double_digestRecommend a single NEB buffer (and flag caveats) for digesting with two enzymes in one tube.
| Name | Required | Description | Default |
|---|---|---|---|
| enzymeA | Yes | First enzyme name (e.g. EcoRI). | |
| enzymeB | Yes | Second enzyme name (e.g. BamHI). |
Changes observed during successful MCP inspections. Dates show when Glama detected each change.
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint and idempotentHint as true, indicating safe, idempotent operation. The description adds behavioral context by mentioning 'flag caveats', which warns about potential issues (e.g., incompatibility). No contradiction with annotations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence that captures the full purpose, including both the primary action and a note about caveats. Every word earns its place; no unnecessary information.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's simplicity (no output schema, two string parameters), the description fully conveys what the tool does and what it returns (a recommendation with caveats). No missing information for an agent to invoke it correctly.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Input schema coverage is 100% with descriptions for both parameters ('First enzyme name' and 'Second enzyme name'). The description does not add additional meaning beyond the schema, so baseline of 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description uses a specific verb ('Recommend') and resource ('a single NEB buffer') with clear context ('digesting with two enzymes in one tube'). It uniquely identifies the tool among siblings like 'restriction_sites' which deals with site mapping, not buffer selection.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description clearly implies when to use: when performing a double digest with two enzymes needing a buffer recommendation. No explicit when-not or alternatives are provided, but the narrow scope makes it distinct from siblings, and the context is clear enough for an agent to infer usage.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Add one secure layer between your agents and this server.
Most tools have highly specific purposes (e.g., crispr_grna_design vs base_editing_design vs prime_editing_design). However, there is some overlap in sequence analysis tools (characterize_sequence, sequence_report) and plasmid annotation tools (plasmid_annotate vs plasmid_deep_annotate) which could cause confusion.
The naming pattern is largely consistent with snake_case verb_noun or noun_descriptor (e.g., primer_design, plasmid_annotate, fastq_trim). However, there are exceptions like 'batch', 'workflow', 'gc_content', and 'cloning_diagnose' which don't follow the verb_noun pattern consistently. Also, some names are phrases like 'golden_gate_from_parts'.
With 101 tools, this server is extremely large and likely overwhelming for agents. Even for a comprehensive bioinformatics toolkit, this exceeds a manageable scope, risking agent confusion and inefficient tool selection. A more modular approach would be advisable.
The tool surface covers a wide range of bioinformatics workflows including sequence analysis, primer design, cloning, CRISPR, NGS, expression analysis, and data export. There are minor gaps such as lack of a dedicated protein structure prediction tool and limited off-target genome coverage, but overall the set is impressively complete for its domain.