Gives access to the metano metabolic modeling toolbox.
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The example model is a genome-scale metabolic model of Sulfolobus acidocaldarius (from my Thesis. The model and a standard scenario can be found in the following folder: /home/metano/example.
You can run a flux balance analysis (FBA) using the following commands:
cd /home/metano/example
fba.py -r reactions.txt -p scenario.txt -o fba.csv
You should get the following output:
Info: The metabolic network has 799 reactions and 730 metabolites.
Info: The reduced network has 589 reactions and 490 metabolites.
Value of objective function at solution: 0.0788084602571737
Total absolute flux: 141.30154722970948
For more information about the open-source metabolic modeling toolbox Metano, please visit the project page.
The Docker image is build on top of debian 10 (buster) using the following dockerfile:
FROM debian:buster
WORKDIR /home/metano
# install all dependencies and the metano python package
RUN apt-get update && apt-get install -y --force-yes python3 python3-pip wget cmake
RUN pip3 install numpy future
RUN pip3 install metano
# create example folder and fetch example model from MMTB
RUN mkdir example
RUN wget -O example/reactions.txt https://mmtb.brenda-enzymes.org/model-download/rea/1
RUN wget -O example/scenario.txt https://mmtb.brenda-enzymes.org/model-download/sce/1
RUN echo "fba.py -r reactions.txt -p scenario.txt -o fba.csv" >> example/example.sh
Content type
Image
Digest
Size
387.9 MB
Last updated
almost 6 years ago
docker pull jhelmecke/metano