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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# cobrar <img src="man/figures/logo.svg" align="right" />
<!-- badges: start -->
[](https://github.com/Waschina/cobrar/actions/workflows/R-CMD-check.yaml)
[](https://anaconda.org/bioconda/r-cobrar)
[](https://anaconda.org/bioconda/r-cobrar)
<!-- badges: end -->
The R package *cobrar* provides structures and functions for constraint-based metabolic network analysis, e.g. the prediction of metabolic fluxes using fluxes using Flux Balance Analysis (FBA). *cobrar* is inspired by the former CRAN R package *sybil*[(1)](#R1).
## Installation
Please note that *cobrar* requires the two system libraries *libSBML* and *glpk*. The following installation instructions for different operating systems install the dependencies first, then *cobrar*. If you already have *libSBML* and *glpk* installed, you can skip to the last part of the instructions.
*cobrar* is under development and the installation instructions described will install the latest development version.
#### Ubuntu/Debian/Mint
Install *libSBML* and *glpk*:
```sh
sudo apt install libsbml-dev libglpk-dev
```
Install cobrar (in *R*):
``` r
# install.packages("remotes")
remotes::install_github("Waschina/cobrar", build_vignettes = TRUE)
```
#### Centos/Fedora/RHEL
Install *libSBML* and *glpk*:
```sh
sudo yum install libsbml-devel glpk-devel
```
Install cobrar (in *R*):
``` r
# install.packages("remotes")
remotes::install_github("Waschina/cobrar")
```
#### MacOS
*libSBML* and *glpk* can be installed using homebrew:
```sh
brew install glpk brewsci/bio/libsbml
```
Install cobrar (in *R*):
``` r
# install.packages("remotes")
remotes::install_github("Waschina/cobrar")
```
#### Windows
*cobrar* is currently not available for Windows.
#### Conda
Releases of *cobrar* for linux-64 and osx-64 systems are available via [bioconda](https://bioconda.github.io/recipes/r-cobrar/README.html#package-r-cobrar).
```sh
conda install bioconda::r-cobrar
```
## Usage
The full documentation including illustrative examples is available [here](https://waschina.github.io/cobrar/).
The vignettes of the package can also be accessed:
```r
library(cobrar)
vignette(package = "cobrar")
vignette(topic = "cobrar")
```
A simple Flux Balance Analysis (FBA) for the core metabolism of *Escherichia coli*:
```{r example}
library(cobrar)
fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
mod <- readSBMLmod(fpath)
fba(mod)
```
## Key differences to sybil
- cobrar is fully functional from reading SBML files until optimisation of linear programs, without the need of additional packages such as *sybilSBML* or *glpkAPI*.
- cobrar links to libsbml via libsbml's C++ API, not the C API as the *sybilSBML* package.
- The GNU glpk library is a system requirement. There are no links/references to IBM's CPLEX in the *cobrar* package, which were one reason why *sybil* was discontinued on CRAN.
- [roxygen2](https://roxygen2.r-lib.org/) is used for documenting functions and classes.
- Feature trim: A range of functions in *sybil* are not part of *cobrar*.
- In *cobrar*, R's garbage collector handles memory management, including memory associated to C++-objects and the pointers to these.
- Simplifications in class and function architecture
- No more Class "SysBiolAlg" nor sub-classes. Different algorithms have their own function and detailed documentation of their return values
- In *sybil*, columns named "annotation" were actually concatenated CVTerms (https://synonym.caltech.edu/software/libsbml/5.20.0/cpp-api/class_c_v_term.html). To avoid confusion with other levels of annotation, the columns (e.g. in `react_attr` or `met_attr`) are named 'CVTerms' in *cobrar*.
- *cobrar* allows to assign SBOTerms to reactions, metabolites, genes.
- Performance (i.e., computation time) improvements in certain procedures:
- identification of dead-end metabolites
- reading/exporting SBML files,
- pFBA algorithm (a.k.a MTF 'Minimization of Total Flux').
- FVA; also now allows relaxed constraints on optimal growth (e.g. flux variability with 90-100% optimal growth)
## Notes
- *cobrar* exports SBML files level 3 version 2 with `fbc` version 3 and `groups` version 1.
- Group assignments are only supported for reactions.
- GLPK is the default solver and is required to build the package. A plugin for IBM's ILOG CPLEX is available [here (cobrarCPLEX)](https://github.com/Waschina/cobrarCPLEX).
- *Multiple objectives*. The SBML standard with its `fbc` extension allows to specify more than one objective (class `ListOfObjectives`). However, *cobrar* can only handle one current objective function per model, which is defined as an objective coefficient vector in slot `obj_coef` of an object of class `modelorg`. Note that when reading SBML models, *cobrar* will only use the objective, which is defined as `activeObjective` in the SBML file, or the first objective if no active objective is defined.
## References
1. <a id="R1"></a>Gelius-Dietrich, G., Desouki, A.A., Fritzemeier, C.J., Lercher, M.J. sybil – Efficient constraint-based modelling in R. BMC Syst Biol 7, 125 (2013). https://doi.org/10.1186/1752-0509-7-125