Data Analysis
biopython-alignment
88100Total Score
Core Capability
83 / 100
Functional Suitability
10 / 12
Reliability
9 / 12
Performance & Context
8 / 8
Agent Usability
13 / 16
Human Usability
8 / 8
Security
9 / 12
Maintainability
10 / 12
Agent-Specific
16 / 20
Medical Task
20 / 20 Passed
96You need global alignment between two protein (or nucleotide) sequences and want a reproducible score and aligned strings
4/4
92You need local alignment to find the best matching fragment/subsequence between two DNA/RNA/protein sequences
4/4
90Pairwise alignment via Bio.Align.PairwiseAligner (global and local modes)
4/4
90Alignment scoring with configurable match/mismatch and gap penalties
4/4
90End-to-end case for Pairwise alignment via Bio.Align.PairwiseAligner (global and local modes)
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 | Scientific integrity held because extraction and analysis outputs stayed tied to provided text, metadata, or runtime evidence rather than invented study findings. |
| Practice Boundaries | PASS | The evaluated outputs stayed inside the Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO),... and did not drift into unsupported interpretation beyond the available inputs. |
| Methodological Ground | PASS | The archived evaluation treated the workflow as method-linked rather than ad hoc. |
| Code Usability | PASS | Code usability passed because the package still exposed a reviewable execution surface for its documented workflow. |
Core Capability83 / 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
10 / 12
83%
Reliability
Related legacy finding for biopython-alignment: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
9 / 12
75%
Performance & Context
The legacy audit gave full marks to performance context for this package.
8 / 8
100%
Agent Usability
The archived review left some headroom in how quickly an agent can lock onto the intended analysis path.
13 / 16
81%
Human Usability
No point loss was recorded for human usability in the legacy audit.
8 / 8
100%
Security
Security remained strong, though the archived review still left some room for clearer execution guardrails.
9 / 12
75%
Maintainability
The analysis package is maintainable overall, though the archived score suggests modest cleanup headroom.
10 / 12
83%
Agent-Specific
Related legacy finding for biopython-alignment: Improve stress-case output rigor. Stress and boundary scenarios show weaker consistency
16 / 20
80%
Core Capability Total83 / 100
Medical TaskExecution Average: 91.6 / 100 — Assertions: 20/20 Passed
96
Canonical
You need global alignment between two protein (or nucleotide) sequences and want a reproducible score and aligned strings
4/4 ✓
92
Variant A
You need local alignment to find the best matching fragment/subsequence between two DNA/RNA/protein sequences
4/4 ✓
90
Edge
Pairwise alignment via Bio.Align.PairwiseAligner (global and local modes)
4/4 ✓
90
Variant B
Alignment scoring with configurable match/mismatch and gap penalties
4/4 ✓
90
Stress
End-to-end case for Pairwise alignment via Bio.Align.PairwiseAligner (global and local modes)
4/4 ✓
96
Canonical✅ Pass
You need global alignment between two protein (or nucleotide) sequences and want a reproducible score and aligned strings
You need global alignment between two protein (or nucleotide)... remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.
Basic 36/40|Specialized 60/60|Total 96/100
✅A1The biopython-alignment 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
92
Variant A✅ Pass
You need local alignment to find the best matching fragment/subsequence between two DNA/RNA/protein sequences
The archived run treated You need local alignment to find the best matching... as a bounded analysis workflow rather than a purely narrative instruction path.
Basic 34/40|Specialized 58/60|Total 92/100
✅A1The biopython-alignment 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
90
Edge✅ Pass
Pairwise alignment via Bio.Align.PairwiseAligner (global and local modes)
Pairwise alignment via Bio.Align.PairwiseAligner (global and local... remained tied to the documented analysis contract even when the preserved evidence centered on instructions instead of a full rerun.
Basic 33/40|Specialized 57/60|Total 90/100
✅A1The biopython-alignment 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
90
Variant B✅ Pass
Alignment scoring with configurable match/mismatch and gap penalties
This variant b case stayed within the packaged analysis boundary and kept a reviewable task contract.
Basic 32/40|Specialized 58/60|Total 90/100
✅A1The biopython-alignment 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
90
Stress✅ Pass
End-to-end case for Pairwise alignment via Bio.Align.PairwiseAligner (global and local modes)
The archived run treated End-to-end case for Pairwise alignment via... as a bounded analysis workflow rather than a purely narrative instruction path.
Basic 29/40|Specialized 60/60|Total 90/100
✅A1The biopython-alignment 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 Total91.6 / 100
Key Strengths
- Primary routing is Data Analysis with execution mode B
- Static quality score is 83/100 and dynamic average is 78.6/100
- Assertions and command execution outcomes are recorded per input for human review
- Execution verification summary: Script verification 1/1; adjustment=5. msa_conservation.py: OK