release history Release notifications | RSS feed

1.58.0

1.57.18

1.57.17

1.57.16

1.57.15

1.57.14

1.57.13

1.57.12

1.57.11

1.57.10

1.57.9

1.57.8

1.57.7

1.57.6

1.57.5

1.57.4

1.57.3

1.57.2

1.57.1

1.57.0

1.56.8

1.56.7

1.56.6

1.56.5

1.56.4

1.56.3

1.56.2

1.56.1

1.55.0

1.54.0

1.53.4

1.53.3

1.53.2

1.53.1

1.53.0

1.52.1

1.52.0

1.51.5

1.51.4

1.51.3

1.51.2

1.51.1

1.51.0

1.50.9

1.50.8

1.50.7

1.50.6

1.50.5

1.50.4

1.50.3

1.50.2

1.50.1

1.50.0

1.49.11

1.49.10

1.49.9

1.49.8

1.49.7

1.49.6

1.49.5

1.49.4

1.49.3

1.49.2

1.49.1

1.49.0

1.48.0

1.47.2

1.47.1

1.47.0

1.46.0

1.45.0

1.44.0

1.43.7

1.43.6

1.43.5

1.43.4

1.43.3

1.43.2

1.43.1

1.43.0

1.42.4

1.42.3

1.42.2

1.42.1

1.42.0

1.41.1

1.41.0

1.40.0

1.39.1

1.39.0

1.38.1

1.38.0

1.37.3

1.37.2

1.37.1

1.37.0

1.36.1

1.36.0

1.35.0

1.34.4

1.34.3

1.34.2

1.34.1

1.34.0

1.33.4

1.33.3

1.33.2

1.33.1

1.33.0

1.32.0

1.31.2

1.31.1

1.31.0

1.30.0

1.29.2

1.29.1

1.29.0

1.28.2

1.28.1

1.28.0

1.27.0

1.26.2

1.26.1

1.26.0

1.25.6

1.25.5

1.25.4

1.25.3

1.25.2

1.25.1

1.25.0

1.24.2

1.24.1

1.24.0

1.23.0

1.22.3

1.22.2

1.22.1

1.22.0

1.21.1

1.21.0

1.20.0

1.19.0

1.18.11

1.18.10

1.18.9

1.18.8

1.18.7

1.18.6

1.18.5

1.18.4

1.18.3

1.18.2

1.18.1

1.18.0

1.17.4

1.17.3

1.17.2

1.17.1

1.17.0

1.16.0

1.15.0

1.14.3

1.14.2

1.14.1

1.14.0

1.13.1

1.13.0

1.12.0

1.11.0

1.10.1

1.10.0

1.9.3

1.9.2

1.9.1

1.8.4

1.8.2

1.8.1

1.8.0

1.7.1

1.7.0

1.6.2

1.6.1

1.6.0

This version

1.5.17

1.5.15

1.5.14

1.5.13

1.5.12

1.5.11

1.5.10

1.5.9

1.5.8

1.5.7

1.5.6

1.5.5

1.5.4

1.5.3

1.5.2

1.5.1

1.5.0

1.4.1

1.4.0

1.3.9

1.3.8

1.3.7

1.3.6

1.3.5

1.3.4

1.3.3

1.3.2

1.3.1

1.3.0

1.2.3

1.2.2

1.2.1

1.2.0

1.1.post1

1.1

1.0.post1

1.0

1rc2 pre-release

0.4.5

0.4.4

0.4.3

0.4.2

0.4.1

0.4.0

0.2.5

0.2.4

0.2.3

0.2.2

0.2.1

0.2

0.1.9

0.1.8

0.1.7

0.1.6

0.1.5

0.1.4

0.1.3

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

modelbase-1.5.17.tar.gz (79.4 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

modelbase-1.5.17-py3-none-any.whl (94.6 kB view details)

Uploaded Python 3

File details

Details for the file modelbase-1.5.17.tar.gz.

File metadata

  • Download URL: modelbase-1.5.17.tar.gz
  • Upload date:
  • Size: 79.4 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: poetry/1.1.13 CPython/3.9.10 Linux/5.4.109+

File hashes

Hashes for modelbase-1.5.17.tar.gz
Algorithm Hash digest
SHA256 42be799dc9e9f5337ad68ae26ea8f3edb93ce039cc767b584fedfd8e3560c97e
MD5 0601d4f3e56f13ecfbb35d9299eeeb2c
BLAKE2b-256 50db93046623f3b7faa73d2886187458a367d2749bddabb92d9937c1f92f7dcf

See more details on using hashes here.

File details

Details for the file modelbase-1.5.17-py3-none-any.whl.

File metadata

  • Download URL: modelbase-1.5.17-py3-none-any.whl
  • Upload date:
  • Size: 94.6 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: poetry/1.1.13 CPython/3.9.10 Linux/5.4.109+

File hashes

Hashes for modelbase-1.5.17-py3-none-any.whl
Algorithm Hash digest
SHA256 0f25ba2c32b179dc757240147f6dc9ea9a0d55e2e2ca27ed879ee80020b918a2
MD5 30db868288ea96fb1e1ded857a077b6a
BLAKE2b-256 e126c287d65e293d9191807c06553b2639219cac6746b201fccc2d02235b542f

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page