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immunology-assays

Computational analysis of immunology experimental data. ATAC-seq differential accessibility, immune cell tracking from microscopy, ELISA data processing with 4-parameter logistic fitting, immunohistochemistry quantification, antibody titer analysis, and cell cycle phase duration estimation. For flow cytometry use flow-cytometry-analysis; for scRNA-seq use scanpy.

54

Quality

68%

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SecuritybySnyk

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tessl review fix ./backend/cli/skills/biology/immunology-assays/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

53%Weight 40%Scale 1-5

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

The body delivers highly actionable, executable domain code with sensible best practices and troubleshooting, but it is structurally mis-organized: it inlines the entire implementation while five equivalent script files sit unreferenced in the bundle, and it repeats the ELISA example three times. Workflow guidance reads as usage examples rather than validated, checkpointed sequences.

Suggestions

Replace the inlined implementations with an overview plus pointers to the existing bundle scripts (e.g. "Run `python scripts/process_elisa.py --data plate.csv --output-dir results/`"), keeping only one compact example per capability in SKILL.md.

Deduplicate the ELISA material: the four_pl function appears in Quick Start and Section 2, and Workflow 1 repeats Section 2's example verbatim — keep one worked example only.

Add explicit validation checkpoints inside the workflows, e.g. "after fitting, verify R² > 0.99 before reporting concentrations; re-run out-of-range samples at appropriate dilutions" as a step in the ELISA workflow rather than only in Best Practices.

DimensionReasoningScore

Conciseness

The code itself is dense and domain-specific with no padding or explanation of concepts Claude already knows, but the same ELISA 4PL material appears three times — the Quick Start four_pl snippet, Section 2's full worked example (standards/unknowns dicts), and Workflow 1 which repeats the identical process_elisa_plate invocation. Mostly efficient but noticeably could be tightened, matching anchor 3; not 2 since no section is fluffy or over-explained.

3 / 5

Actionability

All seven sections provide complete, realistic, executable functions with worked examples (e.g. the full standards/unknowns ELISA run, the dilution-series titer example) plus install commands. Minor gaps keep it below anchor 5: the differential_accessibility block uses np without importing it in that block, and sections 3, 6, and 7 lack example invocations.

4 / 5

Workflow Clarity

The "Typical Workflows" are usage snippets rather than sequenced multi-step processes, and validation checkpoints are implicit — QC guidance like "verify R² > 0.99", "require minimum track length (>10 frames)", and "flag analytes with CV >15%" lives in Best Practices instead of inline at the workflow steps. The MACS2 wrapper does check returncode and raise on failure, but overall this matches anchor 3 (sequence present, checkpoints missing or implicit) rather than 4.

3 / 5

Progressive Disclosure

The bundle contains five complete scripts (scripts/process_elisa.py, atac_peaks.py, quantify_ihc.py, track_immune_cells.py, antibody_titer.py) that duplicate the inlined implementations, yet the body never references or mentions any of them. Per the guideline to score against the actual bundle structure, ~400 lines of code that clearly belong in those separate files are inlined, making SKILL.md the full implementation rather than an overview pointing to detailed materials — matching anchor 2; not 3 because the failure is total (zero pointers to any bundle file) even though section headers are well organized.

2 / 5

Total

12

/

20

Passed

Description

71%Weight 40%Scale 1-5

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

A strong, specific description that names all major capabilities concretely and includes helpful cross-skill routing. Its main weaknesses are the absence of a positive 'Use when...' trigger clause and a few missing natural trigger terms (cytokine/Luminex, H-score) for capabilities the body actually covers.

Suggestions

Add an explicit 'Use when...' clause with concrete triggers, e.g. "Use when processing ELISA plate data, quantifying IHC staining (H-score), analyzing ATAC-seq peaks, or determining antibody titers from serial dilutions."

Include trigger terms for capabilities present in the body but missing from the description, such as multiplex cytokine assays (Luminex/MSD) and H-score.

Consider mentioning the microscopy-image trigger more specifically (e.g. 'time-lapse microscopy') to reduce overlap with a general bioimage-analysis skill.

DimensionReasoningScore

Specificity

The description lists multiple specific concrete actions covering the full capability set: "ATAC-seq differential accessibility", "ELISA data processing with 4-parameter logistic fitting", "immunohistochemistry quantification", "antibody titer analysis", and "cell cycle phase duration estimation". This matches the anchor for comprehensive coverage of specific actions; it is not 4 because there are no meaningful gaps relative to the body's seven capabilities.

5 / 5

Completeness

The "what" is clear and comprehensive, but there is no "Use when..." clause or equivalent positive trigger guidance; the only conditional sentences ("For flow cytometry use flow-cytometry-analysis; for scRNA-seq use scanpy") route users away to other skills rather than stating when to use this one. Per the judging guideline, a missing 'Use when' clause caps completeness at 3.

3 / 5

Trigger Term Quality

Good natural keyword coverage: "ATAC-seq", "ELISA", "IHC" (as immunohistochemistry), "antibody titer", "cell cycle", "immune cell tracking from microscopy". A few natural terms are missing — "cytokine"/"Luminex" (a body capability absent from the description), "H-score", and no file-format terms — so it falls short of the comprehensive-with-synonyms anchor 5 but clearly exceeds anchor 3's 'some relevant keywords'.

4 / 5

Distinctiveness Conflict Risk

It carves a clear immunology-assay niche and explicitly routes flow cytometry and scRNA-seq to other skills, minimizing those conflicts. Minor overlap risk remains with general bioimage/microscopy analysis for the "immune cell tracking from microscopy" trigger, which the body itself acknowledges via the bioimage-analysis related-skill pointer — mostly distinct with minor overlap, matching anchor 4.

4 / 5

Total

16

/

20

Passed

Validation

81%

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

Validation — 13 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

skill_md_line_count

SKILL.md is long (592 lines); consider splitting into references/ and linking

Warning

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

13

/

16

Passed

Repository

synthetic-sciences/openscience

Path

backend/cli/skills/biology/immunology-assays/SKILL.md

Reviewed

Table of Contents

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