README.md

GENtle Tutorial (Generated)

Generated executable tutorial runtime manifest for GENtle. Used by tutorial-generate / tutorial-check and the GUI Open Tutorial Project... flow to map source-backed chapters onto canonical workflow examples.

This folder is generated from:

• docs/tutorial/sources/catalog_meta.json
• docs/tutorial/sources/*.json
• docs/examples/workflows/*.json

Generated runtime manifest:

• docs/tutorial/manifest.json

Regenerate with:

cargo run --bin gentle_examples_docs -- tutorial-generate

Validate committed generated output:

cargo run --bin gentle_examples_docs -- tutorial-check

Recommended progression:

• Start chapters in the GUI to understand biological intent and visual context.
• Then use the command equivalents for repeatable runs and automation.

These chapters are generated from executable workflow JSON. They are stable, regenerable, and machine-checked, but they are reference material - not first-time walkthroughs. If you are new to GENtle, start with the guided walkthroughs in ../README.md.

Each chapter row includes a review badge from ../review_manifest.json; review unreviewed means the workflow is machine-checked but still needs a readability/biology pass from Codex or a human reviewer.

Online execution was disabled (GENTLE_TEST_ONLINE=0 during generation).

Chapters

Getting Started & Interfaces

• 01.02 Contribute to GENtle development - advanced - example contribute_gentle_development_baseline - executed yes - review unreviewed - file feedback

Sequence Basics & Lineage

• 02.01 Load FASTA, branch, and reverse-complement - core - example load_branch_reverse_complement_pgex_fasta - executed yes - review human_reviewed stale - human 2026-05-18 by smoe - file feedback
• 02.04 Compare TP73 cDNA against TP73 genomic context via dotplot (online) - online - example tp73_cdna_genomic_dotplot_online - executed no - review unreviewed - file feedback

Cloning & Assembly

• 03.01 Load pGEX and digest with BamHI/EcoRI - core - example load_and_digest_pgex - executed yes - review unreviewed - file feedback
• 03.02 Digest -> Ligation -> ExtractRegion minimal slice - core - example digest_ligation_extract_region_minimal - executed yes - review unreviewed - file feedback
• 03.03 Gibson two-fragment overlap planning baseline - core - example gibson_two_fragment_overlap_preview - executed yes - review unreviewed - file feedback
• 03.04 Gibson Specialist Starter Project (offline) - core - example gibson_specialist_testing_baseline - executed yes - review unreviewed - file feedback
• 03.06 Gibson Arrangements Starter Project (offline) - core - example gibson_arrangements_baseline - executed yes - review unreviewed - file feedback

Primers, PCR & qPCR

• 04.01 Simple PCR From a Selected Core Region - core - example simple_pcr_selection_gui - executed yes - review unreviewed - file feedback
• 04.02 Selection-first PCR batch primer design (offline) - core - example pcr_selection_batch_primer_pairs_offline - executed yes - review unreviewed - file feedback
• 04.04 Guide practical filtering and oligo generation - core - example guides_filter_and_generate_oligos - executed yes - review unreviewed - file feedback
• 04.05 Guide oligo export (CSV + protocol) - advanced - example guides_export_csv_and_protocol - executed yes - review unreviewed - file feedback

Genome Context & Coordinates

• 05.01 Find and extend the right genomic target (local catalog) - core - example prepare_extract_extend_localproject_gene - executed yes - review unreviewed - file feedback
• 05.02 Prepare a reference genome cache (online) - online - example prepare_reference_genome_online - executed no - review unreviewed - file feedback
• 05.03 Retrieve TP63 and extend the displayed region by +/-2 kb (online) - online - example tp63_extend_anchor_online - executed no - review unreviewed - file feedback

Transcript, Protein & Projection

• 06.03 TP53 isoform architecture expert panel (online) - online - example tp53_isoform_architecture_online - executed no - review unreviewed - file feedback
• 06.04 TP53 UniProt domain mapping and feature-coding DNA query (online) - online - example tp53_uniprot_projection_online - executed no - review unreviewed - file feedback
• 06.05 Audit a TP73 UniProt Projection Against Ensembl and Derived Coding Sequence (CLI Tutorial) - online - example tp73_uniprot_projection_audit_online - executed no - review unreviewed - file feedback

RNA Reads, Splicing & Expression

• 07.02 Map TP53 locus reads with multi-gene sparse indexing (online) - online - example tp53_multi_gene_sparse_mapping_online - executed no - review unreviewed - file feedback

Regulatory, TFBS & Reporter Design

• 08.03 Promoter Design Artifact Slice (Offline Synthetic TP73 Locus) - core - example promoter_design_artifact_slice_offline - executed yes - review human_reviewed stale - human 2026-05-18 by smoe - file feedback

Concepts and Where They Recur

• Shared Engine Contract (shared_engine_contract): GUI, CLI, shell, and scripting interfaces execute the same operation semantics.
  • Appears in: Chapter 1: Load FASTA, branch, and reverse-complement, Chapter 2: Find and extend the right genomic target (local catalog), Chapter 4: Gibson two-fragment overlap planning baseline, Chapter 8: Contribute to GENtle development, Chapter 10: TP53 isoform architecture expert panel (online), Chapter 11: Retrieve TP63 and extend the displayed region by +/-2 kb (online), Chapter 12: Map TP53 locus reads with multi-gene sparse indexing (online), Chapter 13: Selection-first PCR batch primer design (offline), Chapter 14: Compare TP73 cDNA against TP73 genomic context via dotplot (online), Chapter 15: Gibson Specialist Starter Project (offline), Chapter 16: Gibson Arrangements Starter Project (offline), Chapter 17: TP53 UniProt domain mapping and feature-coding DNA query (online), Chapter 18: Simple PCR From a Selected Core Region, Chapter 19: Audit a TP73 UniProt Projection Against Ensembl and Derived Coding Sequence (CLI Tutorial), Chapter 24: Promoter Design Artifact Slice (Offline Synthetic TP73 Locus).
• Deterministic Workflows (deterministic_workflows): Operation chains should produce stable IDs and comparable outputs across repeated runs.
  • Appears in: Chapter 1: Load FASTA, branch, and reverse-complement, Chapter 2: Find and extend the right genomic target (local catalog), Chapter 3: Load pGEX and digest with BamHI/EcoRI, Chapter 4: Gibson two-fragment overlap planning baseline, Chapter 5: Guide practical filtering and oligo generation, Chapter 6: Digest -> Ligation -> ExtractRegion minimal slice, Chapter 9: Prepare a reference genome cache (online), Chapter 12: Map TP53 locus reads with multi-gene sparse indexing (online), Chapter 13: Selection-first PCR batch primer design (offline), Chapter 14: Compare TP73 cDNA against TP73 genomic context via dotplot (online), Chapter 15: Gibson Specialist Starter Project (offline), Chapter 16: Gibson Arrangements Starter Project (offline), Chapter 18: Simple PCR From a Selected Core Region, Chapter 24: Promoter Design Artifact Slice (Offline Synthetic TP73 Locus).
• Sequence Lineage (sequence_lineage): Derived sequences are explicit products linked to upstream inputs and operations.
  • Appears in: Chapter 1: Load FASTA, branch, and reverse-complement, Chapter 2: Find and extend the right genomic target (local catalog), Chapter 3: Load pGEX and digest with BamHI/EcoRI, Chapter 4: Gibson two-fragment overlap planning baseline, Chapter 6: Digest -> Ligation -> ExtractRegion minimal slice, Chapter 11: Retrieve TP63 and extend the displayed region by +/-2 kb (online), Chapter 13: Selection-first PCR batch primer design (offline), Chapter 14: Compare TP73 cDNA against TP73 genomic context via dotplot (online), Chapter 15: Gibson Specialist Starter Project (offline), Chapter 16: Gibson Arrangements Starter Project (offline).
• Genome Catalog Targeting (genome_catalog_targeting): Prepared genome catalogs, annotation-based gene filters, and anchor extension connect imported entries to genomic context.
  • Appears in: Chapter 2: Find and extend the right genomic target (local catalog), Chapter 9: Prepare a reference genome cache (online), Chapter 10: TP53 isoform architecture expert panel (online), Chapter 11: Retrieve TP63 and extend the displayed region by +/-2 kb (online), Chapter 12: Map TP53 locus reads with multi-gene sparse indexing (online), Chapter 14: Compare TP73 cDNA against TP73 genomic context via dotplot (online), Chapter 17: TP53 UniProt domain mapping and feature-coding DNA query (online).
• Guide Design Pipeline (guide_design_pipeline): Guide sets can be created, filtered, expanded to oligos, and exported with protocol context.
  • Appears in: Chapter 5: Guide practical filtering and oligo generation, Chapter 7: Guide oligo export (CSV + protocol).
• Artifact Exports (artifact_exports): Representative outputs (CSV/protocol/SVG/text) are retained for auditability and sharing.
  • Appears in: Chapter 7: Guide oligo export (CSV + protocol), Chapter 10: TP53 isoform architecture expert panel (online), Chapter 17: TP53 UniProt domain mapping and feature-coding DNA query (online), Chapter 19: Audit a TP73 UniProt Projection Against Ensembl and Derived Coding Sequence (CLI Tutorial), Chapter 24: Promoter Design Artifact Slice (Offline Synthetic TP73 Locus).
• Tutorial Drift Checks (tutorial_drift_checks): Tutorial content is generated from executable examples and verified in automated checks.
  • Appears in: Chapter 8: Contribute to GENtle development, Chapter 24: Promoter Design Artifact Slice (Offline Synthetic TP73 Locus).
• Contribution Loop (contribution_loop): Contributions should couple code edits with docs updates and deterministic tests.
  • Appears in: Chapter 8: Contribute to GENtle development.
• Online Opt-in Execution (online_opt_in): Network-dependent chapters remain explicit opt-in and do not break offline default CI.
  • Appears in: Chapter 9: Prepare a reference genome cache (online), Chapter 10: TP53 isoform architecture expert panel (online), Chapter 11: Retrieve TP63 and extend the displayed region by +/-2 kb (online), Chapter 12: Map TP53 locus reads with multi-gene sparse indexing (online), Chapter 14: Compare TP73 cDNA against TP73 genomic context via dotplot (online), Chapter 17: TP53 UniProt domain mapping and feature-coding DNA query (online), Chapter 19: Audit a TP73 UniProt Projection Against Ensembl and Derived Coding Sequence (CLI Tutorial).
• Isoform Architecture Panels (isoform_architecture_panels): Curated transcript/protein architecture overlays can be imported and rendered as deterministic expert-view SVG outputs.
  • Appears in: Chapter 10: TP53 isoform architecture expert panel (online).
• UniProt Projection Mapping (uniprot_projection_mapping): Reviewed UniProt protein annotations can be projected onto transcript/CDS geometry and reopened as one persisted expert-view artifact.
  • Appears in: Chapter 17: TP53 UniProt domain mapping and feature-coding DNA query (online), Chapter 19: Audit a TP73 UniProt Projection Against Ensembl and Derived Coding Sequence (CLI Tutorial).
• Feature Coding-DNA Attribution (feature_coding_dna_attribution): A persisted UniProt projection can be queried for the exact coding DNA, exon attribution, and splice-junction exon pairs that encode one mapped protein feature.
  • Appears in: Chapter 17: TP53 UniProt domain mapping and feature-coding DNA query (online), Chapter 19: Audit a TP73 UniProt Projection Against Ensembl and Derived Coding Sequence (CLI Tutorial).
• Expert View Parity (expert_view_parity): The same expert-view payloads should be inspectable and renderable from GUI, CLI, and other adapters without frontend-only projection logic.
  • Appears in: Chapter 17: TP53 UniProt domain mapping and feature-coding DNA query (online), Chapter 19: Audit a TP73 UniProt Projection Against Ensembl and Derived Coding Sequence (CLI Tutorial).

Source Summary

• Tutorial schema: gentle.tutorial_manifest.v2
• Chapter count: 20
• Generation report: report.json