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viz.render_metabolic_map

Visualize compiled metabolic constraints on an Escher curated map, with automatic fallback to cytoscape subnetwork when no curated map covers the model.

Instructions

DEFAULT metabolic visualizer: overlay compiled constraints on an Escher curated pathway map (biochemically-correct layout); automatically falls back to the cytoscape subnetwork renderer when no curated map covers the model. Returns {backend, out_path, n_reactions_on_map, map_used, fallback_reason}.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
modelYes
titleNoMetabolic constraint map
preferNoescher
out_pathNo
session_idNo
constraintsYes
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Given no annotations, the description does a good job explaining core behavior: overlay constraints on Escher maps and fallback to cytoscape. It also lists the return fields. It lacks details on error handling or permissions, but these are less critical for a visualization tool.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise (two sentences) and front-loaded with key functionality. Every sentence adds value without redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

While the core logic and return values are described, the description is incomplete due to lack of parameter explanations and usage examples. Given 6 parameters and no output schema, more detail would be beneficial.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0% schema description coverage, the description only mentions 'constraints' indirectly. Parameters like model, title, prefer, out_path, and session_id are not explained, leaving a significant gap.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states it is the default metabolic visualizer that overlays compiled constraints on Escher curated maps, with automatic fallback to cytoscape. This distinguishes it from sibling tools like viz.render_subnetwork.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It positions itself as the default tool and mentions fallback behavior, implicitly guiding when to use it. However, it does not explicitly state when not to use it or name alternatives.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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