CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
pyproject.toml
bench/run.py
benchmarks/genome_writing_bench/LEADERBOARD.md
benchmarks/genome_writing_bench/README.md
benchmarks/genome_writing_bench/SHA256SUMS
benchmarks/genome_writing_bench/SUBMISSIONS.md
benchmarks/genome_writing_bench/tasks.yaml
configs/atlas_families.yaml
configs/bridge_offtarget_profile.yaml
configs/cargo_polish.yaml
configs/datasets.yaml
configs/delivery_rules.yaml
configs/gates_v3.yaml
configs/gsh_validated_heldout.yaml
configs/intent_weights.yaml
configs/llm.yaml
configs/monitor_queries.yaml
configs/score_axes.yaml
configs/universe_crosswalk.yaml
configs/wtkb_curated.yaml
data/curated/bridge_offtarget_profile_measured.parquet
data/curated/gene_coords.parquet
data/curated/unified_editor_universe.parquet
docs/DEPLOY.md
docs/INFRA.md
docs/MCP.md
docs/RELEASING.md
docs/REPRO.md
docs/agent.md
docs/alphagenome_feasibility.md
docs/benchmark_circularity.md
docs/dissemination.md
docs/index.md
docs/positioning.md
docs/private_data_formats.md
docs/quickstart.md
docs/scorecard.md
docs/wtkb.md
docs/cards/atlas.md
docs/cards/durability.md
docs/cards/safety.md
docs/tutorials/compare-families.md
docs/tutorials/score-deliverability.md
docs/tutorials/where-can-i-write.md
docs/tutorials/which-writer-reaches-locus.md
pen_stack/__init__.py
pen_stack/_resources.py
pen_stack/cli.py
pen_stack.egg-info/PKG-INFO
pen_stack.egg-info/SOURCES.txt
pen_stack.egg-info/dependency_links.txt
pen_stack.egg-info/entry_points.txt
pen_stack.egg-info/requires.txt
pen_stack.egg-info/top_level.txt
pen_stack/adapt/__init__.py
pen_stack/adapt/finetune.py
pen_stack/adapt/ingest.py
pen_stack/adapt/pipeline.py
pen_stack/adapt/recalibrate.py
pen_stack/adapt/report.py
pen_stack/agent/__init__.py
pen_stack/agent/guardrails.py
pen_stack/agent/mcp_server.py
pen_stack/agent/orchestrator.py
pen_stack/agent/pen_agent.py
pen_stack/agent/tools.py
pen_stack/atlas/__init__.py
pen_stack/atlas/build_wtkb.py
pen_stack/atlas/crosslink.py
pen_stack/atlas/expand.py
pen_stack/atlas/schema.py
pen_stack/atlas/scorecard.py
pen_stack/atlas/universe.py
pen_stack/atlas/variant_propose.py
pen_stack/bridge/__init__.py
pen_stack/bridge/activity.py
pen_stack/bridge/cli.py
pen_stack/bridge/fold_qc.py
pen_stack/bridge/guide_qc.py
pen_stack/bridge/ingest.py
pen_stack/bridge/offtarget.py
pen_stack/bridge/ortholog_screen.py
pen_stack/bridge/pipeline.py
pen_stack/data/__init__.py
pen_stack/data/encode.py
pen_stack/data/genome.py
pen_stack/data/ingest_chromatin.py
pen_stack/data/ingest_integration.py
pen_stack/data/ingest_safety_annot.py
pen_stack/data/ingest_trip.py
pen_stack/mech/__init__.py
pen_stack/mech/classify_atlas.py
pen_stack/mech/whitelist.py
pen_stack/monitor/__init__.py
pen_stack/monitor/europepmc.py
pen_stack/monitor/run.py
pen_stack/monitor/triage.py
pen_stack/planner/__init__.py
pen_stack/planner/cargo.py
pen_stack/planner/cargo_polish.py
pen_stack/planner/delivery.py
pen_stack/planner/multiplex.py
pen_stack/planner/optimize.py
pen_stack/planner/pipeline.py
pen_stack/planner/report.py
pen_stack/rag/__init__.py
pen_stack/rag/index.py
pen_stack/rag/llm.py
pen_stack/rag/qa.py
pen_stack/score/__init__.py
pen_stack/score/recalibrate.py
pen_stack/score/therapeutic.py
pen_stack/server/__init__.py
pen_stack/server/api.py
pen_stack/ui/__init__.py
pen_stack/ui/app.py
pen_stack/validate/__init__.py
pen_stack/validate/adapt_demo.py
pen_stack/validate/agent_eval.py
pen_stack/validate/blind_gsh_discovery.py
pen_stack/validate/cargo_directionality.py
pen_stack/validate/durability_baselines.py
pen_stack/validate/forward_hypotheses.py
pen_stack/validate/guide_qc_demo.py
pen_stack/validate/intent_specification.py
pen_stack/validate/paper3_benchmark.py
pen_stack/validate/paper4_real_validation.py
pen_stack/validate/paper4_validation.py
pen_stack/validate/seq_vs_measured.py
pen_stack/validate/within_locus_ranking.py
pen_stack/validate/writer_recovery.py
pen_stack/wgenome/__init__.py
pen_stack/wgenome/chromatin_seq.py
pen_stack/wgenome/durability.py
pen_stack/wgenome/export_tracks.py
pen_stack/wgenome/features.py
pen_stack/wgenome/gsh_baseline.py
pen_stack/wgenome/providers.py
pen_stack/wgenome/safety.py
pen_stack/wgenome/structure3d.py
pen_stack/wgenome/writability.py
prereg/SHA256_LOCK_phase0.json
prereg/SHA256_LOCK_phase1_5.json
prereg/SHA256_LOCK_phase2.json
prereg/SHA256_LOCK_phase3.json
prereg/SHA256_LOCK_ws_a.json
prereg/SHA256_LOCK_ws_b.json
prereg/SHA256_LOCK_ws_c.json
prereg/SHA256_LOCK_ws_d.json
prereg/SHA256_LOCK_ws_e.json
prereg/SHA256_LOCK_ws_f.json
prereg/SHA256_LOCK_ws_g.json
prereg/SHA256_LOCK_ws_h.json
prereg/paper1.yaml
prereg/paper2.yaml
prereg/paper3.yaml
prereg/paper4.yaml
prereg/phase0.yaml
prereg/ws_a.yaml
prereg/ws_b.yaml
prereg/ws_c.yaml
prereg/ws_d.yaml
prereg/ws_e.yaml
prereg/ws_f.yaml
prereg/ws_g.yaml
prereg/ws_h.yaml
scripts/p1_build_atlas.py
scripts/p1_build_durability.py
scripts/p1_export_tracks.py
scripts/p1_safety_concordance.py
scripts/p1_train_safety.py
scripts/p1_validation_report.py
scripts/p2_build_atlas.py
scripts/p3_benchmark_report.py
scripts/p4_genome_scan.py
scripts/ws_b_report.py
scripts/ws_c_report.py