Verified Commit 9d3297ea authored by Laurent Heirendt's avatar Laurent Heirendt
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add how to get started section

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# Constraint-Based Reconstruction and EXascale Analysis
[docs-img]:https://img.shields.io/badge/docs-latest-blue.svg
[docs-url]: http://lcsb-biocore.github.io/COBREXA.jl
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[ci-img]: https://github.com/LCSB-BioCore/COBREXA.jl/actions/workflows/ci.yml/badge.svg?branch=master
[ci-url]: https://github.com/LCSB-BioCore/COBREXA.jl/actions/workflows/ci.yml
[cov-img]: https://codecov.io/gh/LCSB-BioCore/COBREXA.jl/branch/master/graph/badge.svg?token=3AE3ZDCJJG
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This is package aims to provide constraint based reconstruction and analysis tools at the exa-scale in Julia.
#### Acknowledgements
## How to get started
`COBREXA.jl` was 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
Heine University, Düsseldorf ([qtb.hhu.de](https://www.qtb.hhu.de/)).
### Prerequisites and requirements
The development was supported by European Union's Horizon 2020 Programme under
PerMedCoE project ([permedcoe.eu](https://www.permedcoe.eu/)) agreement no.
951773.
- **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.
<img src="docs/src/assets/unilu.svg" alt="Uni.lu logo" height="64px">   <img src="docs/src/assets/lcsb.svg" alt="LCSB logo" height="64px">   <img src="docs/src/assets/hhu.svg" alt="HHU logo" height="64px">   <img src="docs/src/assets/qtb.svg" alt="QTB logo" height="64px">   <img src="docs/src/assets/permedcoe.svg" alt="PerMedCoE logo" height="64px">
: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
import Pkg; 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
using COBREXA
```
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
import Pkg; Pkg.test("COBREXA")
```
## Quick Example
## Example
Let's use `COBREXA.jl` to perform classic flux balance analysis on an *E. coli* community.
```julia
......@@ -59,9 +86,22 @@ model_3 = read_model(model_file)
exascale_model = join(model_1, model_2, model_3,...)
```
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
Heine University, Düsseldorf ([qtb.hhu.de](https://www.qtb.hhu.de/)).
The development was supported by European Union's Horizon 2020 Programme under
PerMedCoE project ([permedcoe.eu](https://www.permedcoe.eu/)) agreement no.
951773.
<img src="docs/src/assets/unilu.svg" alt="Uni.lu logo" height="64px">   <img src="docs/src/assets/lcsb.svg" alt="LCSB logo" height="64px">   <img src="docs/src/assets/hhu.svg" alt="HHU logo" height="64px">   <img src="docs/src/assets/qtb.svg" alt="QTB logo" height="64px">   <img src="docs/src/assets/permedcoe.svg" alt="PerMedCoE logo" height="64px">
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