Files

.github
data
doc
ecoli
migration
notebooks
reconstruction
- ecoli
  - compendium
  - dataclasses
  - flat
    - adjustments
    - base_codes
    - cell_wall
    - condition
    - mass_fractions
    - new_gene_data
    - rna_seq_data
    - rrna_options
    - tetracycline
    - trna_data
    - amino_acid_export_kms.tsv
    - amino_acid_export_kms_removed.tsv
    - amino_acid_pathways.tsv
    - amino_acid_uptake_rates.tsv
    - amino_acid_uptake_rates_removed.tsv
    - biomass.tsv
    - compartments.tsv
    - complexation_reactions.tsv
    - complexation_reactions_added.tsv
    - complexation_reactions_modified.tsv
    - complexation_reactions_removed.tsv
    - disabled_kinetic_reactions.tsv
    - dna_sites.tsv
    - dna_supercoiling.tsv
    - dry_mass_composition.tsv
    - endoRNases.tsv
    - equilibrium_reaction_rates.tsv
    - equilibrium_reactions.tsv
    - equilibrium_reactions_added.tsv
    - equilibrium_reactions_removed.tsv
    - fold_changes.tsv
    - fold_changes_nca.tsv
    - fold_changes_removed.tsv
    - footprint_sizes.tsv
    - genes.tsv
    - growth_rate_dependent_parameters.tsv
    - linked_metabolites.tsv
    - mass_parameters.tsv
    - metabolic_reactions.tsv
    - metabolic_reactions_added.tsv
    - metabolic_reactions_modified.tsv
    - metabolic_reactions_removed.tsv
    - metabolism_kinetics.tsv
    - metabolite_concentrations.tsv
    - metabolite_concentrations_removed.tsv
    - metabolites.tsv
    - metabolites_added.tsv
    - modified_proteins.tsv
    - molecular_weight_keys.tsv
    - parameters.tsv
    - ppgpp_fc.tsv
    - ppgpp_regulation.tsv
    - ppgpp_regulation_added.tsv
    - ppgpp_regulation_removed.tsv
    - protein_half_lives_measured.tsv
    - protein_half_lives_n_end_rule.tsv
    - protein_half_lives_pulsed_silac.tsv
    - proteins.tsv
    - relative_metabolite_concentrations.tsv
    - rna_half_lives.tsv
    - rna_maturation_enzymes.tsv
    - rnas.tsv
    - secretions.tsv
    - sequence.fasta
    - sequence_motifs.tsv
    - tf_one_component_bound.tsv
    - transcription_factors.tsv
    - transcription_units.tsv
    - transcription_units_added.tsv
    - transcription_units_removed.tsv
    - transcriptional_attenuation.tsv
    - transcriptional_attenuation_removed.tsv
    - translation_efficiency.tsv
    - trna_charging_reactions.tsv
    - trna_charging_reactions_added.tsv
    - trna_charging_reactions_removed.tsv
    - two_component_system_templates.tsv
    - two_component_systems.tsv
  - scripts
  - __init__.py
  - fit_sim_data_1.py
  - knowledge_base_raw.py
  - simulation_data.py
- sim_data
- tests
- __init__.py
- spreadsheets.py
runscripts
validation
wholecell
.gcloudignore
.gitignore
.gitkeep
.pre-commit-config.yaml
LICENSE
README.md
matplotlibrc
mypy.ini
overview.png
pyproject.toml
pytest.ini
setup.py
uv.lock

footprint_sizes.tsv