dcfba

Dynamic Community FBA repository

https://github.com/systemsbioinformatics/dynamic-community-fba

Science Score: 44.0%

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CITATION.cff file
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Scientific vocabulary similarity
Low similarity (9.9%) to scientific vocabulary

Last synced: 9 months ago · JSON representation ·

Repository

Dynamic Community FBA repository

Basic Info

Host: GitHub
Owner: SystemsBioinformatics
License: mit
Language: Python
Default Branch: main
Size: 14.2 MB

Statistics

Stars: 5
Watchers: 3
Forks: 0
Open Issues: 1
Releases: 0

Created over 4 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

Dynamic Community FBA

Welcome to Dynamic Community FBA (dcFBA): The Python package that makes modeling Microbial Communities dynamically a breeze!

This project is licensed under the MIT License - please refer to the LICENSE file for more details.

About

Dynamic Community FBA (dcFBA) is a versatile tool designed for modeling microbial communities as single organisms using Genome Scale Metabolic Models (GSMMs). This package builds upon the solid foundation of cbmpy and seamlessly integrates with SBML and COBRApy models. dcFBA empowers users with three distinct dynamic modeling methods:

Dynamic Joint FBA - Incrementally updates the concentrations of biomass and metabolites within the combined stoichiometric matrix of the provided models.
Dynamic Parallel FBA - Simultaneously updates the concentrations of biomass and metabolites while performing FBA on individual models.
EndPointFBA - Duplicates the CommunityMatrix N times and performs FBA on the community's time-dependent stoichiometric matrix.

For a comprehensive understanding of these methods and their underlying mathematics, please consult [^1].

Whether you're exploring parasitic interactions or investigating costly cross-feeding behaviors in microbial communities, dcFBA offers an elegant and efficient solution.

Installation

Prerequisites

Before installing dcFBA, make sure you have the following prerequisites in place:

Python >= 3.8, < 3.11
cbmpy
cplex

Installation Steps

To install dcFBA, follow these simple steps:

Install using pip:

bash pip install dcFBA

Usage

For basic usage examples and detailed documentation on both cbmpy and dcFBA, please refer to their respective documentation pages.

[^1]: [Cite paper.]

Owner

Name: Systems Biology Lab, Vrije Universiteit Amsterdam
Login: SystemsBioinformatics
Kind: organization
Location: Amsterdam, The Netherlands

Website: http://teusinkbruggemanlab.nl/
Repositories: 6
Profile: https://github.com/SystemsBioinformatics

This is the code repository of the Systems Biology Lab. Our lab studies the molecular networks inside cells that give rise to cell behaviour and fitness.

Citation (CITATION.cff)

cff-version: 1.2.0

message: "If you use this software, please cite it as below."

# IF THE REPOSITORY ISN'T LINKED TO A SCIENTIFIC PAPER, CITE DIRECTLY THE REPOSITORY

authors:
- family-names: "Moro"
  given-names: "Francesco"
  orcid: "https://orcid.org/0000-0003-3683-187X"
  affiliation: "Vrije Universiteit Amsterdam"
- family-names: "Wijnen"
  given-names: "Steven"
  affiliation: "Vrije Universiteit Amsterdam"
- family-names: "Mendoza"
  given-names: "Sebastián N."
  orcid: "https://orcid.org/0000-0002-2192-5569"
  affiliation: "Vrije Universiteit Amsterdam"
- family-names: "Lischke"
  given-names: "Julia"
  orcid: "https://orcid.org/0000-0002-5524-2838"
  affiliation: "Vrije Universiteit Amsterdam"
- family-names: "Olivier"
  given-names: "Brett G."
  orcid: "https://orcid.org/0000-0002-5293-5321"
  affiliation: "Vrije Universiteit Amsterdam"
- family-names: "Bruggeman"
  given-names: "Frank J."
  orcid: "https://orcid.org/0000-0002-0255-4766"
  affiliation: "Vrije Universiteit Amsterdam"
- family-names: "Teusink"
  given-names: "Bas"
  orcid: "https://orcid.org/0000-0003-3929-0423"
  affiliation: "Vrije Universiteit Amsterdam"

title: "dynamic-community-fba"
version: 0.1.2
#doi: 10.5281/zenodo.1234 # Optional, add your Zenodo DOI if you have one
date-released: 2023-11-13

repository-code: "https://github.com/SystemsBioinformatics/dynamic-community-fba"
license: MIT
url: "https://dynamic-community-fba.readthedocs.io/en/latest/"  # Optional website/docs


# IF THE REPOSITORY IS LINKED TO A SCIENTIFIC PAPER, CITE THE PAPER

# preferred-citation:
#   type: article

#   authors:
#   - family-names: "Lisa"
#     given-names: "Mona"
#     orcid: "https://orcid.org/0000-0000-0000-0000"
#     affiliation: Università degli Studi di Padova
#   - family-names: "Bot"
#     given-names: "Hew"
#     orcid: "https://orcid.org/0000-0000-0000-0000"
#     affiliation: Università degli Studi di Padova

#   doi: "10.0000/00000"
#   journal: "Journal Title"
#   publisher: "Publisher Name"
#   month: 9
#   start: 1 # First page number
#   end: 10 # Last page number
#   title: "A Comprehensive Study on XYZ: Insights from the Template Repository"
#   issue: 1
#   volume: 1
#   year: 2025
#   url: "https://doi.org/10.1000/journal.pone.0123456"

GitHub Events

Total

Watch event: 1
Push event: 1

Last Year

Watch event: 1
Push event: 1

Packages

Total packages: 1
Total downloads:
- pypi 22 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 4
Total maintainers: 3

pypi.org: dcfba

Python package for Dynamic Community FBA

Homepage: https://github.com/SystemsBioinformatics/dynamic-community-fba
Documentation: https://dcfba.readthedocs.io/
License: MIT License Copyright (c) 2023 Steven Wijnen Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Latest release: 0.1.2
published over 2 years ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 22 Last month

Rankings

Dependent packages count: 9.6%

Forks count: 29.9%

Average: 36.6%

Stargazers count: 38.9%

Dependent repos count: 67.9%

Maintainers (3)

bgoli StevenWijnen morof17

Last synced: 10 months ago

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