Project Tolera — Work Archive

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Develop a comprehensive project plan for Phase 1 that includes extensive and exhaustive analysis of all existing datasets, defining scope, methodology, and analysis objectives.

📅 2026-07-07📦 180 artifacts💠 $155.28
GOAL

The session set out to develop a comprehensive Phase 1 project plan — including exhaustive analysis of existing datasets, defined scope, methodology, and analysis objectives — for a protein-therapeutics target-discovery effort in eosinophilic esophagitis (EoE) and related conditions.

WHAT WAS DONE

The session combined dataset-level analysis (single-cell and bulk transcriptomics, cell-cell communication, differential expression, epithelial trajectory/pseudotime, HLA/pMHC epitope prediction, and structural modeling) with packaging of reusable methodology into a public GitHub repository, ruthannepai-tech/inflammatory-target-discovery-skills. The final step of the session was finalizing repo metadata: the agent set 10 topic tags spanning the disease area (eoe, eosinophilic-esophagitis), methods (target-discovery, pmhc, hla, systematic-review), domain (immunology, bioinformatics, drug-discovery), and artifact type (agent-skills) so the repo is discoverable, and confirmed the

Artifacts (180)

FileTypeSize
🗜de_tables_bundle.tar.gz Archive7.1 MB
🗜design_briefs_bundle.tar.gz Archive3 KB
🗜design_specs_bundle.tar.gz Archive482 KB
🗜eoe_exhaustive_litreview_bundle.tar.gz Archive1.0 MB
🗜index_case_deliverables.tar.gz Archive762 KB
🗜phase4_deliverables.tar.gz Archive1.1 MB
🗜tier1_harmonized_bundle.tar.gz externalArchive25.2 MB
💻kernel.py Code4 KB
📈allergen_allele_matrix_13.csv Data696 B
📈allergen_epitope_load.csv Data636 B
📈allergen_epitope_panel.csv Data1.1 MB
📈antigen_immunogenicity_load.csv Data164 B
📈antigen_presentation_scores.csv Data777 B
📈binder_design_targets.csv Data606 B
📈bulk_qc_metrics.csv Data380 B
📈canonical_marker_check.csv Data6 KB
📈cellcomm_eoe_vs_gerd.csv Data10 KB
📈companion_dx_specs.csv Data1 KB
📈confirmation_percohort_de.csv Data4 KB
📈dataset_tiers.csv Data32 KB
📈de_summary.csv Data279 B
📈developability_liabilities.csv Data650 B
📈differentiation_map.csv Data1 KB
📈dx_peptide_pool_spec.csv Data512 B
📈enrich_down.csv Data293 KB
📈enrich_tf_up.csv Data483 KB
📈enrich_up.csv Data568 KB
📈eoe_dataset_inventory.csv Data29 KB
📈eoe_master_reference_library.csv Data2.4 MB
📈eoe_meta_signature.csv Data3.8 MB
📈eoe_meta_signature_highconf.csv Data87 KB
📈eoe_meta_signature_loco_robust.csv Data22 KB
📈eoe_target_shortlist.csv Data5 KB
📈epi_hlai_ifng_persample.csv Data673 B
📈epithelial_pseudotime.csv Data10.8 MB
📈epitope_core_matrix.csv Data391 B
📈epitope_cross_reactivity.csv Data39 B
📈epitope_uniqueness.csv Data1 KB
📈esm_epitope_CCL26.csv Data2 KB
📈esm_epitope_IL1RL1.csv Data8 KB
📈esm_epitope_SIGLEC6.csv Data2 KB
📈gse250595_endotypes.csv Data4 KB
📈gse303169_ppi_labels.csv Data4 KB
📈gwas_target_overlap.csv Data903 B
📈hla_allele_burden_13.csv Data632 B
📈hla_allele_epitope_analysis.csv Data937 B
📈hla_allele_frequencies.csv Data192 B
📈hla_allele_prediction_summary.csv Data306 B
📈hlai_delta_bycelltype.csv Data523 B
📈iface_CCL26.csv Data864 B
📈iface_IL1RL1.csv Data591 B
📈iface_IL1RL1_bsa.csv Data644 B
📈iface_SIGLEC6_igv.csv Data1 KB
📈ifn_module_scores.csv Data2 KB
📈immunogenicity_screen.csv Data178 B
📈independent_confirmation.csv Data940 B
📈interface_residues.csv Data355 B
📈liana_eoe.csv Data1.4 MB
📈liana_gerd.csv Data1.2 MB
📈liana_healthy.csv Data1.0 MB
📈loco_cohort_summary.csv Data348 B
📈loco_gene_robustness.csv Data32 KB
📈mastcell_state_markers.csv Data105 KB
📈mhcnuggets_all_alleles.csv Data1.2 MB
📈mirna_de_GSE36727.csv Data17 KB
📈multiomics_evidence.csv Data89 KB
📈multiomics_support_fullsignature.csv Data1.4 MB
📈novelty_ledger.csv Data5 KB
📈patient_allergen_molecule_matrix.csv Data462 B
📈patient_endotypes_all.csv Data13 KB
📈patient_epitope_burden_tiers.csv Data851 B
📈patient_epitope_burden_tiers_13.csv Data5 KB
📈patient_epitope_panel.csv Data923 KB
📈patient_gwas_annotation.csv Data2 KB
📈patient_target_assessment.csv Data2 KB
📈plan_exhaustive-multi-database-eoe-literature_5eff12f3.json Data11 KB
📈plan_personalized-pmhc-effector-target-therap_5eff12f3.json Data7 KB
📈plan_personalized-pmhc-therapy-plan-for-an-in_5eff12f3.json Data5 KB
📈plan_phase-1-exhaustive-mining-of-public-eoe_5eff12f3.json Data7 KB
📈plan_phase-2-mechanistic-validation-novelty-g_5eff12f3.json Data10 KB
📈plan_phase-3-computational-protein-therapeuti_5eff12f3.json Data8 KB
📈plan_phase-4-prospective-preclinical-pmhc-tcr_5eff12f3.json Data8 KB
📈plan_systematic-literature-review-grounding-t_5eff12f3.json Data6 KB
📈pmhc_candidates.csv Data46 KB
📈pmhc_dual_load.csv Data134 B
📈pmhc_ii_candidates.csv Data89 KB
📈ppi_target_triage.csv Data2 KB
📈predictor_concordance.csv Data290 B
📈protein_design_specs.csv Data1 KB
📈revised_design_dossier.csv Data873 B
📈revised_target_dossier.csv Data5 KB
📈roster_lock.csv Data492 B
📈sc_celltype_de.csv Data21 KB
📈sc_composition.csv Data10 KB
📈strong_epitope_binders.csv Data206 KB
📈structure_inventory.csv Data607 B
📈target_addressable_by_endotype.csv Data415 B
📈target_biomarker_dossier.csv Data4 KB
📈target_druggability.csv Data55 KB
📈target_patient_positivity.csv Data1 KB
📈trajectory_gene_dynamics.csv Data3 KB
🖼allergen_epitope_heatmap.png Figure166 KB
🖼antigen_presentation.png Figure184 KB
🖼atopic_march_prevention.png Figure270 KB
🖼bulk_qc_panels.png Figure246 KB
🖼canonical_marker_heatmap.png Figure140 KB
🖼cellcomm_dotplot.png Figure230 KB
🖼companion_dx.png Figure126 KB
🖼dataset_landscape.png Figure104 KB
🖼dataset_tiers.png Figure53 KB
🖼de_concordance.png Figure112 KB
🖼de_volcanoes.png Figure499 KB
🖼developability_screen.png Figure104 KB
🖼differential_cellcomm.png Figure151 KB
🖼differentiation_map.png Figure117 KB
🖼endotype_crosscohort.png Figure239 KB
🖼eoe_dx_assay_workflow.png Figure259 KB
🖼eoe_evidence_map.png Figure258 KB
🖼eoe_phase1_summary.png Figure133 KB
🖼epithelial_trajectory.png Figure543 KB
🖼epitope_load_by_allergen.png Figure117 KB
🖼esm_epitope_analysis.png Figure425 KB
🖼gwas_overlap.png Figure95 KB
🖼heterogeneity_preview.png Figure130 KB
🖼hla_panel_13allele.png Figure190 KB
🖼ifn_deconvolution.png Figure484 KB
🖼independent_confirmation.png Figure159 KB
🖼index_case_groundtruth_calibration.png Figure180 KB
🖼index_case_profile.png Figure254 KB
🖼interface_analysis.png Figure168 KB
🖼loco_robustness.png Figure165 KB
🖼mastcell_states.png Figure293 KB
🖼meta_forest_topgenes.png Figure85 KB
🖼meta_volcano.png Figure127 KB
🖼multiomics_integration.png Figure126 KB
🖼novelty_ledger.png Figure150 KB
🖼pathway_enrichment.png Figure142 KB
🖼phase2_summary.png Figure175 KB
🖼phase3_summary.png Figure160 KB
🖼pmhc_dual_axis.png Figure102 KB
🖼ppi_response_triage.png Figure172 KB
🖼protein_design_specs.png Figure142 KB
🖼roster_structures.png Figure102 KB
🖼sc_composition.png Figure84 KB
🖼sc_marker_dotplot.png Figure65 KB
🖼sc_umap_overview.png Figure1.2 MB
🖼target_biomarker_dossier.png Figure144 KB
🖼target_druggability.png Figure165 KB
📎epithelial_traj.h5ad externalFile1.04 GB
📎gse218607_slim.h5ad externalFile1.08 GB
🧬4KC3_IL33_ST2.pdb Structure596 KB
🧬AF-IL1RL1-Q01638.pdb Structure368 KB
🧬AF-SIGLEC6-O43699.pdb Structure292 KB
📃allergen_sequences.fasta Text4 KB
📃atopic_march_prevention_review.md Text12 KB
📃binder_validation_protocol.md Text2 KB
📃CCL26_design_brief.md Text2 KB
📃dataset_prioritization_rationale.md Text4 KB
📃eoe_exhaustive_literature_review.md Text8 KB
📃eoe_food_trigger_dx_design.md Text14 KB
📃eoe_phase1_report.md Text10 KB
📃eoe_phase2_report.md Text7 KB
📃eoe_phase3_report.md Text7 KB
📃eoe_phase4_pmhc_therapy_package.md Text11 KB
📃eoe_review_part1_disease.md Text12 KB
📃eoe_review_part2_immune_mechanisms.md Text13 KB
📃eoe_review_part3_pmhc.md Text11 KB
📃eoe_review_part4_targeted.md Text10 KB
📃food_antigen_pmhc_review.md Text6 KB
📃IL1RL1_design_brief.md Text1 KB
📃index_case_groundtruth_calibration.md Text6 KB
📃personalized_therapy_plan_index_case.md Text11 KB
📃pmhc_tcr_mechanism_review.md Text11 KB
📃preclinical_workflow_roadmap.md Text9 KB
📃recruitment_stratification_rationale.md Text9 KB
📃SIGLEC6_design_brief.md Text1 KB
📃SKILL.md Text7 KB
📃t_cell_assay_protocol.md Text29 KB
📃target_sequences.fasta Text3 KB
📃validation_extension_note.md Text6 KB