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
benchmarks/genome_writing_challenge/README.md
benchmarks/genome_writing_challenge/SUBMISSIONS.md
configs/antipeg.yaml
configs/atlas_families.yaml
configs/bridge_offtarget_profile.yaml
configs/capsid_epitope_oracle.yaml
configs/capsid_sequences.fasta
configs/cargo_polish.yaml
configs/cell_types.yaml
configs/datasets.yaml
configs/delivery_constraints.yaml
configs/delivery_rules.yaml
configs/delivery_vehicles.yaml
configs/gates_v3.yaml
configs/genotoxicity_oracle.yaml
configs/gsh_validated_heldout.yaml
configs/intent_weights.yaml
configs/known_unknowns.yaml
configs/llm.yaml
configs/metric_guide.yaml
configs/monitor_queries.yaml
configs/score_axes.yaml
configs/seroprevalence.yaml
configs/target_sites.yaml
configs/universe_crosswalk.yaml
configs/write_types.yaml
configs/wtkb_curated.yaml
configs/calibration/preexisting_nab_independent.yaml
configs/expression/modifiers.yaml
configs/expression/promoters.yaml
configs/oracles/execution.yaml
configs/oracles/scope_cards.yaml
configs/rules/delivery.yaml
configs/rules/fold.yaml
configs/rules/multiplex.yaml
configs/rules/payload.yaml
configs/rules/reachability.yaml
configs/safety/hazard_registry.yaml
configs/safety/policy.yaml
configs/safety/probes.yaml
data/curated/bridge_offtarget_energetics.json
data/curated/bridge_offtarget_profile_measured.parquet
data/curated/gene_coords.parquet
data/curated/unified_editor_universe.parquet
docs/BACKLOG.md
docs/DEPLOY.md
docs/INFRA.md
docs/MCP.md
docs/RELEASING.md
docs/REPRO.md
docs/STABILITY.md
docs/agent.md
docs/alphagenome_feasibility.md
docs/autonomy.md
docs/benchmark_circularity.md
docs/biosecurity.md
docs/build_interface.md
docs/challenge.md
docs/closed_loop.md
docs/co_scientist.md
docs/co_scientist_loop.md
docs/delivery.md
docs/delivery_immunology.md
docs/digital_twin.md
docs/dissemination.md
docs/environment.md
docs/experiment_design.md
docs/generative_design.md
docs/index.md
docs/integrations.md
docs/live_oracles.md
docs/mechanistic_constraints.md
docs/oracles.md
docs/positioning.md
docs/private_data_formats.md
docs/quickstart.md
docs/responsible_use.md
docs/rules.md
docs/scope.md
docs/scorecard.md
docs/uncertainty.md
docs/verify.md
docs/world_model.md
docs/writer_verification.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/active/__init__.py
pen_stack/active/acquire.py
pen_stack/active/design.py
pen_stack/active/validate.py
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/cite.py
pen_stack/agent/co_scientist.py
pen_stack/agent/epistemic.py
pen_stack/agent/guardrails.py
pen_stack/agent/mcp_server.py
pen_stack/agent/orchestrator.py
pen_stack/agent/orchestrator_live.py
pen_stack/agent/pen_agent.py
pen_stack/agent/scope.py
pen_stack/agent/tools.py
pen_stack/api/__init__.py
pen_stack/api/manifest.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/atlas/writer_verify.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/offtarget_energetics.py
pen_stack/bridge/ortholog_screen.py
pen_stack/bridge/pipeline.py
pen_stack/build/__init__.py
pen_stack/build/ingest.py
pen_stack/build/protocol.py
pen_stack/build/simlab.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/design/__init__.py
pen_stack/design/generate.py
pen_stack/design/pareto.py
pen_stack/design/space.py
pen_stack/env/__init__.py
pen_stack/env/genome_writing_env.py
pen_stack/env/policies.py
pen_stack/graph/__init__.py
pen_stack/graph/build.py
pen_stack/graph/cell_types.py
pen_stack/graph/ingest.py
pen_stack/graph/query.py
pen_stack/graph/schema.py
pen_stack/loop/__init__.py
pen_stack/loop/continual.py
pen_stack/loop/cycle.py
pen_stack/loop/drift.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/oracles/__init__.py
pen_stack/oracles/cache.py
pen_stack/oracles/energetics.py
pen_stack/oracles/genome.py
pen_stack/oracles/protein_design.py
pen_stack/oracles/rna.py
pen_stack/oracles/schema.py
pen_stack/oracles/status.py
pen_stack/oracles/structure.py
pen_stack/oracles/vcell.py
pen_stack/planner/__init__.py
pen_stack/planner/antipeg_oracle.py
pen_stack/planner/capsid_epitope_oracle.py
pen_stack/planner/cargo.py
pen_stack/planner/cargo_polish.py
pen_stack/planner/delivery.py
pen_stack/planner/delivery_constraints.py
pen_stack/planner/delivery_immunology.py
pen_stack/planner/delivery_vehicles.py
pen_stack/planner/genotoxicity_oracle.py
pen_stack/planner/immune_profile.py
pen_stack/planner/innate_sensing.py
pen_stack/planner/multiplex.py
pen_stack/planner/optimize.py
pen_stack/planner/pipeline.py
pen_stack/planner/report.py
pen_stack/planner/router.py
pen_stack/planner/seroprevalence_oracle.py
pen_stack/planner/target_site.py
pen_stack/rag/__init__.py
pen_stack/rag/index.py
pen_stack/rag/llm.py
pen_stack/rag/qa.py
pen_stack/rules/__init__.py
pen_stack/rules/evaluators.py
pen_stack/rules/loader.py
pen_stack/rules/schema.py
pen_stack/rules/solver.py
pen_stack/safety/__init__.py
pen_stack/safety/audit.py
pen_stack/safety/gate.py
pen_stack/safety/policy.py
pen_stack/safety/redteam.py
pen_stack/safety/registry.py
pen_stack/safety/screen.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/twin/__init__.py
pen_stack/twin/calibrate.py
pen_stack/twin/mechanistic.py
pen_stack/twin/outcome.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/bench_adversarial_tasks.py
pen_stack/validate/bench_coscientist_tasks.py
pen_stack/validate/bench_graph_tasks.py
pen_stack/validate/bench_rule_tasks.py
pen_stack/validate/bench_trust_tasks.py
pen_stack/validate/bench_writetype_tasks.py
pen_stack/validate/blind_gsh_discovery.py
pen_stack/validate/cargo_directionality.py
pen_stack/validate/closed_loop.py
pen_stack/validate/durability_baselines.py
pen_stack/validate/experiment_design.py
pen_stack/validate/forward_hypotheses.py
pen_stack/validate/generative_design.py
pen_stack/validate/guide_qc_demo.py
pen_stack/validate/immune_calibration.py
pen_stack/validate/intent_specification.py
pen_stack/validate/offtarget_energetics_eval.py
pen_stack/validate/out_of_scope_refusal.py
pen_stack/validate/outcome_calibration.py
pen_stack/validate/outcome_prediction.py
pen_stack/validate/paper3_benchmark.py
pen_stack/validate/paper4_real_validation.py
pen_stack/validate/paper4_validation.py
pen_stack/validate/protocol_safety.py
pen_stack/validate/safety_screening.py
pen_stack/validate/selective_prediction.py
pen_stack/validate/seq_vs_measured.py
pen_stack/validate/target_site_controls.py
pen_stack/validate/uncertainty_eval.py
pen_stack/validate/ungrounded_baseline.py
pen_stack/validate/within_locus_ranking.py
pen_stack/validate/writer_recovery.py
pen_stack/verify/__init__.py
pen_stack/verify/schema.py
pen_stack/verify/service.py
pen_stack/web/__init__.py
pen_stack/web/guide.py
pen_stack/web/llm.py
pen_stack/web/router.py
pen_stack/web/server.py
pen_stack/web/tools.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/mesh_features.py
pen_stack/wgenome/ood.py
pen_stack/wgenome/providers.py
pen_stack/wgenome/safety.py
pen_stack/wgenome/structure3d.py
pen_stack/wgenome/uncertainty.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_acq.json
prereg/SHA256_LOCK_ws_aldesign.json
prereg/SHA256_LOCK_ws_alvalidate.json
prereg/SHA256_LOCK_ws_atlas.json
prereg/SHA256_LOCK_ws_b.json
prereg/SHA256_LOCK_ws_ba.json
prereg/SHA256_LOCK_ws_ba_v33.json
prereg/SHA256_LOCK_ws_ba_v45.json
prereg/SHA256_LOCK_ws_bench.json
prereg/SHA256_LOCK_ws_c.json
prereg/SHA256_LOCK_ws_cal.json
prereg/SHA256_LOCK_ws_calib.json
prereg/SHA256_LOCK_ws_challenge.json
prereg/SHA256_LOCK_ws_chat.json
prereg/SHA256_LOCK_ws_cite.json
prereg/SHA256_LOCK_ws_continual.json
prereg/SHA256_LOCK_ws_cosci2.json
prereg/SHA256_LOCK_ws_crit.json
prereg/SHA256_LOCK_ws_ct.json
prereg/SHA256_LOCK_ws_d.json
prereg/SHA256_LOCK_ws_drift.json
prereg/SHA256_LOCK_ws_e.json
prereg/SHA256_LOCK_ws_env.json
prereg/SHA256_LOCK_ws_ep.json
prereg/SHA256_LOCK_ws_epitope.json
prereg/SHA256_LOCK_ws_f.json
prereg/SHA256_LOCK_ws_frontend.json
prereg/SHA256_LOCK_ws_g.json
prereg/SHA256_LOCK_ws_gen.json
prereg/SHA256_LOCK_ws_genotox.json
prereg/SHA256_LOCK_ws_graph.json
prereg/SHA256_LOCK_ws_h.json
prereg/SHA256_LOCK_ws_hybrid.json
prereg/SHA256_LOCK_ws_immune.json
prereg/SHA256_LOCK_ws_ingest.json
prereg/SHA256_LOCK_ws_innate.json
prereg/SHA256_LOCK_ws_loop.json
prereg/SHA256_LOCK_ws_manifest.json
prereg/SHA256_LOCK_ws_mc.json
prereg/SHA256_LOCK_ws_mcp.json
prereg/SHA256_LOCK_ws_mech.json
prereg/SHA256_LOCK_ws_mon.json
prereg/SHA256_LOCK_ws_o.json
prereg/SHA256_LOCK_ws_openapi.json
prereg/SHA256_LOCK_ws_orch.json
prereg/SHA256_LOCK_ws_outcome.json
prereg/SHA256_LOCK_ws_pareto.json
prereg/SHA256_LOCK_ws_peg.json
prereg/SHA256_LOCK_ws_plan.json
prereg/SHA256_LOCK_ws_policy.json
prereg/SHA256_LOCK_ws_profile.json
prereg/SHA256_LOCK_ws_proto.json
prereg/SHA256_LOCK_ws_r.json
prereg/SHA256_LOCK_ws_redteam.json
prereg/SHA256_LOCK_ws_route.json
prereg/SHA256_LOCK_ws_screen.json
prereg/SHA256_LOCK_ws_seroprev.json
prereg/SHA256_LOCK_ws_simlab.json
prereg/SHA256_LOCK_ws_twincal.json
prereg/SHA256_LOCK_ws_uq.json
prereg/SHA256_LOCK_ws_v.json
prereg/SHA256_LOCK_ws_vcell.json
prereg/SHA256_LOCK_ws_wv.json
prereg/paper1.yaml
prereg/paper2.yaml
prereg/paper3.yaml
prereg/paper4.yaml
prereg/phase0.yaml
prereg/ws_a.yaml
prereg/ws_acq.yaml
prereg/ws_aldesign.yaml
prereg/ws_alvalidate.yaml
prereg/ws_atlas.yaml
prereg/ws_b.yaml
prereg/ws_ba.yaml
prereg/ws_ba_v33.yaml
prereg/ws_ba_v45.yaml
prereg/ws_bench.yaml
prereg/ws_c.yaml
prereg/ws_cal.yaml
prereg/ws_calib.yaml
prereg/ws_challenge.yaml
prereg/ws_chat.yaml
prereg/ws_cite.yaml
prereg/ws_continual.yaml
prereg/ws_cosci2.yaml
prereg/ws_crit.yaml
prereg/ws_ct.yaml
prereg/ws_d.yaml
prereg/ws_drift.yaml
prereg/ws_e.yaml
prereg/ws_env.yaml
prereg/ws_ep.yaml
prereg/ws_epitope.yaml
prereg/ws_f.yaml
prereg/ws_frontend.yaml
prereg/ws_g.yaml
prereg/ws_gen.yaml
prereg/ws_genotox.yaml
prereg/ws_graph.yaml
prereg/ws_h.yaml
prereg/ws_hybrid.yaml
prereg/ws_immune.yaml
prereg/ws_ingest.yaml
prereg/ws_innate.yaml
prereg/ws_loop.yaml
prereg/ws_manifest.yaml
prereg/ws_mc.yaml
prereg/ws_mcp.yaml
prereg/ws_mech.yaml
prereg/ws_mon.yaml
prereg/ws_o.yaml
prereg/ws_openapi.yaml
prereg/ws_orch.yaml
prereg/ws_outcome.yaml
prereg/ws_pareto.yaml
prereg/ws_peg.yaml
prereg/ws_plan.yaml
prereg/ws_policy.yaml
prereg/ws_profile.yaml
prereg/ws_proto.yaml
prereg/ws_r.yaml
prereg/ws_redteam.yaml
prereg/ws_route.yaml
prereg/ws_screen.yaml
prereg/ws_seroprev.yaml
prereg/ws_simlab.yaml
prereg/ws_twincal.yaml
prereg/ws_uq.yaml
prereg/ws_v.yaml
prereg/ws_vcell.yaml
prereg/ws_wv.yaml
scripts/calibrate_immune_axes.py
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/p52_build_genotox_oracle.py
scripts/p53_build_epitope_oracle.py
scripts/ws_b_report.py
scripts/ws_c_report.py