Data Analysis
scikit-bio
A Python bioinformatics toolkit for sequence, phylogeny, and microbiome/community-ecology analysis; use it when you need to compute diversity/ordination/statistics from biological data and standard formats (FASTA/FASTQ/Newick/BIOM).
86100Total Score
Core Capability
85 / 100
Functional Suitability
11 / 12
Reliability
9 / 12
Performance & Context
7 / 8
Agent Usability
14 / 16
Human Usability
8 / 8
Security
11 / 12
Maintainability
9 / 12
Agent-Specific
16 / 20
Medical Task
20 / 20 Passed
91You need to parse, validate, and manipulate biological sequences (DNA/RNA/protein) and their metadata
4/4
87You are running microbiome/community-ecology workflows (alpha/beta diversity, UniFrac, ordination, PERMANOVA)
4/4
85Sequence objects: DNA, RNA, Protein, and generic Sequence with validation, slicing, motif search, reverse complement, transcription/translation, and metadata handling
4/4
85Alignment utilities: pairwise local alignment (SSW-based) and multiple sequence alignment containers (TabularMSA) with consensus support
4/4
85End-to-end case for Sequence objects: DNA, RNA, Protein, and generic Sequence with validation, slicing, motif search, reverse complement, transcription/translation, and metadata handling
4/4
Veto GatesRequired pass for any deployment consideration
Skill Veto✓ All 4 gates passed
✓
Operational Stability
System remains stable across varied inputs and edge cases
PASS✓
Structural Consistency
Output structure conforms to expected skill contract format
PASS✓
Result Determinism
Equivalent inputs produce semantically equivalent outputs
PASS✓
System Security
No prompt injection, data leakage, or unsafe tool use detected
PASSResearch Veto✅ PASS — Applicable
| Dimension | Result | Detail |
|---|---|---|
| Scientific Integrity | PASS | No scientific-integrity problem was surfaced because the package did not claim more than the available records, article text, or script evidence supported. |
| Practice Boundaries | PASS | The archived review kept this package within A Python bioinformatics toolkit for sequence, phylogeny, and microbiome/community-ecology..., not freeform inference detached from source data. |
| Methodological Ground | PASS | Methodological grounding was preserved through the documented inputs, transformations, and expected artifacts. |
| Code Usability | PASS | The legacy audit did not record a code-usability failure in the packaged analysis path. |
Core Capability85 / 100 — 8 Categories
Functional Suitability
The archived deduction in functional suitability traces back to: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
11 / 12
92%
Reliability
The archived deduction in reliability traces back to: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
9 / 12
75%
Performance & Context
The archived review left minor headroom in how this analysis workflow scales across heavier contexts.
7 / 8
88%
Agent Usability
The packaged analysis path is understandable, though the archived score suggests slightly clearer routing would help.
14 / 16
88%
Human Usability
Human usability reached full score in the archived evaluation.
8 / 8
100%
Security
The packaged workflow stayed safe overall, with only a small remaining deduction around boundary signaling.
11 / 12
92%
Maintainability
The archived review treated the package as maintainable, while still preserving some room for cleanup.
9 / 12
75%
Agent-Specific
The archived deduction in agent specific traces back to: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
16 / 20
80%
Core Capability Total85 / 100
Medical TaskExecution Average: 86.6 / 100 — Assertions: 20/20 Passed
91
Canonical
You need to parse, validate, and manipulate biological sequences (DNA/RNA/protein) and their metadata
4/4 ✓
87
Variant A
You are running microbiome/community-ecology workflows (alpha/beta diversity, UniFrac, ordination, PERMANOVA)
4/4 ✓
85
Edge
Sequence objects: DNA, RNA, Protein, and generic Sequence with validation, slicing, motif search, reverse complement, transcription/translation, and metadata handling
4/4 ✓
85
Variant B
Alignment utilities: pairwise local alignment (SSW-based) and multiple sequence alignment containers (TabularMSA) with consensus support
4/4 ✓
85
Stress
End-to-end case for Sequence objects: DNA, RNA, Protein, and generic Sequence with validation, slicing, motif search, reverse complement, transcription/translation, and metadata handling
4/4 ✓
91
Canonical✅ Pass
You need to parse, validate, and manipulate biological sequences (DNA/RNA/protein) and their metadata
You need to parse, validate, and manipulate biological sequences... remained an analysis-style extraction path whose value came from structured data capture rather than a freeform narrative response.
Basic 36/40|Specialized 55/60|Total 91/100
✅A1The scikit-bio output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
87
Variant A✅ Pass
You are running microbiome/community-ecology workflows (alpha/beta diversity, UniFrac, ordination, PERMANOVA)
You are running microbiome/community-ecology workflows (alpha/beta... remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.
Basic 34/40|Specialized 53/60|Total 87/100
✅A1The scikit-bio output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Edge✅ Pass
Sequence objects: DNA, RNA, Protein, and generic Sequence with validation, slicing, motif search, reverse complement, transcription/translation, and metadata handling
The archived run treated Sequence objects: DNA, RNA, Protein, and generic Sequence with... as a bounded extraction workflow, keeping attention on source fields, fallback logic, and output shape.
Basic 33/40|Specialized 52/60|Total 85/100
✅A1The scikit-bio output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Variant B✅ Pass
Alignment utilities: pairwise local alignment (SSW-based) and multiple sequence alignment containers (TabularMSA) with consensus support
Alignment utilities: pairwise local alignment (SSW-based) and... remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.
Basic 32/40|Specialized 53/60|Total 85/100
✅A1The scikit-bio output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
85
Stress✅ Pass
End-to-end case for Sequence objects: DNA, RNA, Protein, and generic Sequence with validation, slicing, motif search, reverse complement, transcription/translation, and metadata handling
The archived run treated End-to-end case for Sequence objects: DNA, RNA, Protein, and... as a bounded extraction workflow, keeping attention on source fields, fallback logic, and output shape.
Basic 29/40|Specialized 56/60|Total 85/100
✅A1The scikit-bio output structure matches the documented deliverable
✅A2The instruction path remains actionable for the documented case
✅A3The output stays fully within the documented skill boundary
✅A4The response quality is acceptable for the documented path
Pass rate: 4 / 4
Medical Task Total86.6 / 100
Key Strengths
- Primary routing is Data Analysis with execution mode A
- Static quality score is 85/100 and dynamic average is 78.6/100
- Assertions and command execution outcomes are recorded per input for human review
- Execution verification summary: No script verification was applicable