HGD editing resource for alkaptonuria: code, data and reproducibility records
Year: 2026
Type: software
Abstract: Code, retained reference inputs and derived data for a computational HGD editing resource for alkaptonuria. Version 8.5 preserves HGD_CBC_resource.zip from version 8.4 byte for byte and adds the independent verification addendum and production support for the worked-example Figure 3 in "An auditable HGD editing design resource for alkaptonuria". All three ZIP archives are unchanged from the files prepared for the submitted manuscript. README_v8_5.txt explains the package contents, public-release status, reuse terms and SHA-256 checksums. HGD_verification_addendum.zip (Supplementary Resource 3) supplies the seed-based PE3b verification, coordinate and target-exclusion audits, labelled rule-relaxation sensitivity, baseline replay and reconciliation of historical routing with the 237-locus inventory, including Tables S16 and S17. HGD_Figure_3_support.zip supplies retained inputs, source hashes and the portable generation script for the submitted worked example at HGD c.879+1G>A. These additions do not change the original selected guide configurations. The review-draft and pending-deposit wording retained inside the addendum describes its status before this public version 8.5 release. The unchanged version 8.4 archive preserves the 8.3 scientific baseline and adds selection decomposition, comparison of the full 237-locus inventory with pinned PrimeDesign, full-text-adjudicated cohort tables, and a portable PrimeDesign output-limit verification. Under shared screens, 70 fixed canonical prime configurations are retained and reselection adds 79; with the constant base-editing arm, variant representation is 110 versus 188. PrimeDesign component agreement is 225/233 selected pairs, with four separate availability comparators. Raising the normal-mode peg-count parameter to 1000 produces byte-identical output. Candidate counts do not establish biological efficiency, specificity or clinical utility. The original version 8.4 remains available at https://doi.org/10.5281/zenodo.23073297. The Mathematics, Engineering, and Science Achievement (MESA) program and Emerging Technologies Institute (ETI) at Foothill College provided funding and program support. Investigators controlled study design, analysis, manuscript preparation and the decision to submit. Original code is MIT; original project data, figures and documentation are CC BY 4.0. Third-party terms remain in the included rights records.
Institution: Foothill College
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7213615226