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BioNexus

Warrant-first scientific reliability layer for AI bioinformatics that audits analytical assumptions, calibrates evidence strength, caps unsupported claims, and verifies execution provenance

bionexus-team/bionexus-reliability · v1.0.0-rc.8 · Development & Workflow

BioNexus Teamreview

Install Source Claim this plugin

Trust Score

67

Security

71

Surfaces

21

What is BioNexus?

BioNexus is a published development & workflow plugin for AI coding agents in the codex ecosystem, developed by BioNexus Team and distributed through the HOL AI plugin registry. Warrant-first scientific reliability layer for AI bioinformatics that audits analytical assumptions, calibrates evidence strength, caps unsupported claims, and verifies execution provenance

Canonical slug: bionexus-team/bionexus-reliability
Version: v1.0.0-rc.8 · updated Sep 20, 2026
Open data: entity.json (JSON-LD)

Trust & Reputation

HOL Trust Score

67

Factor Analysis

Per-metric points (0–100 each) combined via a weighted average into the overall score.

Installability

76pts

Maintenance

55pts

MCP Posture

100pts

Plugin Security

71pts

Provenance

70pts

Publisher Quality

75pts

Registry Snapshot

Repository: https://github.com/HERRY423/BioNexus
Homepage: https://github.com/HERRY423/BioNexus
Canonical profile: https://hol.org/registry/plugins/bionexus-team%2Fbionexus-reliability
Publisher verification: No
Marketplace source: Unknown
Scanner: Broker fallback
Safety label: review
Digest verified: Yes

20 bundled skills — copy or download SKILL.mdOpen skills

Trust & reputation

Trust & Reputation

HOL Trust Score

67

Factor Analysis

Per-metric points (0–100 each) combined via a weighted average into the overall score.

Installability

76pts

Maintenance

55pts

MCP Posture

100pts

Plugin Security

71pts

Provenance

70pts

Publisher Quality

75pts

Provenance

Plugin root: .
Source repo: https://github.com/HERRY423/BioNexus
Source commit: 683018420a75…
Publisher verified: No
Owner verified: Not owner verified

Continuous scanner CI not detected

This plugin remains listed. Its overall trust score is reduced by 10% because security checks are not maintained in the source repository's CI.

Optional: maintain the scanner in the source repository's CI to receive the full trust score. Listing does not require that change.

Verified badge not detected

Add the HOL verified badge to the repository README to score +2% trust. Plugin owners can open that pull request from Guard Plugins.

Security Posture

review

Safety label

71

Security score

0

High findings

Provider: registry-broker-fallback
Grade: C · review
Version: Unknown

cisco-skill-scanner: unknown

Findings

mediumpublishabilitypublishability.link.missing.privacyPolicyURL

privacyPolicyURL should be present for marketplace readiness.

mediumpublishabilitypublishability.link.missing.termsOfServiceURL

termsOfServiceURL should be present for marketplace readiness.

lowoperational-securitysupply-chain.lockfile-missing

Repository snapshot does not include a lockfile.

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BioNexus — Frequently asked questions

What is BioNexus?: BioNexus is an AI plugin in the HOL registry. Warrant-first scientific reliability layer for AI bioinformatics that audits analytical assumptions, calibrates evidence strength, caps unsupported claims, and verifies execution provenance
How do I install BioNexus?: Install BioNexus in your harness: Codex — codex plugin marketplace add HERRY423/BioNexus; Claude Code — /plugin marketplace add HERRY423/BioNexus; Any agent — npx skills add HERRY423/BioNexus. Full step-by-step guidance is on the HOL plugin page.
How do I install BioNexus in Codex?: To install BioNexus in Codex, start with codex plugin marketplace add HERRY423/BioNexus. The complete step-by-step install guide for Codex is on the HOL plugin page.
How do I install BioNexus in Claude Code?: To install BioNexus in Claude Code, start with /plugin marketplace add HERRY423/BioNexus. The complete step-by-step install guide for Claude Code is on the HOL plugin page.
Is BioNexus free?: Pricing for BioNexus is published on its HOL plugin page when the maker schedules a launch.
Who publishes BioNexus?: BioNexus is published by BioNexus Team and listed on HOL.
Is BioNexus available now?: BioNexus availability is listed on its HOL plugin page.

Install Guidance

Install in Claude Code

Install through the Claude Code plugin marketplace.

Claude Code plugin docs

1
Add the marketplace
Run this inside a Claude Code session.
claude code
2
Install the plugin
Use the plugin name and the marketplace name shown by the previous command.
claude code
3
Scripted alternative
Non-interactive equivalent for scripts and CI pipelines. Add --scope project to pin the install to one repository.
shell

Plugin Manifest

{
  "name": "bionexus-reliability",
  "version": "1.0.0-rc.8",
  "description": "Scientific Reliability Layer for AI-Assisted Biology. Know what your evidence actually warrants: pre-submission shadow review of multi-donor single-cell differential expression, evidence gap location, and human scientific review support.",
  "author": {
    "name": "BioNexus Team",
    "url": "https://github.com/HERRY423/BioNexus"
  },
  "homepage": "https://github.com/HERRY423/BioNexus",
  "repository": "https://github.com/HERRY423/BioNexus",
  "license": "Apache-2.0",
  "keywords": [
    "bionexus",
    "scientific-reliability",
    "warrant-engine",
    "bioinformatics",
    "single-cell",
    "differential-expression",
    "pseudobulk",
    "reproducibility",
    "mcp"
  ],
  "skills": "./",
  "interface": {
    "displayName": "BioNexus",
    "developerName": "BioNexus Team",
    "shortDescription": "The Scientific Reliability Layer for Agentic Biology",
    "longDescription": "Scientific Reliability Layer for AI-Assisted Biology. Know what your evidence actually warrants: pre-submission shadow review of multi-donor single-cell differential expression, evidence gap location, and human scientific review support.",
    "category": "Science",
    "capabilities": [
      "Interactive",
      "Read",
      "Write"
    ],
    "websiteURL": "https://github.com/HERRY423/BioNexus",
    "defaultPrompt": [
      "Audit evidence returned by another science plugin",
      "Check whether this result warrants the proposed claim",
      "Verify provenance, backend identity, and claim ceiling"
    ]
  },
  "mcpServers": "./.registry/mcp.json",
  "registryIndexVersion": 5
}

Marketplace Source

Repo URL: https://github.com/HERRY423/BioNexus
Marketplace path: Unknown
Source path: .
Install policy: Unspecified

Skills

20 SKILL.md files ship with this plugin. Preview, copy, or download each one, then install them with the Skills CLI.

skills-cli

external-evidence-audit
plugins/bionexus/skills/external-evidence-audit/SKILL.md
Audit completed results from literature, database, analysis, sequence, structure, or slide capabilities, then optionally assemble an explicitly adjudicated multi-source claim assessment. Passive only; never select tools, infer evidence relationships, or make the final scientific decision.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
instrument-data-to-allotrope
plugins/bionexus/skills/instrument-data-to-allotrope/SKILL.md
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV using native allotropy or declarative YAML mapping rules. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
nextflow-development
plugins/bionexus/skills/nextflow-development/SKILL.md
Prepare nf-core samplesheets, cluster nextflow.config, and write launch artifacts. nfcore_launch.py only wraps nf-core/rnaseq and nf-core/scrnaseq with optional nextflow -preview. Other pipelines still use generate_samplesheet.py plus a hand-written nextflow run. Does not reimplement the pipelines.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
provenance-and-audit
plugins/bionexus/skills/provenance-and-audit/SKILL.md
SHA-256 hashes, environment snapshot, and activity-aware Methods text. Use to attach a reproducibility sidecar to an analysis. Do not use for 21 CFR Part 11, GxP, ALCOA+, or CLIA audit claims.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
scientific-problem-selection
plugins/bionexus/skills/scientific-problem-selection/SKILL.md
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
scvi-tools
plugins/bionexus/skills/scvi-tools/SKILL.md
Train official scvi-tools models (scVI/scANVI/totalVI/PeakVI/MultiVI/veloVI) on raw counts after the scRNA gold chain. Use for probabilistic batch integration or those named models. Does not run DestVI/Cell2location. Do not log-normalize before setup_anndata.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
single-cell-de-audit
plugins/bionexus/skills/single-cell-de-audit/SKILL.md
Review completed multi-donor single-cell differential expression before submission. Accept existing DE tables, sample sheets, AnnData, scripts and claims; produce located findings, evidence gaps, repairs and human review. Record pilot observations without claiming validated benefit.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
single-cell-rna-qc
plugins/bionexus/skills/single-cell-rna-qc/SKILL.md
scverse scRNA gold chain on .h5ad/.h5 — inspect, convert, MAD QC, optional scanpy.pp.scrublet, preprocess, Harmony/ComBat, PCA-UMAP-Leiden, Wilcoxon markers, subset, pseudobulk, pydeseq2, stable plots. Use when the user has scRNA-seq counts. Does not assign cell-type labels. rank_genes_groups is not condition DE. Do not call local doublet/ambient helpers SoupX, CellBender, or scDblFinder.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
spatial-transcriptomics
plugins/bionexus/skills/spatial-transcriptomics/SKILL.md
squidpy spatial gold chain on SpatialData .zarr or AnnData .h5ad with obsm['spatial']. Use when the user has Visium/Slide-seq/generic spots or cells with coordinates. Builds a knn spatial graph, Moran SVGs, and spatial_scatter plots. Multi-table SpatialData requires --table. Does not run Cell2location, BayesSpace, SpaGCN, or vendor HD/Xenium pipelines. Numeric clusters only.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
start
plugins/bionexus/skills/start/SKILL.md
Orient a session on this plugin. BioNexus is a Scientific Reliability Layer for AI-Assisted Biology. Route completed single-cell DE to the pre-submission shadow review; check backend readiness before a requested analysis. Do not assign cell-type labels or run analyses from this skill.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
external-evidence-audit
skills/external-evidence-audit/SKILL.md
Audit completed results from literature, database, analysis, sequence, structure, or slide capabilities, then optionally assemble an explicitly adjudicated multi-source claim assessment. Passive only; never select tools, infer evidence relationships, or make the final scientific decision.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
instrument-data-to-allotrope
skills/instrument-data-to-allotrope/SKILL.md
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV using native allotropy or declarative YAML mapping rules. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
nextflow-development
skills/nextflow-development/SKILL.md
Prepare nf-core samplesheets, cluster nextflow.config, and write launch artifacts. nfcore_launch.py only wraps nf-core/rnaseq and nf-core/scrnaseq with optional nextflow -preview. Other pipelines still use generate_samplesheet.py plus a hand-written nextflow run. Does not reimplement the pipelines.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
provenance-and-audit
skills/provenance-and-audit/SKILL.md
SHA-256 hashes, environment snapshot, and activity-aware Methods text. Use to attach a reproducibility sidecar to an analysis. Do not use for 21 CFR Part 11, GxP, ALCOA+, or CLIA audit claims.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
scientific-problem-selection
skills/scientific-problem-selection/SKILL.md
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
scvi-tools
skills/scvi-tools/SKILL.md
Train official scvi-tools models (scVI/scANVI/totalVI/PeakVI/MultiVI/veloVI) on raw counts after the scRNA gold chain. Use for probabilistic batch integration or those named models. Does not run DestVI/Cell2location. Do not log-normalize before setup_anndata.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
single-cell-de-audit
skills/single-cell-de-audit/SKILL.md
Review completed multi-donor single-cell differential expression before submission. Accept existing DE tables, sample sheets, AnnData, scripts and claims; produce located findings, evidence gaps, repairs and human review. Record pilot observations without claiming validated benefit.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
single-cell-rna-qc
skills/single-cell-rna-qc/SKILL.md
scverse scRNA gold chain on .h5ad/.h5 — inspect, convert, MAD QC, optional scanpy.pp.scrublet, preprocess, Harmony/ComBat, PCA-UMAP-Leiden, Wilcoxon markers, subset, pseudobulk, pydeseq2, stable plots. Use when the user has scRNA-seq counts. Does not assign cell-type labels. rank_genes_groups is not condition DE. Do not call local doublet/ambient helpers SoupX, CellBender, or scDblFinder.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
spatial-transcriptomics
skills/spatial-transcriptomics/SKILL.md
squidpy spatial gold chain on SpatialData .zarr or AnnData .h5ad with obsm['spatial']. Use when the user has Visium/Slide-seq/generic spots or cells with coordinates. Builds a knn spatial graph, Moran SVGs, and spatial_scatter plots. Multi-table SpatialData requires --table. Does not run Cell2location, BayesSpace, SpaGCN, or vendor HD/Xenium pipelines. Numeric clusters only.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.
start
skills/start/SKILL.md
Orient a session on this plugin. BioNexus is a Scientific Reliability Layer for AI-Assisted Biology. Route completed single-cell DE to the pre-submission shadow review; check backend readiness before a requested analysis. Do not assign cell-type labels or run analyses from this skill.
Raw SKILL.md
SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

File Inventory

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