LICENSE
README.md
README_PYPI.md
pyproject.toml
src/helixlang/__init__.py
src/helixlang/__main__.py
src/helixlang/ast_nodes.py
src/helixlang/bio_data.py
src/helixlang/biocodec.py
src/helixlang/bytecode.py
src/helixlang/cell.py
src/helixlang/cell_body.py
src/helixlang/central_dogma.py
src/helixlang/cli.py
src/helixlang/codon_table.py
src/helixlang/compiler.py
src/helixlang/crispr.py
src/helixlang/debugger.py
src/helixlang/disassembler.py
src/helixlang/dna_codec.py
src/helixlang/environment.py
src/helixlang/epigenetics.py
src/helixlang/errors.py
src/helixlang/evolution.py
src/helixlang/flow.py
src/helixlang/grn.py
src/helixlang/hxbc.py
src/helixlang/interop.py
src/helixlang/lexer.py
src/helixlang/lsystem.py
src/helixlang/metabolism.py
src/helixlang/morphology_3d.py
src/helixlang/parser.py
src/helixlang/population.py
src/helixlang/protein_fitness.py
src/helixlang/protein_structure.py
src/helixlang/protein_structure_predictor.py
src/helixlang/reaction_diffusion.py
src/helixlang/semantic.py
src/helixlang/seq_utils.py
src/helixlang/server.py
src/helixlang/sim_runtime.py
src/helixlang/sparse_grn.py
src/helixlang/stochastic.py
src/helixlang/type_system.py
src/helixlang/units.py
src/helixlang/vectorized.py
src/helixlang/virtual_cell.py
src/helixlang/vm.py
src/helixlang.egg-info/PKG-INFO
src/helixlang.egg-info/SOURCES.txt
src/helixlang.egg-info/dependency_links.txt
src/helixlang.egg-info/entry_points.txt
src/helixlang.egg-info/requires.txt
src/helixlang.egg-info/top_level.txt
src/helixlang/annotation/__init__.py
src/helixlang/annotation/blast.py
src/helixlang/annotation/ec_mapping.py
src/helixlang/annotation/kegg_mapping.py
src/helixlang/annotation/sequences.py
src/helixlang/annotation/tf_detection.py
src/helixlang/annotation/transporter.py
src/helixlang/apps/__init__.py
src/helixlang/apps/consortium.py
src/helixlang/apps/digital_evolution.py
src/helixlang/apps/dna_storage.py
src/helixlang/apps/ecosystem.py
src/helixlang/apps/fate_analysis.py
src/helixlang/apps/full_pipeline.py
src/helixlang/apps/gem_pipeline.py
src/helixlang/apps/genome_scale.py
src/helixlang/apps/lattice_boltzmann.py
src/helixlang/apps/lattice_boltzmann_3d.py
src/helixlang/apps/morphogen_gradient.py
src/helixlang/apps/omics_calibration.py
src/helixlang/apps/population_calibration.py
src/helixlang/apps/population_dbtl.py
src/helixlang/apps/protein_evolution.py
src/helixlang/apps/spatial_dfba.py
src/helixlang/apps/spatial_evolution.py
src/helixlang/apps/synbio_automation.py
src/helixlang/apps/synbio_designer.py
src/helixlang/apps/virtual_cell_bench.py
src/helixlang/apps/whole_cell_calibration.py
src/helixlang/apps/whole_cell_scale.py
src/helixlang/data/ecoli_core_model.json
src/helixlang/gem/__init__.py
src/helixlang/gem/biomass.py
src/helixlang/gem/bottom_up.py
src/helixlang/gem/bridge.py
src/helixlang/gem/community.py
src/helixlang/gem/consensus.py
src/helixlang/gem/ecgem.py
src/helixlang/gem/full_model.py
src/helixlang/gem/gapfill.py
src/helixlang/gem/grn_inference.py
src/helixlang/gem/organism_registry.py
src/helixlang/gem/sbml_export.py
src/helixlang/gem/sbml_import.py
src/helixlang/gem/top_down.py
src/helixlang/gem/validation.py
src/helixlang/kinetics/__init__.py
src/helixlang/kinetics/kcat_predictor.py
src/helixlang/kinetics/km_estimator.py
src/helixlang/kinetics/sequence_predictor.py
src/helixlang/omics/__init__.py
src/helixlang/omics/_spatial_omics.py
src/helixlang/omics/expression_inference.py
src/helixlang/web/index.html
src/helixlang/web/labs.html
src/helixlang/web/serializers.py
tests/test_api_sim_run.py
tests/test_benchmark.py
tests/test_biocodec.py
tests/test_cell.py
tests/test_cell_body.py
tests/test_central_dogma.py
tests/test_central_dogma_pipeline.py
tests/test_cli.py
tests/test_codon_table.py
tests/test_community_fba.py
tests/test_compiler.py
tests/test_consortium.py
tests/test_crispr.py
tests/test_dFBA.py
tests/test_debugger.py
tests/test_digital_evolution.py
tests/test_dna_codec.py
tests/test_dna_codec_bench.py
tests/test_dna_storage.py
tests/test_doc25_phase_vii_x.py
tests/test_ecgem.py
tests/test_ecosystem.py
tests/test_end_to_end.py
tests/test_environment.py
tests/test_epigenetics.py
tests/test_evolution.py
tests/test_fate_analysis.py
tests/test_fba_simplex.py
tests/test_flow.py
tests/test_full_gem_import.py
tests/test_full_pipeline.py
tests/test_g9.py
tests/test_gem_integration.py
tests/test_genome_scale.py
tests/test_grn.py
tests/test_grn_continuous.py
tests/test_helixc.py
tests/test_integration.py
tests/test_interop.py
tests/test_lattice_boltzmann.py
tests/test_lattice_boltzmann_3d.py
tests/test_lexer.py
tests/test_lsystem.py
tests/test_metabolism.py
tests/test_metabolism_proxy.py
tests/test_morphogen_gradient.py
tests/test_morphology_3d.py
tests/test_mutate_consistency.py
tests/test_omics.py
tests/test_omics_calibration.py
tests/test_pamindex_fallback.py
tests/test_parser.py
tests/test_population.py
tests/test_population_3d.py
tests/test_population_advances.py
tests/test_population_calibration.py
tests/test_population_dbtl.py
tests/test_population_dfba.py
tests/test_protein_evolution.py
tests/test_protein_fitness.py
tests/test_protein_structure.py
tests/test_protein_structure_predictor.py
tests/test_reaction_diffusion.py
tests/test_realism.py
tests/test_semantic.py
tests/test_sequence_kinetics.py
tests/test_server.py
tests/test_sim_runtime.py
tests/test_spatial_evolution.py
tests/test_species.py
tests/test_stochastic.py
tests/test_synbio_automation.py
tests/test_synbio_designer.py
tests/test_type_system.py
tests/test_units.py
tests/test_vectorized.py
tests/test_virtual_cell.py
tests/test_vm.py
tests/test_whole_cell_calibration.py
tests/test_whole_cell_scale.py