Repositories list

• cbmpy-metadraft

  Public
  CBMPy Metadraft: a flexible and extensible genome-scale model reconstruction tool

  genome-scale-modelscbmpymodel-reconstruction+ 1python

  Python

  •

  GNU General Public License v3.0

  •2•2•5•0•Updated Jul 19, 2024Jul 19, 2024

• GECKO

  Public
  Toolbox for including enzyme constraints on a genome-scale model.

  MATLAB

  •

  MIT License

  •51•0•0•0•Updated Jul 18, 2024Jul 18, 2024

• ecmtool

  Public
  Uncover organisms' metabolic blueprints

  Python

  •

  MIT License

  •6•12•1•1•Updated Jun 18, 2024Jun 18, 2024

• parcr

  Public
  Construct parser combinators in R

  parserparsinghigher-order-functions+ 2r-packagecombinators

  HTML

  •

  Other

  •0•4•0•0•Updated Jun 7, 2024Jun 7, 2024

• pub-data

  Public archive
  Repository for published, public supplementary material (archived, for new data please use a data repository)

  HTML

  •3•0•0•0•Updated Jun 1, 2024Jun 1, 2024

• cbmpy

  Public
  CBMPy is a Python based platform for constraint based modelling and analysis.

  bioinformaticssystems-biologyconsole-application+ 5modelling-frameworksbmlconstraint-based-modelingcbmpypython

  Python

  •

  GNU General Public License v3.0

  •6•18•14•0•Updated May 12, 2024May 12, 2024

• dynamic-community-fba

  Public
  Dynamic Community FBA repository

  Python

  •

  MIT License

  •0•3•1•0•Updated Jan 10, 2024Jan 10, 2024

• stochpy

  Public
  StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

  pythonbioinformaticssystems-biology+ 3console-applicationstochastic-simulation-algorithmkinetic-modeling

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11•40•3•0•Updated Nov 14, 2022Nov 14, 2022

• analysis-of-EDA-data

  Public
  HTML

  •0•0•0•0•Updated Apr 21, 2022Apr 21, 2022

• anaerobic-benzene-degrading-culture

  Public
  Code repository for Chrats paper

  speciesbioreactorbenzene-degradation

  Other

  •1•0•0•0•Updated May 8, 2021May 8, 2021

• elementary-mode-based-FBA-rationale

  Public
  Code that uses Elementary Conversion Mode computation to obtain all relevant conversions for a constraint-based optimization problem, i.e., all possible optimal yields between the constrained nutrients and the objective function. As published in Metabolites https://doi.org/10.3390/metabo11050257

  pythonsystems-biologyfba+ 2efmmetabolic-model

  Python

  •0•1•0•0•Updated Apr 15, 2021Apr 15, 2021

• cbmpy-metadraft-templates

  Public
  Template models for MetaDraft

  Other

  •1•0•0•0•Updated Nov 3, 2020Nov 3, 2020

• funciminer

  Public
  R

  •1•0•0•0•Updated Oct 2, 2020Oct 2, 2020

• sbl-template-pub

  Public template
  Template for new SysBioLab repositories

  0•0•0•0•Updated Jul 15, 2020Jul 15, 2020

• metadraft

  Public
  MetaToolkit-MetaDraft GUI based reconstruction of genome scale metabolic models

  0•0•1•0•Updated Apr 27, 2020Apr 27, 2020

• memesa-tools

  Public
  This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function

  linear-programmingflux-balance-analysispolyhedron+ 2solution-enumerationpipeline

  Python

  •3•0•0•0•Updated Feb 27, 2020Feb 27, 2020

• HILIC-MS-Detrending

  Public
  R

  •0•0•0•0•Updated May 21, 2018May 21, 2018

• yeast_metabolic_map

  Public
  visualisation of the yeast metabolic network

  Python

  •2•1•0•0•Updated Jul 11, 2017Jul 11, 2017

• vonda

  Public
  VoNDA: Visualization of Network DAta

  Python

  •2•0•0•0•Updated Jan 19, 2017Jan 19, 2017