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by com.seqbench

Virtual gel

virtual_gel
Read-onlyIdempotent

Predict restriction-digest fragment sizes and their gel migration positions against a chosen DNA ladder.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
ladderNoDNA ladder to plot alongside the sample lane.1 kb
enzymesNoEnzyme names to digest with, from the curated common-enzyme set (see restriction_sites for the full list). An unrecognised name is rejected rather than skipped, so an empty band pattern always means "no sites".
circularNoTreat the sequence as circular (plasmid).
sequenceYesNucleotide sequence (raw or FASTA; IUPAC accepted).

TDQS

A4/5.0
Behavior3/5

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

The annotations already declare readOnlyHint and idempotentHint, so the description doesn't need to repeat safety info. The description adds the key behavioral aspect (predicts fragment sizes and positions) but does not disclose output format or edge-case behavior. However, no contradictions 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.

Conciseness5/5

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

The description is a single, focused sentence that gets straight to the point without extraneous details.

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

Completeness4/5

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

The tool has no output schema, but the description conveys the core purpose and the parameter schema covers inputs thoroughly. It lacks explicit return-value details, but the purpose statement sufficiently covers what the tool produces for an agent to understand high-level behavior.

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

Parameters3/5

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

Schema description coverage is 100%, with detailed descriptions for all four parameters including enum values and error semantics for enzymes. The description itself adds no parameter-level detail, so the baseline of 3 applies.

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 the tool's function with a specific verb ('Predict') and resource ('restriction-digest fragment sizes and their gel migration positions'), and distinguishes it from sibling tools like 'double_digest' and 'restriction_sites' by its focus on gel migration against a chosen ladder.

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?

The description implies the use case (simulating a gel with a chosen ladder) but does not explicitly state when to prefer this over alternatives like 'restriction_sites' or 'double_digest'. There are no exclusions or alternative references, but the context is clear enough for an agent to infer when to use it.

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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TDQS

A3.6/5.0
Disambiguation4/5

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.

Naming Consistency3/5

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'.

Tool Count2/5

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.

Completeness4/5

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.

Resources