Acknowledgements & licences
Acknowledgements & licences
Vanguard Biotech Systems builds on open-source software, fonts, tools and public reference databases. Only verified attributions are listed here. A complete, versioned and reproducible Software Bill of Materials (with each component's exact licence and integrity hash) is published separately.
Typeface
JetBrains Mono (latin subset) — © JetBrains, licensed under the SIL Open Font License 1.1. It is self-hosted on VBS's own infrastructure at /fonts/jetbrains-mono-latin.woff2, so the browser makes no third-party font request.
JavaScript libraries
The website is built with open-source JavaScript libraries — including React, TanStack Start & Router, Radix UI, Tailwind CSS, Zod, Motion and Recharts — under permissive licences (MIT / ISC / Apache-2.0). The complete list, with each library's exact version, licence and lockfile integrity hash, is in the machine-readable SBOM.
Bioinformatics tools
The NextGenAMR pipeline integrates the following third-party tools (integrated, not modified). Attribution and licence are shown for each.
| Tool | Project | Licence | Source |
|---|---|---|---|
| Snakemake | Snakemake community | MIT | snakemake.github.io |
| fastp | OpenGene | MIT | github.com/OpenGene/fastp |
| Kraken2 | Derrick Wood / Johns Hopkins | MIT | github.com/DerrickWood/kraken2 |
| Bracken | Jennifer Lu et al. | GPL-3.0 | github.com/jenniferlu717/Bracken |
| minimap2 | Heng Li | MIT | github.com/lh3/minimap2 |
| SAMtools | SAMtools / htslib | MIT/Expat | www.htslib.org |
| BWA-MEM2 | bwa-mem2 | MIT | github.com/bwa-mem2/bwa-mem2 |
| Qualimap | Qualimap (CIPF/Conesa lab) | GPL-2.0 | qualimap.conesalab.org |
| SPAdes | SPAdes (ABLab) | GPL-2.0 | github.com/ablab/spades |
| CheckM2 | CheckM2 (Chklovski et al.) | GPL-3.0 | github.com/chklovski/CheckM2 |
| Pyrodigal | Martin Larralde (Prodigal) | GPL-3.0 | github.com/althonos/pyrodigal |
| Sma3s | Sma3s (Universidad Pablo de Olavide) | GPL-3.0 | www.bioinfocabd.upo.es/sma3s |
| DIAMOND | Benjamin Buchfink | GPL-3.0 | github.com/bbuchfink/diamond |
| AMRFinderPlus | NCBI | NCBI — public domain | github.com/ncbi/amr |
Reference databases
The pipeline uses public reference databases. These are data resources governed by their own terms and conditions — not software licences. Terms are stated by each source; consult the source for the authoritative, current terms.
| Database | Project | Terms | Source |
|---|---|---|---|
| CARD (Comprehensive Antibiotic Resistance Database) | McMaster University | See source (pending verification) | card.mcmaster.ca |
| ResFinder database | Center for Genomic Epidemiology (DTU) | See source (pending verification) | bitbucket.org/genomicepidemiology/resfinder_db |
| PointFinder database | Center for Genomic Epidemiology (DTU) | See source (pending verification) | bitbucket.org/genomicepidemiology/pointfinder_db |
| AMRFinderPlus database | NCBI | NCBI data — see source (pending verification) | www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder |
| UniProt | UniProt Consortium (EMBL-EBI, SIB, PIR) | CC BY 4.0 per source — see source (pending verification) | www.uniprot.org |
Software Bill of Materials (SBOM)
A reproducible CycloneDX SBOM enumerating every production dependency, tool and database is published at /docs/security/sbom.cdx.json in the source repository, with a human-readable summary at /docs/security/sbom.md.