genomi
Local-first, open-source Claude Science alternative, before Claude Science is a thing. Turn your AI agent into personal DNA expert.
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- _install_for_agents_downloads.py
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- build_dashboard.py
- build_llms.py
- install_for_agents.py
- SKILL.md
- SKILL.md
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- SKILL.md
- context-routing.md
- evidence-quality.md
- SKILL.md
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- openai.yaml
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- SKILL.md
- _output-rules.md
- __init__.py
- agi_store.py
- arrays.py
- detection.py
- dispatch.py
- genome_bundle.py
- sequencing.py
- text_io.py
- vcf.py
- __init__.py
- _agi_build.py
- _agi_query.py
- _agi_readiness.py
- _agi_schema.py
- active_genome_index.py
- alignment.py
- array_genotypes.py
- build.py
- canonical.py
- clinvar.py
- dosage.py
- export.py
- filtering.py
- genotype_qc.py
- genotype_resolver.py
- identity.py
- normalize.py
- observations.py
- parallel_build.py
- query.py
- reader.py
- readiness.py
- record_kinds.py
- revisions.py
- source_capabilities.py
- tool_catalog.json
- vcf.py
- vcf_info.py
- genomi-logo-transparent.png
- __init__.py
- api.py
- cell_markers.py
- constants.py
- gene_coordinates.py
- helpers.py
- library.py
- pathways.py
- regions.py
- responses.py
- __init__.py
- constants.py
- helpers.py
- ordering.py
- retrieval.py
- sources.py
- __init__.py
- tool_catalog.json
- __init__.py
- overlap.py
- panel_build.py
- pca.py
- policy.py
- reference_panels.py
- source_context.py
- tool_catalog.json
- __init__.py
- _helpers.py
- build.py
- queries.py
- __init__.py
- tool_catalog.json
- dashboard.compiled.001.js
- dashboard.compiled.002.js
- dashboard.compiled.003.js
- react-dom.production.min.js
- react.production.min.js
- dashboard.jsx
- dashboard_helpers.js
- shell.html
- __init__.py
- dashboard.py
- evidence_builder.py
- local_server.py
- panel_adapters.py
- panel_states.py
- pgx_panel_rows.py
- tool_catalog.json
- __init__.py
- client.py
- response.py
- tables.py
- text_utils.py
- __init__.py
- helpers.py
- native_sources.py
- ranking.py
- __init__.py
- evidence_acquisition.py
- tool_catalog.json
- __init__.py
- tool_catalog.json
- __init__.py
- compare.py
- constants.py
- parsing.py
- phenotype_match.py
- ranking.py
- text_utils.py
- __init__.py
- tool_catalog.json
- __init__.py
- _constants.py
- _helpers.py
- _operations.py
- __init__.py
- tool_catalog.json
- __init__.py
- catalog.py
- operations.py
- source_context.py
- tool_catalog.json
- gene_requirements.json
- star_marker_definitions.json
- __init__.py
- _common.py
- artifacts.py
- execution.py
- matrix.py
- preflight.py
- record_payloads.py
- __init__.py
- _common.py
- evidence_matrix.py
- interaction.py
- medication_matrix.py
- record_research.py
- sample_evidence.py
- source_state.py
- stored_research.py
- __init__.py
- clinpgx.py
- evidence_matrix.py
- fda_pgx.py
- pgx_envelope.py
- pgx_outside_calls.py
- pgx_requirements.py
- pgx_star.py
- pgxdb.py
- readiness.py
- sample_context.py
- source_summaries.py
- tool_catalog.json
- __init__.py
- _base.py
- comparison.py
- locus.py
- trait_records.py
- __init__.py
- _base.py
- annotations.py
- comparison.py
- __init__.py
- _base.py
- builders.py
- investigation.py
- review_groups.py
- __init__.py
- _base.py
- comparison.py
- disease_targets.py
- __init__.py
- comparison.py
- gencc.py
- hpo_annotation.py
- normalization.py
- tool_catalog.json
- __init__.py
- harmonize.py
- pgs_catalog.py
- scorer.py
- scoring_files.py
- source_context.py
- tool_catalog.json
- __init__.py
- intent_research.py
- tool_catalog.json
- __init__.py
- sequence.py
- tool_catalog.json
- __init__.py
- context.py
- core.py
- parsing.py
- queries.py
- runs.py
- __init__.py
- annotation.py
- gene_variants.py
- tool_catalog.json
- __init__.py
- __init__.py
- candidate_groups.py
- candidate_scoring.py
- candidates.py
- clinvar_annotation.py
- clinvar_import.py
- clinvar_match.py
- clinvar_match_provenance.py
- clinvar_query.py
- connection.py
- constants.py
- gather.py
- helpers.py
- population.py
- research.py
- __init__.py
- candidate_evidence.py
- candidate_inventory.py
- clinvar.py
- envelope.py
- investigation.py
- population.py
- research.py
- schema.py
- sources.py
- task_profiles.py
- variant_context.py
- __init__.py
- cli.py
- mcp.py
- presentation.py
- api.js
- app.js
- brief.css
- connections-controller.js
- form-controls.js
- index.html
- investigation-controller.js
- portal-state.js
- profile-controller.js
- profile-entities.js
- render-brief.js
- render-connections.js
- render-dom.js
- render-evidence.js
- render-profile.js
- render-research-artifacts.js
- render-specialist-board.js
- render.js
- responsive.css
- styles.css
- workspace.css
- __init__.py
- agent_application.py
- agent_artifacts.py
- agent_runtime.py
- agi_authority.py
- approval_store.py
- artifact_payload.py
- artifact_types.py
- artifact_validation.py
- authorization_candidate_receipts.py
- authorization_derivation_store.py
- authorization_store.py
- brief_provenance.py
- candidate_gene_capability.py
- capability_registry.py
- capability_store.py
- context_candidate_receipts.py
- disease_evidence_capabilities.py
- disease_evidence_catalog.py
- disease_evidence_external.py
- disease_relation_contract.py
- disease_relations.py
- encrypted_sqlite.py
- esm_transport.py
- evidence_application_contract.py
- evidence_artifact_store.py
- evidence_disclosure_service.py
- evidence_envelope.py
- evidence_gateway.py
- evidence_job_service.py
- evidence_normalization.py
- evidence_record_store.py
- evidence_service.py
- evidence_service_support.py
- evidence_snapshot_store.py
- evidence_source.py
- evidence_store.py
- evidence_types.py
- genomic_scope.py
- health_store.py
- hypothesis_contract.py
- hypothesis_store.py
- investigation_authorization.py
- investigation_authorized_flow.py
- investigation_capabilities.py
- investigation_capability_catalog.py
- investigation_capability_dispatch.py
- investigation_capability_protocols.py
- investigation_capability_support.py
- investigation_event_store.py
- investigation_round_store.py
- investigation_rounds.py
- investigation_store.py
- model_policy.py
- models.py
- narrative_contract.py
- narrative_forms.py
- narrative_safety_patterns.py
- native_keyring.py
- paperclip_adapter.py
- paperclip_authorization_config.py
- paperclip_contract.py
- paperclip_transport.py
- portal_context.py
- profile_context_application.py
- profile_entities.py
- proto_modal_probe_worker.py
- proto_transport.py
- provider_connection_store.py
- provider_connections.py
- provider_credentials.py
- provider_policy.py
- research_artifact_application.py
- research_artifact_contract.py
- research_artifact_store.py
- research_narrative.py
- research_scientific_operations.py
- schema.py
- schema_migrations.py
- scientific_executor_config.py
- server.py
- service.py
- service_errors.py
- snapshot_store.py
- specialist_board.py
- store.py
- tool_catalog.json
- user_authority.py
- workspace_application.py
- __init__.py
- pharmacogenomics.py
- phenotype.py
- runtime.py
- __init__.py
- agi_access.py
- catalog_meta.py
- coerce.py
- errors.py
- execution.py
- handlers_admin.py
- handlers_admin_next_actions.py
- handlers_agi_lifecycle.py
- handlers_ancestry_prs.py
- handlers_clinvar.py
- handlers_evidence_phenotype.py
- handlers_genomilab.py
- handlers_pgx.py
- handlers_screen_journal.py
- handlers_sequence.py
- handlers_variant_gene.py
- handlers_vcf_variant.py
- model.py
- table.py
- __init__.py
- catalog.py
- catalog_base.json
- defaults.py
- discovery.py
- types.py
- __init__.py
- hybrid.py
- index.py
- semantic.py
- __init__.py
- agi.py
- agi_access.py
- agi_inference.py
- agi_inventory.py
- agi_records.py
- agi_registry.py
- agi_removal.py
- agi_selection.py
- agi_summary.py
- normalize.py
- storage.py
- users.py
- __init__.py
- manager.py
- materialization.py
- registry.py
- spec.py
- transforms.py
- __init__.py
- background_jobs.py
- external.py
- handoff.py
- host_response.py
- host_response_profiles.json
- host_skills.py
- http_json.py
- http_text.py
- job_worker.py
- liftover.py
- paths.py
- private_storage.py
- resources.py
- skill_assets.py
- source_fetch.py
- sqlite_support.py
- static_dependencies.py
- tool_catalog.json
- __init__.py
- __main__.py
- clinvar_match_model.py
- genomilab_synthetic_patient_a.vcf
- genomilab_synthetic_patient_b.vcf
- pgp_hms_public_genetic_data_manifest.json
- tiny.clinvar.vcf
- tiny.fa
- tiny.fa.fai
- tiny.gvcf.vcf
- tiny.normalize.fa
- tiny.normalize.fa.fai
- tiny.normalize.vcf
- tiny.population.vcf
- genomilab_brief.test.mjs
- genomilab_claims.test.mjs
- genomilab_connections.test.mjs
- genomilab_personal_genome.test.mjs
- genomilab_research_artifacts.test.mjs
- genomilab_security.test.mjs
- genomilab_specialist_board.test.mjs
- genomilab_state.test.mjs
- __init__.py
- contract_cases.py
- contract_fixtures.py
- source_fixture_inventory.py
- __init__.py
- candidates.py
- external_layers.py
- gwas.py
- pgx_review.py
- prs_contract.py
- __init__.py
- capability_contract.py
- result_states.py
- source_external_operations.py
- source_runtime_operations.py
- source_support_operations.py
- __init__.py
- genomi.py
- __init__.py
- __init__.py
- genomilab_e2e_support.py
- genomilab_support.py
- pharmcat_test_support.py
- test_active_genome_index_canonical_dependencies.py
- test_active_genome_index_downstream_contract.py
- test_active_genome_index_reader_boundary.py
- test_active_genome_index_sequencing_e2e.py
- test_agi_access.py
- test_agi_revision_integrity.py
- test_analytical_grounding.py
- test_ancestry.py
- test_ancestry_panel_build.py
- test_background_jobs.py
- test_capability_matrix_contract.py
- test_clinpgx.py
- test_clinvar_liftover.py
- test_clinvar_observed_alleles.py
- test_decode_dashboard.py
- test_decode_dashboard_adapters.py
- test_decode_dashboard_assets.py
- test_decode_dashboard_builder.py
- test_decode_dashboard_catalog.py
- test_decode_dashboard_presentation.py
- test_decode_dashboard_registry.py
- test_dispatcher.py
- test_entity_relationships.py
- test_envelope.py
- test_envelope_contract.py
- test_evidence_db_current_contract.py
- test_external_layers_candidates.py
- test_external_layers_clinvar_context.py
- test_external_layers_evidence.py
- test_external_layers_genotype_context.py
- test_external_layers_population.py
- test_external_layers_research_context.py
- test_external_layers_static.py
- test_external_layers_wrappers.py
- test_fda_pgx.py
- test_gene_variant_scan.py
- test_genomi_install.py
- test_genomi_runtime_annotations.py
- test_genomi_runtime_array_intake.py
- test_genomi_runtime_catalog.py
- test_genomi_runtime_context.py
- test_genomi_runtime_intake.py
- test_genomi_runtime_mcp.py
- test_genomi_runtime_operations.py
- test_genomi_runtime_provider_detection.py
- test_genomi_runtime_sequencing_intake.py
- test_genomi_runtime_settings.py
- test_genomi_runtime_variant.py
- test_genomilab_agent_event_atomicity.py
- test_genomilab_agent_guide.py
- test_genomilab_agent_multiturn.py
- test_genomilab_agent_read_security.py
- test_genomilab_agent_runtime.py
- test_genomilab_artifact_validation.py
- test_genomilab_assets.py
- test_genomilab_authorization.py
- test_genomilab_capability_job_resume.py
- test_genomilab_capability_jobs.py
- test_genomilab_capability_registry.py
- test_genomilab_disease_evidence_capabilities.py
- test_genomilab_disease_investigation.py
- test_genomilab_disease_relation_contract.py
- test_genomilab_encrypted_sqlite.py
- test_genomilab_evidence_gateway.py
- test_genomilab_evidence_http.py
- test_genomilab_http_security.py
- test_genomilab_investigation_authorization_store.py
- test_genomilab_investigation_capabilities.py
- test_genomilab_investigation_events.py
- test_genomilab_investigation_rounds.py
- test_genomilab_mcp_presentation.py
- test_genomilab_model_transports.py
- test_genomilab_molecular_profile.py
- test_genomilab_paperclip_adapter.py
- test_genomilab_paperclip_authorization_config.py
- test_genomilab_paperclip_transport.py
- test_genomilab_portal_context.py
- test_genomilab_profile_integrity.py
- test_genomilab_proto_modal_probe_worker.py
- test_genomilab_proto_transport.py
- test_genomilab_provider_connections.py
- test_genomilab_provider_credentials.py
- test_genomilab_provider_policy.py
- test_genomilab_research_artifacts.py
- test_genomilab_schema_migrations.py
- test_genomilab_scientific_executor_config.py
- test_genomilab_snapshot.py
- test_genomilab_specialist_board.py
- test_genomilab_store.py
- test_genomilab_transport_security.py
- test_genomilab_workspace.py
- test_gwas.py
- test_gwas_variant.py
- test_host_skills.py
- test_implementation_catalogs.py
- test_install_for_agents.py
- test_journal.py
- test_library_manager.py
- test_library_registry.py
- test_library_transforms.py
- test_liftover.py
- test_mcp_http.py
- test_no_prose_contract.py
- test_nutrigenomics.py
- test_operation_error_contract.py
- test_parse_source_path_expansion.py
- test_paths.py
- test_pgp_hms_public_format_manifest.py
- test_pgx_capabilities.py
- test_pgx_outside_calls.py
- test_pgx_requirements.py
- test_pgx_review_composition.py
- test_pgx_review_sample.py
- test_pgx_review_stored_sources.py
- test_pgx_star.py
- test_pgxdb.py
- test_pharmcat.py
- test_pharmcat_matrix.py
- test_pharmcat_real_jar.py
- test_phenotype.py
- test_presentation_pgx.py
- test_private_storage.py
- test_prs.py
- test_prs_calculation.py
- test_prs_dosage.py
- test_prs_import_cache.py
- test_prs_score_cache_contracts.py
- test_reference_pass.py
- test_risk_investigation.py
- test_runtime_contracts.py
- test_screen.py
- test_sequence.py
- test_skill_assets.py
- test_skill_tool_sections.py
- test_source_detection.py
- test_source_fetch.py
- test_targets.py
- test_vcf.py
- .gitignore
- AGENTS.md
- CITATION.cff
- CLAUDE.md
- GENOMILAB_PRODUCT_DEFINITION.md
- INSTALL_FOR_AGENTS.md
- LICENSE
- llms-full.txt
- llms.txt
- MANIFEST.in
- pyproject.toml
- README.md
- README.zh-CN.md
- RELEASE_NOTES.md
- SKILL.md
- uv.lock
# Installation Guide
1. Get the code
git clone https://github.com/exon-research/genomi
Downloads the entire project code from GitHub to your computer.
cd genomi
Moves into the project folder you just downloaded.
2. Python
Easy RecommendedPrerequisites
"args": ["-lc", "cd /path/to/genomi && PYTHONPATH=src python3 -m genomi serve"]
Runs the Python script (or module).
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
// repository documentation
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