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ecoli
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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
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matplotlibrc
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pyproject.toml
pytest.ini
setup.py
uv.lock

dry_mass_composition.tsv

prismofeverything

update for new underscore sim_data names

Sep 22, 2020

bb99967 · Sep 22, 2020

1	doublingTime (units.min)	proteinMassFraction	rnaMassFraction	dnaMassFraction	lipidMassFraction	lpsMassFraction	mureinMassFraction	glycogenMassFraction	solublePoolMassFraction	inorganicIonMassFraction	averageDryMass (units.fg)
2	100	0.675675676	0.135135135	0.051351351	0.065536395	0.023959542	0.017617311	0.017617311	0.006060355	0.007046924	148
3	60	0.604651163	0.151162791	0.034883721	0.099514909	0.036381795	0.02675132	0.02675132	0.009202454	0.010700528	258
4	40	0.540415704	0.177829099	0.026096998	0.121555279	0.044439564	0.03267615	0.03267615	0.011240596	0.01307046	433
5	30	0.530421217	0.205928237	0.022464899	0.114674158	0.041923886	0.030826386	0.030826386	0.010604277	0.012330555	641
6	24	0.520231214	0.243930636	0.021156069	0.102072768	0.037316926	0.027438916	0.027438916	0.009438987	0.010975567	865