Example data#

The models that the pages of the user guide load are copied here and not 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`	Building a model from scratch: an empty SBML model with compartments defined, to build a model from scratch
`smallYeastBad.yml`	45 kB	`RAVEN/tutorials/data/models/smallYeastBad.yml`	Quality control and Comparing models, 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: Reading and writing models, Simulating growth with FBA, Growth media and conditions, Biomass composition and annotation
`yeast-GEM.xml`	11.6 MB	yeast-GEM v9.1.0, `model/yeast-GEM.xml`	the same model as SBML, for Reading and writing models
`anaerobic.yml`	2 kB	transcribed from yeast-GEM's `anaerobicModel.m`	Growth media and conditions: a condition file, yeast-GEM under anaerobic conditions
`tasks.txt`	0.5 kB	written for this guide	Metabolic tasks and Gap-filling: a task list for `smallYeast.yml`
`curation-mets.tsv`	0.3 kB	written for this guide	Table-driven curation: a metabolite curation table
`hpa-sample.tsv`	1 kB	a ten-row excerpt in Human Protein Atlas format	Context-specific models with ftINIT

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). It is 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 the copies#

The two RAVEN tutorial copies are deliberate duplicates and do not follow the RAVEN submodule automatically. After a submodule bump that changes either model, refresh the copies 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

A change of the pinned tag is a deliberate act, and it changes every number that the guide prints from the model. 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 makes the guide's numbers unreproducible, without a warning, for a reader who takes the model from RAVEN.

Proteomes for homology reconstruction#

hanpo.faa and sce-template.faa back 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 restricted to the genes of the model. BLAST against 61 subjects keeps the example of the homology page to about fifteen seconds per language, and a template protein that no reaction uses cannot contribute to the draft.

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