-
Scott, William authored
- /License.txt - /data/supplementary/random_sampling_recovery_v4_crossfeeding_FIXED.tsv - /data/supplementary/random_sampling_recovery_v4_medium_exchange_FIXED.tsv - /data/supplementary/pairwiseDiagnostics_sampling_recovery_v4.csv - /data/supplementary/README.md - /data/supplementary/target_network_random_sampling_withMedium_mean_summary.tsv - /data/supplementary/random_sampling_recovery_v4_metabolite_summary_FIXED.tsv - /data/annotations/seed_metabolites_edited-2.tsv - /data/media/Edlab_Mineral_Medium_modelseed_final.tsv - /docs/repository_contents.md - /docs/reproducibility_notes.md - /environment/software_requirements.md - /figures/README.md - /figures/pairwise_ecological_interactions_recovery_v4_notitle_600dpi.png - /figures/random_sampling_crossfeeding_catabolic_metabolites_highres_notitle.png - /figures/random_sampling_crossfeeding_requested_metabolites_pyvis_stable_highres_notitle.png - /figures/random_sampling_crossfeeding_top10_metabolites_highres.png - /models/constrainedModels_EdlabMM_modelseed/mediumCoverage_singleModels.csv - /models/constrainedModels_EdlabMM_modelseed/Rectinema_sp002441395.mat - /models/constrainedModels_EdlabMM_modelseed/Rectinema_sp015657395.mat - /models/constrainedModels_EdlabMM_modelseed/f__Cloacimonadaceae_g__Cloacimonas_s__.mat - /models/constrainedModels_EdlabMM_modelseed/o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865.mat - /models/constrainedModels_EdlabMM_modelseed/Dehalobacter_sp004343605_cur.mat - /models/constrainedModels_EdlabMM_modelseed/Rectinema_subterraneum.mat - /models/constrainedModels_EdlabMM_modelseed/Dehalobacter_restrictus_cur.mat - /models/constrainedModels_EdlabMM_modelseed/o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s__.mat - /models/constrainedModels_EdlabMM_modelseed/Acetobacterium_sp003260995.mat - /models/constrainedModels_EdlabMM_modelseed/o__Bacteroidales_f__VadinHA17_g__LD21_s__.mat - /models/constrainedModels_EdlabMM_modelseed/Methanobacterium_C_congolense.mat - /models/constrainedModels_EdlabMM_modelseed/g__Methanothrix_s__.mat - /models/converted_models_modelseed/README.md - /models/converted_models_modelseed/Dehalobacter_restrictus_cur.xml - /models/converted_models_modelseed/Dehalobacter_sp004343605_cur.xml - /models/converted_models_modelseed/f__Cloacimonadaceae_g__Cloacimonas_s__.xml - /models/converted_models_modelseed/g__Methanothrix_s__.xml - /models/converted_models_modelseed/Rectinema_subterraneum.xml - /models/converted_models_modelseed/Rectinema_sp002441395.xml - /models/converted_models_modelseed/Acetobacterium_sp003260995.xml - /models/converted_models_modelseed/Methanobacterium_C_congolense.xml - /models/converted_models_modelseed/o__Bacteroidales_f__TTA-H9_g__TTA-H9_s__TTA-H9_sp002418865.xml - /models/converted_models_modelseed/Rectinema_sp015657395.xml - /models/converted_models_modelseed/o__Bacteroidales_f__VadinHA17_g__SR-FBR-E99_s__.xml - /models/converted_models_modelseed/o__Bacteroidales_f__VadinHA17_g__LD21_s__.xml - /notebooks/ecological_interaction_figure_notebook.ipynb - /notebooks/random_sampling_network_figures_notebook.ipynb - /notebooks/README.md - /reports/MEMOTE_Reports/Memote_gapseq_GEMs.zip - /reports/MEMOTE_Reports/Memote_Carveme_GEMs.zip - /reports/MEMOTE_Reports/README.md - /results/pairwiseModels_EdlabMM_modelseed/pairwiseSolutions_sampling_recovery_v4.mat - /results/pairwiseModels_EdlabMM_modelseed/pairwiseInteractions_sampling_recovery_v4.mat - /results/pairwiseModels_EdlabMM_modelseed/pairwiseDiagnostics_sampling_recovery_v4.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_g__Methanothrix_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Rectinema_sp002441395_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/README.md - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Dehalobacter_sp004343605_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Dehalobacter_restrictus_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_g__Methanothrix_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__LD21_s___Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__LD21_s___Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Dehalobacter_sp004343605_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Dehalobacter_restrictus_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___g__Methanothrix_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__LD21_s___o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_g__Methanothrix_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Rectinema_sp002441395_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Rectinema_sp015657395_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Dehalobacter_sp004343605_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__LD21_s___Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_f__Cloacimonadaceae_g__Cloacimonas_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /scripts/pipeline/build_exchange_tables_from_paired_samples_recovery_v4_fixed.m - /scripts/pipeline/run_FluxSampling_EdlabMM_pipeline_modelSEED_recovery_v4.m - /scripts/pipeline/patch_corrinoid_annotations_and_rebuild.m - /scripts/pipeline/simulatePairwiseInteractions_Sampling_recovery_v4.m - /scripts/pipeline/resamplePairedFluxes_recovery_v4_strict_fixed.m - /scripts/pipeline/build_exchange_tables_from_paired_samples_recovery_v4.m - /scripts/pipeline/build_target_network_from_paired_samples.m - /scripts/legacy/samplingCostlessExchange.m - /scripts/legacy/older_exploratory_scripts_README.md - /scripts/legacy/resamplePairedFluxes.m - /scripts/utilities/processCostlessData.m - /scripts/utilities/helper_placeholder.m - /scripts/utilities/costlessGrowth.m - /scripts/utilities/assertRHMCready.m - /scripts/utilities/costlessGrowthSCC.m - /scripts/utilities/GenerateAll_Sampling_DiffThresholds.m - /scripts/utilities/defineMedium.m - /scripts/utilities/README.md - /scripts/utilities/applyDietSmart.m - /scripts/utilities/Prepare_Csources.m - /scripts/utilities/samplingCostlessExchange.m - /LICENSE.txt - /LICENSE-data
Scott, William authored- /License.txt - /data/supplementary/random_sampling_recovery_v4_crossfeeding_FIXED.tsv - /data/supplementary/random_sampling_recovery_v4_medium_exchange_FIXED.tsv - /data/supplementary/pairwiseDiagnostics_sampling_recovery_v4.csv - /data/supplementary/README.md - /data/supplementary/target_network_random_sampling_withMedium_mean_summary.tsv - /data/supplementary/random_sampling_recovery_v4_metabolite_summary_FIXED.tsv - /data/annotations/seed_metabolites_edited-2.tsv - /data/media/Edlab_Mineral_Medium_modelseed_final.tsv - /docs/repository_contents.md - /docs/reproducibility_notes.md - /environment/software_requirements.md - /figures/README.md - /figures/pairwise_ecological_interactions_recovery_v4_notitle_600dpi.png - /figures/random_sampling_crossfeeding_catabolic_metabolites_highres_notitle.png - /figures/random_sampling_crossfeeding_requested_metabolites_pyvis_stable_highres_notitle.png - /figures/random_sampling_crossfeeding_top10_metabolites_highres.png - /models/constrainedModels_EdlabMM_modelseed/mediumCoverage_singleModels.csv - /models/constrainedModels_EdlabMM_modelseed/Rectinema_sp002441395.mat - /models/constrainedModels_EdlabMM_modelseed/Rectinema_sp015657395.mat - /models/constrainedModels_EdlabMM_modelseed/f__Cloacimonadaceae_g__Cloacimonas_s__.mat - /models/constrainedModels_EdlabMM_modelseed/o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865.mat - /models/constrainedModels_EdlabMM_modelseed/Dehalobacter_sp004343605_cur.mat - /models/constrainedModels_EdlabMM_modelseed/Rectinema_subterraneum.mat - /models/constrainedModels_EdlabMM_modelseed/Dehalobacter_restrictus_cur.mat - /models/constrainedModels_EdlabMM_modelseed/o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s__.mat - /models/constrainedModels_EdlabMM_modelseed/Acetobacterium_sp003260995.mat - /models/constrainedModels_EdlabMM_modelseed/o__Bacteroidales_f__VadinHA17_g__LD21_s__.mat - /models/constrainedModels_EdlabMM_modelseed/Methanobacterium_C_congolense.mat - /models/constrainedModels_EdlabMM_modelseed/g__Methanothrix_s__.mat - /models/converted_models_modelseed/README.md - /models/converted_models_modelseed/Dehalobacter_restrictus_cur.xml - /models/converted_models_modelseed/Dehalobacter_sp004343605_cur.xml - /models/converted_models_modelseed/f__Cloacimonadaceae_g__Cloacimonas_s__.xml - /models/converted_models_modelseed/g__Methanothrix_s__.xml - /models/converted_models_modelseed/Rectinema_subterraneum.xml - /models/converted_models_modelseed/Rectinema_sp002441395.xml - /models/converted_models_modelseed/Acetobacterium_sp003260995.xml - /models/converted_models_modelseed/Methanobacterium_C_congolense.xml - /models/converted_models_modelseed/o__Bacteroidales_f__TTA-H9_g__TTA-H9_s__TTA-H9_sp002418865.xml - /models/converted_models_modelseed/Rectinema_sp015657395.xml - /models/converted_models_modelseed/o__Bacteroidales_f__VadinHA17_g__SR-FBR-E99_s__.xml - /models/converted_models_modelseed/o__Bacteroidales_f__VadinHA17_g__LD21_s__.xml - /notebooks/ecological_interaction_figure_notebook.ipynb - /notebooks/random_sampling_network_figures_notebook.ipynb - /notebooks/README.md - /reports/MEMOTE_Reports/Memote_gapseq_GEMs.zip - /reports/MEMOTE_Reports/Memote_Carveme_GEMs.zip - /reports/MEMOTE_Reports/README.md - /results/pairwiseModels_EdlabMM_modelseed/pairwiseSolutions_sampling_recovery_v4.mat - /results/pairwiseModels_EdlabMM_modelseed/pairwiseInteractions_sampling_recovery_v4.mat - /results/pairwiseModels_EdlabMM_modelseed/pairwiseDiagnostics_sampling_recovery_v4.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_g__Methanothrix_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Rectinema_sp002441395_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/README.md - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Dehalobacter_sp004343605_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Dehalobacter_restrictus_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_g__Methanothrix_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__LD21_s___Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__LD21_s___Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Dehalobacter_sp004343605_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Dehalobacter_restrictus_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___g__Methanothrix_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__LD21_s___o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_g__Methanothrix_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Rectinema_sp002441395_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Rectinema_sp015657395_Rectinema_subterraneum_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_g__Methanothrix_s___Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___Methanobacterium_C_congolense_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___o__Bacteroidales_f__VadinHA17_g__LD21_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Methanobacterium_C_congolense_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_sp004343605_cur_Rectinema_sp015657395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Dehalobacter_restrictus_cur_Dehalobacter_sp004343605_cur_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_o__Bacteroidales_f__TTA_H9_g__TTA_H9_s__TTA_H9_sp002418865_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_o__Bacteroidales_f__VadinHA17_g__LD21_s___Rectinema_sp002441395_Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_Acetobacterium_sp003260995_f__Cloacimonadaceae_g__Cloacimonas_s___Paired_samples.mat - /results/pairwiseModels_EdlabMM_modelseed/sampling_flux_recovery_v4/pairedModel_f__Cloacimonadaceae_g__Cloacimonas_s___o__Bacteroidales_f__VadinHA17_g__SR_FBR_E99_s___Paired_samples.mat - /scripts/pipeline/build_exchange_tables_from_paired_samples_recovery_v4_fixed.m - /scripts/pipeline/run_FluxSampling_EdlabMM_pipeline_modelSEED_recovery_v4.m - /scripts/pipeline/patch_corrinoid_annotations_and_rebuild.m - /scripts/pipeline/simulatePairwiseInteractions_Sampling_recovery_v4.m - /scripts/pipeline/resamplePairedFluxes_recovery_v4_strict_fixed.m - /scripts/pipeline/build_exchange_tables_from_paired_samples_recovery_v4.m - /scripts/pipeline/build_target_network_from_paired_samples.m - /scripts/legacy/samplingCostlessExchange.m - /scripts/legacy/older_exploratory_scripts_README.md - /scripts/legacy/resamplePairedFluxes.m - /scripts/utilities/processCostlessData.m - /scripts/utilities/helper_placeholder.m - /scripts/utilities/costlessGrowth.m - /scripts/utilities/assertRHMCready.m - /scripts/utilities/costlessGrowthSCC.m - /scripts/utilities/GenerateAll_Sampling_DiffThresholds.m - /scripts/utilities/defineMedium.m - /scripts/utilities/README.md - /scripts/utilities/applyDietSmart.m - /scripts/utilities/Prepare_Csources.m - /scripts/utilities/samplingCostlessExchange.m - /LICENSE.txt - /LICENSE-data
This project is licensed under the MIT License.
Learn more
Loading