Metabolic modelling simulation and analysis tools for diverse yeast species.
This repository contains a collection of scripts for simulation, modification, data integration and visualization using Genome-scale mEtabolic Models (GEMs) for probing metabolic capabilities of yeast organisms.
KeyWords
Utilisation: GEMs reconstruction, FBA, metabolic engineering, data integration; Field: Constraint-based methods; Omic Source: NA
Last update: 2020-12-11
This repository is administered by @IVANDOMENZAIN, Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology
Anybody is welcome to contribute to the development of this modeling and simulation Toolbox, but please abide by the following guidelines.
Each function should start with a commented section describing the function and explaining the parameters. Existing functions can clarify what style should be used. When making any changes to an existing function (*.m
-file), change the date and name of developer near the bottom of this commented section in the last modified line.
devel
and name the branch for instance after the function/feature you are fixing/developing. If you work on a fix, start the branch name with fix/
, if you work on a feature, start the branch name with feat/
. Examples: fix/format_reactions
or feat/new_algorithms
.devel
branch. Also, see Pull request below.Use semantic commit messages to make it easier to show what you are aiming to do:
chore
: updating binaries (model MATLAB
structures), UniProt databases, physiology and protemics data files, etc.doc
: updating documentation (in doc
folder) or explanatory comments in functions.feat
: new feature added, e.g. new function introduced / new parameters / new algorithm / etc.fix
: bugfix.refactor
: see code refactoring.style
: minor format changes of functions (spaces, semi-colons, etc., no code change).Examples:
feat: exportModel additional export to YAML
chore: update UniProt database for CENPK113-7D
fix: optimizeProb parsing results from Gurobi
More detailed explanation or comments can be left in the commit description.
master
or devel
branches. Commits are made to side-branches, after which pull requests are made for merging with master
or devel
.