Constraint-Based Reconstruction and EXascale Analysis
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This is package aims to provide constraint based reconstruction and analysis tools at the exa-scale in Julia.
Acknowledgements
COBREXA.jl was developed at the Luxembourg Centre for Systems Biomedicine of
the University of Luxembourg (uni.lu/lcsb),
cooperating with Institute for Quantitateve and Theoretical Biology of Heinrich
Heine University, Düsseldorf (qtb.hhu.de).
The development was supported by European Union's Horizon 2020 Programme under PerMedCoE project (permedcoe.eu) agreement no. 951773.
Installation
To install this package: ] add ???. See the documentation for more information.
Quick Example
Let's use COBREXA.jl to perform classic flux balance analysis on an E. coli community.
using COBREXA
# download the model
model_file = COBREXA.Downloads.download("http://bigg.ucsd.edu/static/models/iJO1366.json", "iJO1366.json")
# Import E. coli models (models have pretty printing)
model_1 = read_model(model_file)
model_2 = read_model(model_file)
model_3 = read_model(model_file)
# Build an exascale model
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
- 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
- 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
- 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
- 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