cff-version: 1.2.0
title: >-
  Codex Vivum — browser client-side tools for
  privacy-compliant sequence analysis in teaching
message: >-
  If you use this work, please cite it using the metadata
  from this file.
type: software
authors:
  - given-names: Thomas
    family-names: Schüller
    email: forschung@tschueller.com
    orcid: 'https://orcid.org/0009-0003-9799-6747'
    affiliation: independent research, Vienna
abstract: >-
  A browser client-side tool family for three routine tasks in
  molecular biology teaching: restriction site mapping (40
  enzymes, REBASE specificities), PCR primer design with
  nearest-neighbor thermodynamics (SantaLucia 1998, Owczarzy
  2004 salt correction) and FASTA processing. All computation
  runs in the browser; no sequence data is transmitted to a
  server. Accompanied by a concept paper and a completed
  validation of the melting temperature calculation against an
  independent implementation (120 comparisons, all within
  ±2 °C). Not a medical device (EU 2017/745), not an in-vitro
  diagnostic (EU 2017/746) — teaching and research only.
keywords:
  - bioinformatics education
  - client-side computing
  - local-first
  - PCR primer design
  - melting temperature
  - restriction enzymes
  - GDPR
  - open science
license: AGPL-3.0-or-later
license-url: 'https://www.gnu.org/licenses/agpl-3.0.html'
version: v1.0
date-released: '2026-05-12'
references:
  - type: article
    title: >-
      A unified view of polymer, dumbbell, and oligonucleotide
      DNA nearest-neighbor thermodynamics
    authors:
      - given-names: John
        family-names: SantaLucia
    journal: PNAS
    volume: 95
    issue: 4
    year: 1998
    doi: 10.1073/pnas.95.4.1460
  - type: article
    title: >-
      Effects of sodium ions on DNA duplex oligomers: improved
      predictions of melting temperatures
    authors:
      - given-names: Richard
        family-names: Owczarzy
    journal: Biochemistry
    volume: 43
    issue: 12
    year: 2004
    doi: 10.1021/bi034621r
  - type: article
    title: >-
      REBASE — a database for DNA restriction and modification
    authors:
      - given-names: Richard J.
        family-names: Roberts
    journal: Nucleic Acids Research
    volume: 43
    year: 2015
    doi: 10.1093/nar/gku1046