workbench

siRNA / shRNA Designer

sirna_design

Read-onlyIdempotent

Design siRNA duplexes against an mRNA target using the established Reynolds (2004) 8-criteria score and the Ui-Tei (2004) rules, plus the siDirect seed-duplex Tm off-target flag (≥21.5 °C, computed on siDirect's own RNA/RNA scale: Freier 1986 nearest-neighbour parameters, helix initiation A = −10.8, CT = 100 µM, 100 mM Na⁺). Returns ranked candidates with sense/guide oligos (with UU 3' overhangs) and, per candidate, a ready shRNA cassette (sense–loop–antisense–Pol III terminator). Heuristic sequence rules only — no RNA-folding accessibility model and no transcriptome-wide off-target search. PREDICTED, NOT MEASURED. These are rule counts, not a regression, and no skill statistic is claimed for the ranking. Target-site accessibility is not modelled (no folding) and no transcriptome-wide off-target search is performed, so a top-ranked candidate is a starting point for a knockdown panel, not a predicted knockdown level. Valid for: mRNA targets. The seed Tm is computed on siDirect's own RNA/RNA scale (Freier 1986 parameters, helix initiation A = -10.8, CT = 100 µM, 100 mM Na+) and is not comparable with the DNA/DNA Tm reported elsewhere in the toolkit.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`target`	Yes	Nucleotide sequence (raw or FASTA; IUPAC accepted).
`shRnaLoop`	No	Loop sequence used when assembling the shRNA cassette.	TTCAAGAGA
`minReynolds`	No	Minimum Reynolds score (0–8) to keep; falls back to best-ranked if none qualify.

TDQS

A4.4/5.0

Behavior5/5

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

Annotations (readOnlyHint, idempotentHint) indicate safe, deterministic operation. The description adds substantial behavioral context: disclaimers ('PREDICTED, NOT MEASURED'), absence of RNA-folding accessibility and off-target search, details on scoring and seed Tm computation on a custom scale, and the note that no skill statistic is claimed. These disclosures go well beyond annotations and are critical for correct agent decision-making.

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

Conciseness4/5

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

The description is moderately long but every sentence adds value: purpose, method, output, limitations, and seed Tm details are all covered. It is well-structured, front-loading the core action and then providing necessary caveats. Minor wordiness (e.g., repeated seed Tm note) prevents a perfect score, but it remains efficient for the complexity.

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

Completeness5/5

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

Given the tool has 3 parameters, no output schema, and 100% schema coverage, the description covers all essential aspects: what it designs, how it scores, what it returns (candidates with oligos and shRNA cassette), validity range, and key limitations. It is self-contained enough for an agent to understand when and how to invoke the tool without additional context.

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 coverage is 100% with adequate descriptions for all three parameters (target, shRnaLoop, minReynolds). The description adds conceptual context (e.g., Reynolds scoring) but does not elaborate on parameter syntax or behavior beyond the schema. Baseline of 3 is appropriate; the description does not significantly enhance parameter understanding.

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 'Design siRNA duplexes against an mRNA target' with specific scoring methods (Reynolds, Ui-Tei, siDirect). It distinguishes from sibling tools (e.g., aso_design, crispr_grna_design) by explicitly focusing on siRNA/shRNA design and detailing what it does not do (no folding, no off-target search).

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 specifies valid targets ('mRNA targets') and clarifies limitations (heuristic rules only, no folding, no off-target search), implying when not to rely on the tool. However, it does not explicitly name alternative tools for complementary analyses (e.g., folding models or transcriptome-wide checks) nor provide a when-not-to-use directive. Clear context but lacks explicit exclusions.

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.

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