tooluniverse-dose-response-f5162e — independently scanned and version-tracked by SaferSkills.
SaferSkills independently audited tooluniverse-dose-response-f5162e (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.
Findings & checks · 0 flagged
Every scanned point with the score it earned and what moved between them.
First recorded scan — no prior version to compare against.
The primary manifest — the file an agent reads to learn what this artifact does.
Turn paired concentration vs response measurements into a potency (IC50/EC50), a Hill slope, an efficacy (Emax), and a quality judgment — and compare potency between compounds.
The model is the 4-parameter logistic (4PL) / Hill sigmoidal: f(x) = Emin + (Emax − Emin) / (1 + (EC50/x)^n) — where n is the Hill slope.
| Issue | What to do |
|---|---|
| Concentration units | Pick ONE unit (µM, nM, M) and use it for every point. The IC50 comes back in that unit. Don't mix. |
| Log vs linear concentrations | Pass concentrations on the linear scale (e.g. 0.01, 0.1, 1, 10), not log10. The fitter logs internally. |
| Zero/control concentration | Drop a literal 0 concentration (log(0) is undefined). Keep it only as the Emin/Emax reference if normalizing. |
| Direction | Inhibition curves go high→low (IC50); activation curves go low→high (EC50). The tools handle both; just be consistent. |
| Normalization | Convert raw signal to % of control if you want Emax/Emin near 100/0: % = 100 × (raw − blank)/(control − blank). Raw values also fit, but plateaus are then in raw units. |
| Replicates | Average technical replicates per concentration before fitting, or pass all points (the fit weights them equally). |
Coverage requirement: you need ≥4 points (the tools require it) and ideally 6–8 spanning both plateaus — points clearly above and clearly below the inflection. A curve that never plateaus gives an unreliable, extrapolated IC50 (see Step 4).
Single curve → IC50 or EC50 (same math; "IC50" for inhibition, "EC50" for activation):
tu run DoseResponse_calculate_ic50 '{"operation":"calculate_ic50",
"concentrations":[0.001,0.01,0.1,1,10,100],
"responses":[98,95,80,45,12,3]}'Returns ic50, ic50_95_confidence_interval, hill_slope, emax, emin, r_squared, log_ic50.
Full 4PL parameters only → DoseResponse_fit_curve (same inputs). Two compounds → DoseResponse_compare_potency with conc_a/resp_a/conc_b/resp_b (returns each IC50 + ic50_fold_shift_b_over_a + more_potent).
For non-standard needs (constrained plateaus, weighting, plotting), scripts/fit_dose_response.py runs a scipy 4PL fit from a CSV and matches the tool.
| Parameter | Meaning | Sanity check | ||
|---|---|---|---|---|
| IC50 / EC50 | Concentration giving half-maximal effect — the potency. Lower = more potent. | Should fall within your tested range; if it's at/beyond an endpoint, the curve is incomplete (Step 4). | ||
| Hill slope `n` | Steepness / apparent cooperativity. ~1 = simple one-site. >1.5 = steep/positive cooperativity (or non-specific). <0.5 = shallow/multiple sites or heterogeneity. | A wildly large ` | n | ` (>4) usually means a bad fit or too few transition points, not real cooperativity. |
| Emax | Maximal response (top plateau) = efficacy. | For % data, full agonist ≈100; a partial agonist plateaus well below 100 even at saturating dose. | ||
| Emin | Bottom plateau (baseline/floor). | For % inhibition data, ≈0 for a complete inhibitor. | ||
| r² | Fit quality. | ≥0.95 good; <0.90 → inspect for outliers, wrong model, or incomplete curve before trusting the IC50. |
Potency comparison: report the fold-shift in IC50/EC50 (e.g. "A is 6.2× more potent than B"), and only call it meaningful if both fits are good (r²≥0.95) and the Hill slopes are comparable — a potency ratio between curves of very different slope is not a clean comparison.
tooluniverse-image-analysis — dose-response on image-derived measurements (.tif, colony, fluorescence).tooluniverse-gpcr-structural-pharmacology / tooluniverse-network-pharmacology — receptor pharmacology context.tooluniverse-statistical-modeling — general regression, EC50 via spline, power analysis.~30 seconds. Free. No account. Every finding cites a rule and a line of evidence.