M

Mycelium

arjun-raj-laboratory/mycelium · v0.9.1+codex.20261014183651 · Development & Workflow

by Arjun Raj LaboratoryOwner verifiedreview

Gives Claude Code and Codex analytical repositories durable memory for decisions, findings, provenance, reusable conventions, and analysis workflows

InstallSourceFollow0
Trust Score67Security71Surfaces12

Is Mycelium a fit?

From the plugin's manifest and HOL's scan. Anything the plugin does not declare is shown as not declared.

Works with

  • Codex
  • Claude Code
  • 12 skills

Before you install

Sign-in
Not declared
Declared access
Interactive, Read, Write
License
MIT

Check before relying on it

What is Mycelium?

Mycelium is a published development & workflow plugin for AI coding agents in the codex ecosystem, developed by Arjun Raj Laboratory and distributed through the HOL AI plugin registry. Gives Claude Code and Codex analytical repositories durable memory for decisions, findings, provenance, reusable conventions, and analysis workflows

Canonical slug
arjun-raj-laboratory/mycelium
Version
v0.9.1+codex.20261014183651 · updated Oct 15, 2026

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

Project link
Mycelium
Publisher verification
No
Marketplace source
Unknown
Scanner
Broker fallback
Security result
Needs review
Digest verified
Yes
12 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/arjunrajlaboratory/mycelium
Source commit
8f8b167b0259…
Publisher verified
No
Owner verified
@arjunrajlab

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.

README badge not detected

Plugin owners can add the HOL badge to the repository README from Guard Plugins. Distribution, not security evidence. It adds a 2% engagement adjustment to the overall trust score and never changes the security result.

Security Posture

See how the Trust Score is computed
Needs review
Security result
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.

infoskill-securityskill-scan.unavailable

Cisco skill scanner timed out after 60000 ms

infoskill-securityskill-scan.unavailable

Cisco skill scanner exited with code 1: Error loading skill: No SKILL.md and no .md files found in /tmp/hol-skill-safety-0tNyTH (lenient mode requires at least one markdown file)

infoskill-securityskill-scan.unavailable

Cisco skill scanner exited with code 1: Error loading skill: No SKILL.md and no .md files found in /tmp/hol-skill-safety-O5jjm3 (lenient mode requires at least one markdown file)

infoskill-securityskill-scan.unavailable

Cisco skill scanner timed out after 60000 ms

infoskill-securityskill-scan.unavailable

Cisco skill scanner timed out after 60000 ms

infoskill-securityskill-scan.unavailable

Cisco skill scanner exited with code 1: Error loading skill: No SKILL.md and no .md files found in /tmp/hol-skill-safety-FUd0rc (lenient mode requires at least one markdown file)

infoskill-securityskill-scan.unavailable

Cisco skill scanner exited with code 1: Error loading skill: No SKILL.md and no .md files found in /tmp/hol-skill-safety-motxek (lenient mode requires at least one markdown file)

infoskill-securityskill-scan.unavailable

Cisco skill scanner exited with code 1: Error loading skill: No SKILL.md and no .md files found in /tmp/hol-skill-safety-NXOvP8 (lenient mode requires at least one markdown file)

infoskill-securityskill-scan.unavailable

Cisco skill scanner exited with code 1: Error loading skill: No SKILL.md and no .md files found in /tmp/hol-skill-safety-nz0JdQ (lenient mode requires at least one markdown file)

infoskill-securityskill-scan.unavailable

Cisco skill scanner exited with code 1: Error loading skill: No SKILL.md and no .md files found in /tmp/hol-skill-safety-hwsKca (lenient mode requires at least one markdown file)

infoskill-securityskill-scan.unavailable

Cisco skill scanner timed out after 60000 ms

infoskill-securityskill-scan.unavailable

Cisco skill scanner exited with code 1: Error loading skill: No SKILL.md and no .md files found in /tmp/hol-skill-safety-6g4HMD (lenient mode requires at least one markdown file)

Mycelium — Frequently asked questions

What is Mycelium?
Mycelium is an AI plugin in the HOL registry. Gives Claude Code and Codex analytical repositories durable memory for decisions, findings, provenance, reusable conventions, and analysis workflows
How do I install Mycelium?
Install Mycelium in your harness: Codex — codex plugin marketplace add arjunrajlaboratory/mycelium; Claude Code — /plugin marketplace add arjunrajlaboratory/mycelium; Any agent — npx [email protected] add arjunrajlaboratory/mycelium. Full step-by-step guidance is on the HOL plugin page.
How do I install Mycelium in Codex?
To install Mycelium in Codex, start with codex plugin marketplace add arjunrajlaboratory/mycelium. The complete step-by-step install guide for Codex is on the HOL plugin page.
How do I install Mycelium in Claude Code?
To install Mycelium in Claude Code, start with /plugin marketplace add arjunrajlaboratory/mycelium. The complete step-by-step install guide for Claude Code is on the HOL plugin page.
Is Mycelium free?
Pricing for Mycelium is published on its HOL plugin page when the maker schedules a launch.
How is the Trust Score for Mycelium computed?
Mycelium has a HOL Trust Score of 67 out of 100. The score is a weighted sum of six components from a static scan of the source, capped for high-severity findings and adjusted by two disclosed policies. Memberships and payments are not inputs, and a scan is not a safety guarantee. Full breakdown: https://hol.org/registry/plugins/arjun-raj-laboratory%2Fmycelium/trust
Who publishes Mycelium?
Mycelium is published by Arjun Raj Laboratory and listed on HOL.
Is Mycelium available now?
Mycelium 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

Optional: install HOL Guard for Claude Code first, so it can check this plugin's tools on your machine before Claude Code uses them.

  1. 1

    Add the marketplace

    Run this inside a Claude Code session. It registers the marketplace manifest shipped at the repository root. If the repository ships none, add the generated entry from the Advanced section below first.

    claude code
  2. 2

    Find the marketplace and plugin names

    The install id is <plugin-entry>@<marketplace-name>, and the marketplace name is declared inside the manifest — it can differ from the repository name. List registered marketplaces to read both names.

    shell
  3. 3

    Install the plugin

    Substitute the plugin entry name and the marketplace name shown by the previous step.

    claude code

Did setup work in Claude Code?

No setup reports for Claude Code yet. Self-reported by signed-in visitors. Copying a command is not counted, and most installs are never reported.

Attested installs: Fewer than 10 attested installs of this plugin in week 2026-W43, so no number is shown. Counted from opt-in HOL Guard install reports, once per machine and runtime, and never mixed with the answers above. How install reports work.

Loading reviews

Plugin Manifest

{
  "name": "mycelium",
  "version": "0.9.1+codex.20261014183651",
  "description": "Self-documenting, self-improving framework for analytical repositories",
  "author": {
    "name": "Arjun Raj Laboratory",
    "url": "https://github.com/arjunrajlaboratory"
  },
  "homepage": "https://github.com/arjunrajlaboratory/mycelium",
  "repository": "https://github.com/arjunrajlaboratory/mycelium",
  "license": "MIT",
  "keywords": [
    "research",
    "analysis",
    "provenance",
    "knowledge-management"
  ],
  "skills": "./",
  "interface": {
    "displayName": "Mycelium",
    "developerName": "Arjun Raj Laboratory",
    "shortDescription": "Living repositories for analytical work",
    "longDescription": "Capture analytical decisions, learnings, findings, provenance, and reusable conventions as projects evolve.",
    "category": "Productivity",
    "capabilities": [
      "Interactive",
      "Read",
      "Write"
    ],
    "websiteURL": "https://github.com/arjunrajlaboratory/mycelium",
    "defaultPrompt": [
      "Set up Mycelium in this repository.",
      "Analyze this dataset using the project conventions.",
      "Review this analysis for scientific correctness."
    ]
  },
  "holManifestOrigin": "repository",
  "registryIndexVersion": 5
}

Marketplace Source

Repo URL
https://github.com/arjunrajlaboratory/mycelium
Marketplace path
Unknown
Source path
.
Install policy
Unspecified

Skills

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

Share
skills-cli

  • skill

    SKILL.md

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • analyze

    skills/analyze/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • codex-review

    skills/codex-review/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • core

    skills/core/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • develop

    skills/develop/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • harden

    skills/harden/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • ideas

    skills/ideas/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • ingest

    skills/ingest/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • lifecycle-audit

    skills/lifecycle-audit/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • report

    skills/report/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • review

    skills/review/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

  • transfer

    skills/transfer/SKILL.md

    >

    Raw SKILL.md

    SKILL.md content is not in this snapshot. Open the raw file to copy it from the source repository.

File Inventory

.claude-plugin/marketplace.json

file

471 bytes

87b510665665fc38…

.claude-plugin/plugin.json

file

269 bytes

4a760304ba1aa517…

.codex-plugin/plugin.json

plugin-manifest

1,075 bytes

24236dcb347546ce…

.github/ISSUE_TEMPLATE/convention-gap.md

file

946 bytes

97e1a42af63b5254…

.github/ISSUE_TEMPLATE/new-domain-request.md

file

1,090 bytes

084bdb36a8f28a0c…

.github/ISSUE_TEMPLATE/skill-improvement.md

file

843 bytes

7b2d339f9228a929…

.github/PULL_REQUEST_TEMPLATE.md

file

1,290 bytes

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.github/workflows/validate-skill.yml

file

7,783 bytes

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analysis/skill-pack-assessment/SKILL_PACK_ASSESSMENT.md

file

34,547 bytes

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CHANGELOG.md

file

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CONTRIBUTING.md

file

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docs/cross-host-review-checklist.md

file

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docs/plans/2026-06-14-knowledge-map-design.md

file

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docs/plans/2026-08-02-multi-session-concurrency-design.md

file

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docs/release-process.md

file

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docs/superpowers/plans/2026-04-25-learnings-access-path-overhaul.md

file

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docs/superpowers/specs/2026-06-18-codex-review-skill-design.md

file

5,074 bytes

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hooks/hooks.json

file

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hooks/mycelium-codex-dispatch.sh

file

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mycelium-setup-prompt.md

file

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network/conventions/bioinformatics/analysis-conventions.md

file

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network/conventions/bioinformatics/CONVENTION_PACK.yaml

file

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network/conventions/bioinformatics/qc-checklist.md

file

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network/conventions/bioinformatics/statistical-conventions.md

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network/conventions/bioinformatics/templates/rnaseq-analysis.md

file

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network/conventions/idea-generator/analysis-conventions.md

file

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network/conventions/idea-generator/CONVENTION_PACK.yaml

file

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network/conventions/idea-generator/execution-protocol.md

file

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network/conventions/idea-generator/idea-template.md

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network/conventions/idea-generator/persona-catalog.md

file

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network/conventions/image-analysis/analysis-conventions.md

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network/conventions/image-analysis/CONVENTION_PACK.yaml

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network/conventions/image-analysis/qc-checklist.md

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network/conventions/image-analysis/segmentation-standards.md

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network/conventions/image-analysis/templates/segmentation-benchmark.md

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network/conventions/report-generator/analysis-conventions.md

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network/conventions/report-generator/assets/html-example/build_example.py

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network/conventions/report-generator/assets/html-example/outputs/figures/dose_response.svg

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network/conventions/report-generator/assets/html-example/outputs/growth_counts.json

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network/conventions/report-generator/assets/html-example/reports/.manifest.json

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network/conventions/report-generator/assets/html-example/reports/example-report.html

file

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network/conventions/report-generator/assets/report-template.html

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network/conventions/report-generator/CONVENTION_PACK.yaml

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network/conventions/report-generator/html-conventions.md

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network/conventions/report-generator/qc-checklist.md

file

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network/conventions/report-generator/references/manifest-example.json

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network/conventions/report-generator/references/phase-prompts.md

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network/conventions/report-generator/references/section-guide.md

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network/conventions/robust-analysis/adversarial-probing.md

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network/conventions/robust-analysis/analysis-conventions.md

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network/conventions/robust-analysis/CONVENTION_PACK.yaml

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network/conventions/robust-analysis/failure-mode-analysis.md

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network/conventions/robust-analysis/null-hypothesis-protocol.md

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network/conventions/robust-analysis/qc-checklist.md

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network/conventions/robust-analysis/sensitivity-analysis.md

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network/conventions/robust-analysis/spot-check-protocol.md

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network/conventions/robust-analysis/strict-execution-rules.md

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network/conventions/robust-analysis/templates/sensitivity-report.md

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network/conventions/robust-analysis/validation-checks.md

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network/conventions/skill-bridge/analysis-conventions.md

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network/conventions/skill-bridge/CONVENTION_PACK.yaml

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network/conventions/skill-bridge/persona-routing.md

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network/conventions/skill-bridge/qc-checklist.md

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network/conventions/skill-bridge/references/single-cell-workflow.md

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network/conventions/skill-bridge/skill-routing.md

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network/conventions/skill-bridge/skill-sources.yaml

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network/conventions/skill-bridge/templates/persona-review-log.md

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network/conventions/skill-bridge/templates/skill-invocation-log.md

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network/conventions/skill-bridge/templates/validation-report.md

file

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network/README.md

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README.md

file

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SECURITY.md

file

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SKILL.md

skill

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skillpacks/README.md

file

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skills/analyze/agents/openai.yaml

skill

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skills/analyze/SKILL.md

skill

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skills/codex-review/agents/openai.yaml

skill

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skills/codex-review/SKILL.md

skill

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skills/core/agents/openai.yaml

skill

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skills/core/hooks/mycelium-activity-tracker.sh

skill

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skills/core/hooks/mycelium-data-lineage-stop.sh

skill

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skills/core/hooks/mycelium-data-tracker.sh

skill

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skills/core/hooks/mycelium-health.sh

skill

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skills/core/hooks/mycelium-hook-lib.sh

skill

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skills/core/hooks/mycelium-post-action.sh

skill

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skills/core/hooks/mycelium-read-tracker.sh

skill

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skills/core/hooks/mycelium-stop-check.sh

skill

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skills/core/hooks/test_hooks_stress.sh

skill

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skills/core/hooks/test_stop_hook.sh

skill

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skills/core/references/analysis-conventions.md

skill

4,787 bytes

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skills/core/references/data-contract-check.md

skill

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skills/core/references/data-ingest-conventions.md

skill

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skills/core/references/data-lineage.md

skill

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skills/core/references/decision-status.md

skill

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skills/core/references/environment-setup.md

skill

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skills/core/references/folder-structure.md

skill

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skills/core/references/marketplace-guide.md

skill

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skills/core/references/report-values-guide.md

skill

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skills/core/references/review/bioinformatics.md

skill

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skills/core/references/review/code-quality.md

skill

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Browse all 241 files

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Alternatives in Development & Workflow

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History, reviews, and alternatives

Launch history

No public launch record yet.

User reviews

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The first substantive review can be added on this page.