Example data#

The models the user guide pages load. They are copied here, rather than read from the RAVEN submodule, so that every snippet can use a short, stable path (smallYeast.yml) that works the same way for a reader who downloads the file and for the example runner in CI.

File	Size	Source	Used by
`smallYeast.yml`	45 kB	`RAVEN/tutorials/data/models/smallYeast.yml`	the default example model for most guide pages
`empty.xml`	4 kB	`RAVEN/tutorials/data/empty.xml`	7. Building: an empty SBML model with compartments defined, to build a model from scratch
`smallYeastBad.yml`	45 kB	`RAVEN/tutorials/data/models/smallYeastBad.yml`	9. Quality control and 21. Comparing, which need a model with known errors
`yeast-GEM.yml`	3.6 MB	yeast-GEM v9.1.0, `model/yeast-GEM.yml`	pages that need a genome-scale model: 3. I/O, 4. FBA, 5. Media, 11. Biomass
`yeast-GEM.xml`	11.6 MB	yeast-GEM v9.1.0, `model/yeast-GEM.xml`	the same model as SBML, for 3. I/O
`anaerobic.yml`	2 kB	transcribed from yeast-GEM's `anaerobicModel.m`	5. Media: a condition file, yeast-GEM under anaerobic conditions
`tasks.txt`	0.5 kB	written for this guide	15. Metabolic tasks and 17. Gap-filling: a task list for `smallYeast.yml`
`curation-mets.tsv`	0.3 kB	written for this guide	10. Table-driven curation: a metabolite curation table
`hpa-sample.tsv`	1 kB	a ten-row excerpt in Human Protein Atlas format	14. Context-specific models

The two small yeast models are part of the RAVEN Toolbox (MIT licence). yeast-GEM is the consensus genome-scale model of Saccharomyces cerevisiae (SysBioChalmers/yeast-GEM, CC-BY-4.0), pinned here at release v9.1.0 so the numbers printed in the guide stay reproducible while the model keeps developing.

The .yml files are RAVEN YAML, read by readYAMLmodel in MATLAB and read_yaml_model in Python; yeast-GEM.xml is SBML, read by importModel and cobrapy's read_sbml_model.

Refreshing them#

The two RAVEN tutorial copies are deliberate duplicates, so they do not follow the RAVEN submodule automatically. After a submodule bump that changes either model, refresh them and re-run the examples:

cp "RAVEN/tutorials/data/models/smallYeast.yml" docs/data/smallYeast.yml
cp "RAVEN/tutorials/data/empty.xml" docs/data/empty.xml
cp "RAVEN/tutorials/data/models/smallYeastBad.yml" docs/data/smallYeastBad.yml
python scripts/run_examples.py

Moving to a newer yeast-GEM is a deliberate act, not a routine one: every number the guide prints from it changes, so bump the tag, re-download both files, and re-generate the affected output blocks in one commit.

YEAST_GEM=v9.1.0   # the release the guide currently documents
curl -sSL -o docs/data/yeast-GEM.yml "https://raw.githubusercontent.com/SysBioChalmers/yeast-GEM/${YEAST_GEM}/model/yeast-GEM.yml"
curl -sSL -o docs/data/yeast-GEM.xml "https://raw.githubusercontent.com/SysBioChalmers/yeast-GEM/${YEAST_GEM}/model/yeast-GEM.xml"
python scripts/run_examples.py --update

Do not edit the files in place: any change here silently makes the guide's numbers unreproducible for a reader who takes the model from RAVEN instead.

Proteomes, for the homology page#

hanpo.faa and sce-template.faa back 12. Reconstruction from homology.

file	what it is
`hanpo.faa`	the Hansenula polymorpha proteome, 5177 sequences, copied unchanged from the `hanpo-GEM` submodule (`data/genomes/hanpo.faa`)
`sce-template.faa`	61 S. cerevisiae sequences (exactly the genes of `smallYeast.yml`) extracted from the same submodule's `data/genomes/sce.faa`

The template proteome is cut down to the model's own genes on purpose: BLAST against 61 subjects instead of a whole proteome is what keeps the page's example to about fifteen seconds per language, and a template protein that no reaction uses could not have contributed to the draft anyway.

Regenerate sce-template.faa after a change to smallYeast.yml:

python - <<'EOF'
from pathlib import Path
from raven_toolbox.io import read_yaml_model
ids = {g.id for g in read_yaml_model("docs/data/smallYeast.yml").genes}
out, keep = [], False
for line in Path("hanpo-GEM/data/genomes/sce.faa").read_text().splitlines():
    if line.startswith(">"):
        keep = line[1:].strip().split()[0] in ids
    if keep:
        out.append(line)
Path("docs/data/sce-template.faa").write_text("\n".join(out) + "\n")
EOF
python scripts/run_examples.py docs/guide/homology.md --update