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pkpd-modeling

Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug monitoring. Use when analysing concentration-time data, deriving exposure metrics, fitting PK or PD models, or evaluating dosing regimens. Triggers include "pharmacokinetics", "pharmacodynamics", "PK/PD", "NCA", "non-compartmental", "AUC", "Cmax", "lambda z", "half-life", "clearance", "volume of distribution", "compartmental model", "population PK", "popPK", "NONMEM", "nlmixr2", "Pharmpy", "Monolix", "exposure-response", "Emax", "EC50", "indirect response", "effect compartment", "TMDD", "PBPK", "bioequivalence", "RSABE", "ABEL", "allometric scaling", "first-in-human", "MABEL", "drug-drug interaction", "DDI", "ICH M12", "concentration-QTc", "therapeutic drug monitoring", "MIPD", and "dosing regimen".

76

Quality

96%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is pkpd-modeling in K-Dense-AI/scientific-agent-skills

SKILL.md
Quality
Evals
Security

Quality

Content

92%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.

An exceptionally strong skill body: fully executable commands with real outputs for all nine workflows, explicit validation checkpoints wired into tool exit codes and findings, and clean one-level-deep progressive disclosure into a well-organized reference bundle. The only weakness is minor: the Software ecosystem and Citing sections carry inline time-sensitive version and protocol detail that duplicates the references and could be trimmed or delegated.

Suggestions

Conciseness: reduce the Software ecosystem section to the verified date plus a one-line pointer to references/software-ecosystem.md, moving the per-version breaking-change details (Pharmpy 2.0.0/2.1.0 changes, NONMEM 7.5-to-7.6 additions) out of the body since they already live in that reference file.

Conciseness: condense the citation section to the reference itself plus a single pointer line, and move the arXiv fetch-and-version-resolution protocol into a reference or asset file.

Conciseness: trim the worked-example output blocks (e.g., the full NCA metric table and the scaling parameter table) to only the rows that illustrate the stated teaching point, keeping the findings lines that carry the decision content.

DimensionReasoningScore

Conciseness

The body is dense, expert-level prose with no padding and no explanation of concepts Claude already knows — every paragraph carries non-obvious domain judgment ("AIC picks the three-compartment model. BIC and the F test both reject it"). It falls short of the score 5 anchor only because some inline detail could move to the bundle: the Software ecosystem section duplicates per-version, dated changelog material ("2.0.0 (2026-02-12) changed dataset row indices to start at 1", the NONMEM 7.5-to-7.6 feature list) that already lives in references/software-ecosystem.md, and the closing citation protocol (arXiv fetch/version-resolution rules) runs long. It is well above score 3, which requires unnecessary explanation or looseness throughout.

4 / 5

Actionability

Every workflow ships a copy-paste-ready command with real flags and arguments ("python3 nca.py -i profile.csv --dose 100 --route extravascular --partial-auc 0-24", the simulate/two-scenario invocation, the tdm_bayes invocation), a script-to-question table routes users to the right tool, I/O conventions are uniform ("All take --format table|tsv|json... Exit code is 0 for no findings, 1 when findings were raised, 2 for bad input"), and real recorded outputs illustrate each common case. This matches the score 5 anchor: fully executable commands covering the common cases, with no gaps.

5 / 5

Workflow Clarity

The Workflow section sequences nine numbered analyses, each with explicit validation checkpoints: "Check the dataset before running anything" for popPK, RSE/correlation flags after fitting ("Q3 has 98% RSE - not estimable"), attainment fractions after simulation, and NCA extrapolation/window findings. Findings plus exit codes create the validate-then-decide feedback loop ("any of them can gate a workflow"), and the closing ten-item checklist enumerates the failure modes the skill exists to prevent. This matches the score 5 anchor (clear sequence, explicit validation, feedback, checklist); none of these analyses are destructive or batch operations, so no cap applies.

5 / 5

Progressive Disclosure

The body is a true overview that pushes depth into 14 one-level-deep reference files (all verified to exist and contain substantive content), 2 assets, and 11 scripts, with no nested references. Navigation is well-signaled both in a dedicated References section with a scope line per file ("references/population-pk.md — NLME estimation, covariate building, BLQ M1-M7, diagnostics, VPC") and at point of need in the text ("see references/population-pk.md for estimation methods"). This matches the score 5 anchor: clear overview, well-signaled one-level-deep references, easy navigation.

5 / 5

Total

19

/

20

Passed

Description

100%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.

An exemplary description: a comprehensive enumeration of what the skill does, an explicit Use-when clause, and a dense list of natural trigger terms with synonyms. It follows the strongest reference pattern (what + when + triggers) with no fluff, buzzwords, or over-claims, and its third-person voice is correct throughout.

DimensionReasoningScore

Specificity

The description enumerates concrete capability areas — "non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug monitoring" — which map one-to-one onto the skill's nine bundled workflows. This matches the anchor "lists multiple specific concrete actions; comprehensive coverage"; it is not score 4 because there is no meaningful coverage gap, and not score 3 because far more than 1-2 actions are named.

5 / 5

Completeness

It explicitly answers both questions: the "what" in the opening enumeration of capabilities, and the "when" via "Use when analysing concentration-time data, deriving exposure metrics, fitting PK or PD models, or evaluating dosing regimens" followed by a concrete "Triggers include..." list. This is the score 5 pattern (clear what AND when with concrete trigger phrases); the score 4 anchor ("when could be more explicit") does not apply because the when-clause is fully explicit.

5 / 5

Trigger Term Quality

Roughly 35 natural trigger terms including synonyms users actually say: "population PK"/"popPK", "drug-drug interaction"/"DDI", "pharmacokinetics", "AUC", "Cmax", "lambda z", "half-life", "clearance", "volume of distribution", plus tool names ("NONMEM", "nlmixr2", "Pharmpy", "Monolix") a user would name directly. This is comprehensive natural-term coverage with synonyms, matching the score 5 anchor; no common phrasing in the domain is missing.

5 / 5

Distinctiveness Conflict Risk

A deep pharmacometrics niche with unambiguous, domain-exclusive triggers ("RSABE", "ABEL", "MABEL", "lambda z", "TMDD", "ICH M12", "MIPD") that no adjacent skill (general statistics, chemistry, data analysis) would fire on. Matches the score 5 anchor "clear niche with distinct triggers; minimal conflict risk"; overlap risk with generic skills is negligible.

5 / 5

Total

20

/

20

Passed

Validation

93%

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

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

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

Warning

Total

15

/

16

Passed

Repository

synthetic-sciences/openscience

Path

backend/cli/skills/chemistry/pkpd-modeling/SKILL.md

Reviewed

Table of Contents

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