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Sabio-rk example

Example parsing sabio-rk SBML files.

Steps to reproduce

First, clone the repository and make sure that jupyter lab and cargo are installed.

git clone https://github.com/computer-aided-biotech/sabio_stuff.git
cd sabio_stuff
  1. Retrieval of information. This is the SBML corresponding to the ethanol dehydrogenase (SabioReactionID 597) (will generate a file sabio.xml).
curl -L http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/sbml\?q\=SabioReactionID:"597" > sabio597.xml
  1. Parsing of the SBML doc into a TSV table (will generate a file sabio.tsv).
cargo build --release
./target/release/sabio_stuff sabio.xml > sabio.tsv
  1. Plotting the results. Open the file ./notebooks/sabio_587.ipynb in jupyter lab.