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… into cofactors # Conflicts: # notebooks/cofactors/buffer_modeling.ipynb
work for yggX supplement figure
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Pull request overview
This PR introduces a set of small functional tweaks plus a large addition of notebooks/data/scripts for cofactor and yggX-homolog analyses, along with updates to metabolism-redux simulation defaults and Python dependencies.
Changes:
- Adjust ParCa config loading to read config files from the repository config directory.
- Add yggX homolog discovery + GEO download tooling and commit supporting artifacts (scripts, readme, output CSV, PDB/PyMOL assets).
- Update metabolism redux classic experiment defaults/output capture and add additional cofactor-related datasets/notebooks.
Reviewed changes
Copilot reviewed 34 out of 83 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| runscripts/parca.py | Changes how --config is resolved/loaded for ParCa runs |
| reconstruction/ecoli/flat/adjustments/translation_efficiencies_adjustments.tsv | Minor TSV row formatting/line correction |
| reconstruction/ecoli/flat/adjustments/rna_expression_adjustments.tsv | Removes several adjustment rows and adds a new one |
| pyproject.toml | Adds new runtime dependencies |
| notebooks/Vivarium_ecoli_processes.ipynb | Adds a new (mostly empty) notebook |
| notebooks/cofactors/yggX_pdb_homologs/yggX_homologs.pymolrc | Adds PyMOL recipe for homolog visualization |
| notebooks/cofactors/yggX_pdb_homologs/AF-A0A1R4GVR5-F1-model_v6.pdb | Adds an AlphaFold structure file for analysis |
| notebooks/cofactors/yggX_homologs/search_gene_across_pathogens.py | Adds an NCBI/GEO-based homolog search + expression extraction script |
| notebooks/cofactors/yggX_homologs/requirements_for_NCBI_script.txt | Adds dependency list for the NCBI/GEO script |
| notebooks/cofactors/yggX_homologs/output/yggX_expression.csv | Adds a committed output CSV artifact |
| notebooks/cofactors/yggX_homologs/homologs_readMe.md | Adds documentation/quickstart for the yggX homolog workflow |
| notebooks/cofactors/yggX_homologs/download_geo_gse152295.py | Adds a helper to download GSE152295 processed GEO files |
| notebooks/cofactors/no3_well_od.csv | Adds experimental OD dataset |
| notebooks/cofactors/no3_df.csv | Adds processed nitrate/molybdenum dataset |
| notebooks/cofactors/no3_df_v2.csv | Adds expanded processed dataset |
| notebooks/cofactors/growth_data/adrian_growth_jan25_indicator.csv | Adds growth plate mapping metadata |
| notebooks/cofactors/growth_data/adrian_growth_jan25_blanks.txt | Adds raw blanks export |
| notebooks/cofactors/growth_data/adrian_growth_jan25_blanks.csv | Adds CSV version of blanks export |
| notebooks/cofactors/data/sim_buf_rich.csv | Adds buffer concentration dataset (rich) |
| notebooks/cofactors/data/sim_buf_minimal.csv | Adds buffer concentration dataset (minimal) |
| notebooks/cofactors/data/metals_plot_data.csv | Adds plotting dataset for metal atoms/cell |
| notebooks/cofactors/data/element_ids.txt | Modifies element ID ordering/content |
| notebooks/cofactors/data/E_matrix.csv | Adds E matrix data |
| notebooks/cofactors/data/buffer_info.csv | Adds buffer reference table with citations |
| notebooks/cofactors/data/buffer_constants.csv | Adds buffer constants table |
| notebooks/cofactors/cofactors_lineage_processing.ipynb | Adds a notebook for lineage processing |
| ecoli/processes/metabolism_redux_classic.py | Extends BAD_RXNS list with additional reaction IDs |
| ecoli/experiments/metabolism_redux_sim.py | Changes classic run defaults, output paths, adds lineage runner, expands saved queries |
| ecoli/composites/ecoli_configs/ecoli/composites/ecoli_configs/run_parca.json | Adds a duplicate config file under a nested/duplicated directory path |
Comments suppressed due to low confidence (2)
notebooks/cofactors/yggX_homologs/search_gene_across_pathogens.py:1077
- Online mode will fail with an AttributeError if Biopython isn't installed (
Entrez/SeqIOare set to None), and it will silently set an empty Entrez email if--emailisn't provided. Add an explicit guard with a clear argparse error message before configuring Entrez.
notebooks/cofactors/yggX_homologs/homologs_readMe.md:103 - Typo: "downlaoded" → "downloaded".
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| if args.config is not None: | ||
| config_file = args.config | ||
| with open(os.path.join(args.config), "r") as f: | ||
| with open(os.path.join(CONFIG_DIR_PATH, args.config), "r") as f: | ||
| SimConfig.merge_config_dicts(config, json.load(f)) |
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| "opencv-python>=4.13.0.92", | ||
| "narwhals==2.21.2", | ||
| "ipykernel>=6.29.5", |
| @@ -0,0 +1,15 @@ | |||
| # Runtime dependencies for the yggX expression analysis. | |||
| # Install into a fresh environment with: pip install -r requirements.txt | |||
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| ap.add_argument( | ||
| "--email", | ||
| default="aj0204@stanford.edu", | ||
| help="Email for NCBI Entrez (required by NCBI)", | ||
| ) |
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| query = [] | ||
| folder = f"out/cofactors/{name}_{total_time}_{datetime.date.today()}/" | ||
| folder = f"out/cofactors/colony/" | ||
| save_sim_output(folder, query, sim, save_model=True) |
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| { | ||
| "sim_data_path": null | ||
| } |
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| yggX_homologs/ | ||
| ├── README.md # this file | ||
| ├── requirements.txt # pip deps (biopython, pandas, numpy, requests, matplotlib, seaborn) | ||
| ├── download_geo_gse152295.py # step 2: downloads the 32 GEO source files |
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