-**Operating system**: Use Linux (Debian, Ubuntu or centOS), MacOS, or Windows 10 as your operating system. `COBREXA` has been tested on these systems.
-**Julia language**: In order to use `COBREXA`, you need to install Julia 1.0 or higher. Download and installation instructions for Julia are [here](https://julialang.org/downloads/).
-**Hardware requirements**: `COBREXA` runs on any hardware that can run Julia, and can easily use resources from multiple computers interconnected by network. For processing large datasets, you require to ensure that the total amount of available RAM on all involved computers is larger than the data size.
:bulb: If you are new to Julia, it is adviseable to [familiarize youself with
the environment
first](https://docs.julialang.org/en/v1/manual/getting-started/). Use the full
Julia [documentation](https://docs.julialang.org) to solve various possible
language-related issues, and the [Julia package manager
docs](https://julialang.github.io/Pkg.jl/v1/getting-started/) to solve
installation-related difficulties.
### Installation
Using the Julia package manager to install `COBREXA` is straightforward -- after starting Julia, type:
```julia
importPkg;Pkg.add("GigaSOM");
```
> All these commands should be run from Julia at the `julia>` prompt.
Then you can load the `COBREXA` package and start using it:
```julia
usingCOBREXA
```
The first loading of the `COBREXA` package may take several minutes to complete due to precompilation of the sources, especially on a fresh Julia installation.
### Test the installation
## Installation
If you run a non-standard platform (e.g. a customized operating systems), or if you added any modifications to the `COBREXA` source code, you may want to run the test suite to ensure that everything works as expected:
To install this package: `] add ???`. See the documentation for more information.
```julia
importPkg;Pkg.test("COBREXA")
```
## Quick Example
## Example
Let's use `COBREXA.jl` to perform classic flux balance analysis on an *E. coli* community.
More funcionality is described in the documention, e.g. model construction and analysis in pure Julia.
## Citations
### Citations
1) Ebrahim, A., Lerman, J.A., Palsson, B.O. & Hyduke, D. R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Systems Biology, 7(74). https://doi.org/10.1186/1752-0509-7-74
2) Heirendt, L., Arreckx, S., Pfau, T. et al. (2019). Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc 14, 639–702. https://doi.org/10.1038/s41596-018-0098-2
3) Noor, E., Bar-Even, A., Flamholz, A., Lubling, Y., Davidi, D., & Milo, R. (2012). An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics, 28(15), 2037–2044. https://doi.org/10.1093/bioinformatics/bts317
4) Chang, A., Jeske, L., Ulbrich, S., Hofmann, J., Koblitz, J., Schomburg, I., Neumann-Schaal, M., Jahn, D., Schomburg, D.. (2021). BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Research, 49(D1). https://doi.org/10.1093/nar/gkaa1025
## Acknowledgements
`COBREXA.jl` is developed at the Luxembourg Centre for Systems Biomedicine of
the University of Luxembourg ([uni.lu/lcsb](https://www.uni.lu/lcsb)),
cooperating with Institute for Quantitateve and Theoretical Biology of Heinrich
