mfa-pipeline-orchestrator

Orchestrate the full metabolic flux analysis pipeline from model loading to phenotype prediction and publication figures. Triggers when the user provides an organism name, BIGG model ID, or custom reaction list and wants end-to-end metabolic modelling run automatically.

Quality

100%

Does it follow best practices?

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Securityby

Passed

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Quality

Content

100%Weight 40%Scale 1-3

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is a tight, fully-actionable orchestration spec: a clear sequenced workflow with per-step I/O contracts, validation via progress-file status checkpoints, and a retry budget. It assumes Claude's competence and avoids padding or concept re-explanation.

Dimension	Reasoning	Score
Conciseness	The body is lean — it never re-explains concepts Claude knows (no "what is FBA" preamble) and every section (overview diagram, step I/O, progress-file templates, conventions) earns its place, matching the lean/efficient anchor.	3 / 3
Actionability	Each step specifies concrete inputs to "Provide" and outputs to "Read" with exact progress-file paths and field names, and the progress-file templates are copy-ready markdown specs rather than pseudocode or vague directions.	3 / 3
Workflow Clarity	A clear Step 0→4 sequence with explicit "Wait for progress/stepN..." checkpoints and PASS/FAIL status fields, plus a retry budget and the rule to check progress before re-invoking, gives explicit validation checkpoints for each stage.	3 / 3
Progressive Disclosure	No bundle files exist and none are needed; the skill is a single well-organized file with clearly labeled sections (Overview, Workflow, Progress File Specification, Key Conventions) and easy navigation, meeting the well-organized-structure bar.	3 / 3
	Total	12 / 12 Passed

Description

100%Weight 40%Scale 1-3

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is concise, specific, and clearly distinguishes itself in a narrow domain, with an explicit trigger clause covering both what and when. It is third-person and free of vague fluff or over-claims.

Dimension	Reasoning	Score
Specificity	"Orchestrate the full metabolic flux analysis pipeline from model loading to phenotype prediction and publication figures" names the domain and a concrete sequenced span of actions (model loading, phenotype prediction, publication figures), matching the multiple-specific-actions anchor; it is more than the partial-action level 2.	3 / 3
Completeness	It answers what (orchestrate the end-to-end pipeline) and when via an explicit "Triggers when the user provides an organism name, BIGG model ID, or custom reaction list..." clause, satisfying both halves of the level-3 anchor.	3 / 3
Trigger Term Quality	Natural trigger terms a user would say are present — "organism name, BIGG model ID, or custom reaction list" plus metadata keywords (MFA, FBA, COBRApy, BIGG, knockout, yield), giving good coverage of common variations rather than jargon-only.	3 / 3
Distinctiveness Conflict Risk	The niche is sharply defined (metabolic flux analysis, BIGG/COBRApy) with distinct triggers, making overlap with generic skills unlikely and matching the clear-niche anchor.	3 / 3
	Total	12 / 12 Passed

Validation

93%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_version	'metadata.version' is missing	Warning

	Total	15 / 16 Passed

Repository: aiming-lab/AutoResearchClaw
Path: external/agents/Biology-Agent/skills/mfa-pipeline-orchestrator/SKILL.md
Commit: e2e23c9

Reviewed: 6 days ago

Table of Contents

Discovery Implementation Validation

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