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

2. 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

3. Plotting the results. Open the file ./notebooks/sabio_587.ipynb in jupyter lab.