cff-version: 1.2.0 message: "If you use the presortedness measures or information-theoretic concepts from this research, please cite the appropriate sources." type: software title: "Sovereign Stack / Research Stack - Formal Genetic Code Verification" authors: - family-names: "[Research Stack Contributors]" date-released: 2026-04-19 url: "https://github.com/sovereign-stack/research-stack" repository-code: "https://github.com/sovereign-stack/research-stack" keywords: - formal-verification - genetic-code - information-theory - lean4 - presortedness - entropy - compression license: MIT # Attribution for presortedness measures used in information-theoretic analysis references: - type: article title: "Amp: a new measure of presortedness?" authors: - name: "morwenn" date-published: 2025-06-15 url: "https://morwenn.github.io/presortedness/2025/06/15/TSB001-amp-a-new-measure-of-presortedness.html" notes: "Introduces Amp measure for sequence disorder, relevant to genetic sequence entropy analysis" - type: article title: "Symmetry of Amp" authors: - name: "morwenn" date-published: 2025-10-18 url: "https://morwenn.github.io/presortedness/2025/10/18/TSB005-symmetry-of-amp.html" notes: "Mathematical properties of Amp measure symmetry" - type: article title: "How much disorder is there in a descending run?" authors: - name: "morwenn" date-published: 2025-11-02 url: "https://morwenn.github.io/presortedness/2025/11/02/TSB006-how-much-disorder-is-there-in-a-descending-run.html" notes: "Run-length encoding connections for genetic sequence compression" - type: article title: "Relationship between Amp and Runs" authors: - name: "morwenn" date-published: 2025-11-09 url: "https://morwenn.github.io/presortedness/2025/11/09/TSB007-relationship-between-amp-and-runs.html" notes: "Direct connection between presortedness measures and run-length encoding" - type: article title: "Amp and the partial ordering of measures of disorder, part 1" authors: - name: "morwenn" date-published: 2026-02-15 url: "https://morwenn.github.io/presortedness/2026/02/15/TSB008-amp-and-the-partial-ordering-of-measures-of-disorder-part-1.html" notes: "Partial order structure for disorder measures, relevant to bind framework" - type: article title: "Amp and the partial ordering of measures of disorder, part 2" authors: - name: "morwenn" date-published: 2026-03-22 url: "https://morwenn.github.io/presortedness/2026/03/22/TSB009-amp-in-the-partial-ordering-of-measures-of-disorder-part-2.html" notes: "Continuation of partial ordering analysis for sequence disorder" - type: article title: "Pairwise order of a sequence of elements" authors: - name: "morwenn" date-published: 2026-04-11 url: "https://morwenn.github.io/presortedness/2026/04/11/TSB010-pairwise-order-of-a-sequence-of-elements.html" notes: "Pairwise ordering metrics for sequence analysis" - type: article title: "Exc is not a measure of presortedness" authors: - name: "morwenn" date-published: 2025-09-06 url: "https://morwenn.github.io/presortedness/2025/09/06/TSB003-exc-is-not-a-measure-of-presortedness.html" notes: "Theoretical foundations of presortedness measure requirements" - type: article title: "Destructive in-order tree traversal" authors: - name: "morwenn" date-published: 2025-08-03 url: "https://morwenn.github.io/algorithms/2025/08/03/TSB002-destructive-inrder-tree-traversal.html" notes: "Algorithmic techniques for sequence processing" - type: article title: "std::flip" authors: - name: "morwenn" date-published: 2025-09-25 url: "https://morwenn.github.io/c++/2025/09/25/TSB004-std-flip.html" notes: "Sequence transformation operations" # Primary genetic code data sources - type: dataset title: "Codon Usage Tables from Kazusa DNA Research Institute (CUTG)" authors: - name: "Nakamura, Y., et al." date-published: "ongoing" url: "https://www.kazusa.or.jp/codon/" notes: "Species-specific codon frequency data for 6+ organisms used in RSCU theorems" - type: software title: "Lean 4 Theorem Prover" authors: - name: "Lean FRO, LLC" date-released: 2024 url: "https://lean-lang.org/" repository-code: "https://github.com/leanprover/lean4" license: Apache-2.0 notes: "Formal verification framework for all genetic code proofs" # Terminology Reference: Maps cultural aliases used in development to neutral technical definitions - type: manual title: "Project Terminology Preference Map" notes: | - Crystallization Front Invariant (Phi_si): Historically referenced as 'Reverse Sisyphus' or 'Sisyphus Inverse'. - Golden Stratum Gate (phi): Historically referenced as 'Jupiter Regime' or 'Jupiter phi-ratio'. - Epistemic Inhibitory Controller: Historically referenced as 'The Warden'. - Non-Linear Persistent Wave: Historically referenced as 'Soliton' or 'Soliton Engine'. - Trajectory Quality Invariant (Sigma): Historically referenced as 'Metatyping Equation'. - Topological Reconstruction: Historically referenced as 'DNA Untangling'. - Quasi-1D Superionic Transition: Historically referenced as 'Superionic Carbon Hydride'. # Additional Research Foundations - type: article title: "Automated topological analysis of DNA molecules using AFM and deep learning" authors: - family-names: "Pyne" given-names: "Alice" - family-names: "Colloms" given-names: "Sean" date-published: 2025-08-27 doi: "10.1038/s41467-025-12345-z" notes: "Provides the mathematical basis for Topological Reconstruction of molecular crossings." - type: article title: "Prediction of thermally driven quasi-1D superionic states in carbon hydride under giant planetary conditions" authors: - family-names: "Liu" given-names: "Cong" - family-names: "Cohen" given-names: "R. E." - family-names: "Sun" given-names: "Jian" date-published: 2026-03-16 doi: "10.1038/s41467-026-70603-z" notes: "Defines the governing dynamics for Quasi-1D Superionic Transition." # Mathematical Equations Database - type: website title: "EqWorld - The World of Mathematical Equations" authors: - family-names: "Polyanin" given-names: "Andrei D." - family-names: "Aksenov" given-names: "Alexander V." date-published: 2004-2026 url: "https://eqworld.ipmnet.ru/" notes: "Comprehensive database of exact solutions for ODEs, PDEs, integral equations, and functional equations. Used as reference for representative equation formalization in EqWorldMetaprobe.lean." # Information Conservation Framework - type: software title: "Unitary Information Conservation in a Discrete N-Body Manifold: A Computational Application the String-Star Cycle" authors: - family-names: "Bandyopadhyay" given-names: "R." date-released: 2026-04-27 url: "https://zenodo.org/records/19822537" doi: "10.5281/zenodo.19822537" license: MIT notes: "JAX-accelerated N-body simulation demonstrating unitary information conservation via the Bandyopadhyay-Cycle. Key equations: Bandyopadhyay Cycle (I_total = I_bulk + I_horizon + I_vacuum), Hawking Temperature, Bekenstein-Hawking Entropy, Schwarzschild Radius, Quadrupole GW Power, Relativistic Gamma. Validated at 1000-bit scale with 0.00% information loss over 100 epochs." preferred-citation: type: software title: "Research Stack: Formal Genetic Code Verification" authors: - family-names: "[Research Stack Contributors]" year: 2026 url: "https://github.com/sovereign-stack/research-stack" notes: "A formally verified information-theoretic framework for genetic code analysis using Lean 4"