# Discovery Toolbox > A routed repertoire of ~90 scientific thinking operators for biological research agents - visual reasoning, detectability and information budgets, search reframing, causal identification, competing explanations, observation and selection processes, pipeline artifact diagnosis, effort allocation, and confirmation hygiene. Use when a screen returns null or weak results, a result looks too good, sea… - **Type:** Skill - **Install:** `agentstack add skill-dekan-aleksandr-biodiscovery-skills-discovery-toolbox` - **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior - **Seller:** [dekan-aleksandr](https://agentstack.voostack.com/s/dekan-aleksandr) - **Installs:** 0 - **Category:** [Search](https://agentstack.voostack.com/c/search) - **Latest version:** 0.1.0 - **License:** MIT - **Upstream author:** [dekan-aleksandr](https://github.com/dekan-aleksandr) - **Source:** https://github.com/dekan-aleksandr/biodiscovery-skills/tree/main/skills/discovery-toolbox ## Install ```sh agentstack add skill-dekan-aleksandr-biodiscovery-skills-discovery-toolbox ``` Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent. ## About # DISCOVERY TOOLBOX **Load on demand, never wholesale.** Route to the smallest relevant section. Usually activate **1–3 operators**, execute them, then return to the research loop. The toolbox is a repertoire, not a checklist. --- ## A · VISUAL REASONING **Trigger:** shape, heterogeneity, ranking, trajectories, subsets, or individual observations may matter. - **RAW + EXTREMES** — inspect representative raw units, argmax/argmin, and matched non-hits. - **RANK / SHAPE VIEW** — inspect the full ordered profile or curve, not only thresholds or summary metrics. - **SMALL MULTIPLES / MULTISCALE** — repeat the same view across subsets, clades, batches, quality strata, sources, time, and analysis scales. - **RESIDUAL / INFLUENCE VIEW** — inspect residual structure and sensitivity to influential observations/groups. - **PREDICTED FIGURES** — generate expected visual patterns under competing hypotheses before looking at decisive evidence. - **CALIBRATED VISUAL INFERENCE** — important visual-only claim → declare the expected pattern, compare against matched nulls/line-ups, and calibrate the visual reader on pure nulls. - **DISPLAY AUDIT** — if a conclusion depends on axes, aspect ratio, encoding, aggregation, or overplotting, compute it directly or re-render appropriately. --- ## B · INSTRUMENT / DETECTABILITY / INFORMATION **Trigger:** new screen, weak/null result, uncertain calibration, lossy representation, or multi-fidelity pipeline. - **PERMANENT CALIBRATION HARNESS** — reusable screen → maintain `structure-preserving null + spike-in/recovery + empirical decoys/negative controls`. - **TARGET RELIABILITY** — estimate target noise, cross-source agreement, test–retest/version agreement, and effective independent units. - **POINT → CURVE** — replace a weak point estimate with signal vs `n / noise / quality / aggregation / threshold / scale`. - **EXISTENCE / INFORMATION BUDGET** — estimate expected detectable hits and whether target information × independent units can support the search space; insufficient capacity → change instrument/design, not estimator. - **TOY TRUTH** — reproduce a known answer on a toy slice and/or generative simulation before interpreting large-scale nulls. - **COMMON-CAUSE FIRST** — before explaining individual hits, test screen-wide technical or biological causes. - **SIGNAL/NOISE AUTOPSY** — assume signal exists; identify what makes it unreadable: target noise, heterogeneity, wrong unit, aggregation, alignment, measurement error, etc. - **DIFFUSE-SIGNAL SWITCH** — if individual hits fail but the statistic distribution shifts, use whole-distribution/set-level modeling. - **INFORMATION-LOSS / RATE–DISTORTION AUDIT** — vary compression, aggregation, or preprocessing and locate where target-relevant information disappears. - **DPI / PROVENANCE LEAKAGE CHECK** — derived features cannot legitimately contain target information unavailable in their declared inputs; violations trigger leakage/provenance investigation. - **MULTI-FIDELITY RECALL** — cheap filters must preserve top-k/rank behavior at the real operating threshold and in important subgroups; otherwise hedge pruning aggressiveness. - **UNDETERMINED ≠ NEGATIVE** — pipeline failure, missingness, timeout, or non-convergence is a third outcome; track its structure. --- ## C · SEARCH / REFRAMING **Trigger:** ideas repeat, experiment space freezes, or marginal exploration yield falls. - **DUAL-SPACE SEARCH** — track `hypothesis space` and `experiment/measurement space` separately; change whichever is stagnant. - **LOCAL → STRUCTURAL ANALOGY** — search nearby mechanisms first, then search the relational skeleton of the problem across fields. - **INVERSE SCREEN** — construct the feature/profile that would explain the phenomenon, then search for nearest real examples. - **CHANGE THE UNIT** — move coarser/finer or to another causal/biological unit. - **DECOMPOSE / RECOMBINE** — split composite targets/features; localize the informative component. - **AUXILIARY TARGET** — solve a related quantity that can be measured better, then transfer back. - **EINSTELLUNG BREAK / RANDOM RESTART** — run a branch where the dominant approach is forbidden, or restart in another region of search space. - **BLIND / HIGH-UPSIDE VARIATION** — preserve some exploration not justified by the current model; require justification only before expensive escalation. - **SPRAY-AND-CUT** — lower per-attempt cost → buy more independent attempts rather than only deeper attempts. - **INTERMEDIATE MODEL CHAIN** — build a sequence of simplified models and treat the residual sequence as the discovery object. - **POSE THE NEXT QUESTION** — after each useful screen, ask what sharper question or measurement it newly makes possible. --- ## D · CAUSAL IDENTIFICATION **Trigger:** causal/mechanistic interpretation, comparative/natural experiment, or major covariate adjustment. - **IDENTIFICATION BEFORE ESTIMATOR** — state the causal quantity, ideal experiment, identifying variation, and unit of inference. No identifying variation → descriptive claim. - **EXOGENOUS-VARIATION SWEEP** — actively search thresholds, timing accidents, protocol/software changes, rollouts, natural discontinuities, independent transitions, and other quasi-experiments. - **DESIGNED CONTRAST** — remove confounding by design when possible: matched pairs, within-unit changes, independent origins, decoupled subsets, change points. - **BOUNDS FIRST** — weak identification → report what the data permit under minimal assumptions, then show what additional assumptions narrow. - **ONTOLOGY / TARGET POPULATION** — state which unit and population the estimate actually describes; do not silently generalize beyond the identifying contrast. - **PLACEBO / PRE-TREND BATTERY** — test outcomes, periods, populations, or thresholds the proposed mechanism should not affect. - **CONFOUNDER-STRENGTH SENSITIVITY** — quantify how strong an unmeasured confounder must be to overturn the result. - **SELECTION TRAJECTORY** — ask why units entered the exposed/selected group and whether they were already changing before selection. - **NUISANCE-MODEL DISAGREEMENT** — result depends on adjustment choice → identify and test the assumption causing the disagreement. - **COMPARISON-WEIGHT AUDIT** — pooled estimate → inspect which elementary comparisons actually contribute and with what weights. --- ## E · COMPETING EXPLANATIONS **Trigger:** a lead may deserve concentration of resources. - **ACH / NONE-OF-THE-ABOVE** — compare evidence across competing hypotheses; discard evidence compatible with all; retain an unconceived-alternative row. - **DIAGNOSTICITY GATE** — if possible test outcomes do not separate hypotheses, choose another test. - **DIFFERENTIAL MEASUREMENT** — find the measurement where the leading explanations predict different values. - **LOCARD TRACE** — each mechanism/artifact should leave collateral traces elsewhere; search for them. - **PAIRED ABLATIONS** — `destroy mechanism, preserve cue` + `destroy cue, preserve mechanism`. - **PERTURBATION / SPECIFICATION STABILITY** — vary defensible subsets, transformations, nuisance models, thresholds, seeds, and analysis choices; distinguish robustness distribution from knob attribution. - **ERROR BUDGET** — express plausible systematic errors in the effect's units. - **SOURCE-INDEPENDENCE CHECK** — apparently independent evidence sharing collection, ontology, preprocessing, or labels counts as less than independent. - **ELIMINATION LEDGER** — track `UNTOUCHED / ALIVE / WOUNDED / DEAD` and the observation that changed state. - **ALTERNATIVE / COLD DERIVATION** — reproduce representative results by a structurally different route, or with artifacts stripped of the original narrative. --- ## F · OBSERVATION / SELECTION PROCESS **Trigger:** filtering, missingness, uneven effort, curation, historical data, protocol drift, or provenance may shape the dataset. - **OBSERVATION-PROCESS AUDIT** — map `generation → measurement → collection → inclusion → QC → preprocessing → loaded data`; record what each stage removes and what removal correlates with. - **ABSENT / UNDETECTED / REMOVED** — distinguish these explicitly; recover upstream QC/filter information when needed. - **CHAIN OF CUSTODY** — trace important derived variables/results back to raw measurements; broken provenance is a leakage/contamination alarm. - **COVERAGE-STANDARDIZED COMPARISON** — unequal measurement/observation effort → compare equivalent coverage/information, not merely equal row count. - **ACTUALISTIC CALIBRATION** — pass known/synthetic material through the real inclusion/QC/join pipeline and measure what survives. - **PALIMPSEST / ERA DETECTION** — detect hidden protocol, schema, curator, or collection-era strata from missingness/provenance patterns. - **PRESERVATION-PROXY CHECK** — test whether completeness, observation effort, metadata richness, collection date, or similar archive variables explain the result. - **SAMPLING-INDUCED GRADIENT CHECK** — apparent gradual onset/decay or endpoints may arise from incomplete sampling; simulate abrupt truth through the observed sampling process. --- ## G · PIPELINE / ARTIFACT DIAGNOSIS **Trigger:** spectacular result, unexplained change, replication failure, or suspicious software/data behavior. - **CHECK THE PLUG** — files, row alignment, labels, units, joins, versions, executed code, and outputs. - **DETERMINISTIC MINIMAL REPRODUCER** — fix randomness and reduce to the smallest input that reproduces the effect. - **PIPELINE BISECTION** — inject known-good signal and bisect where it is lost/corrupted. - **INVARIANTS + LOUD ASSERTIONS** — specify what each transformation must preserve and fail loudly when violated. - **COUNT TWO WAYS** — derive headline quantities through another implementation/path. - **FAULT TREE + FAULT INJECTION** — enumerate plausible failures, deliberately inject them, and identify silent holes. - **REINTRODUCE / SAME-HOLE SWEEP** — restored bug should restore artifact; then inspect all prior results exposed to the same failure mode. - **BISECT HISTORY** — binary-search changes when behavior shifted. - **INHERITED-CONSTANT / VERSION AUDIT** — unexpected yield → inspect mappings, annotations, external constants, resource versions, and producer semantics. - **TIME-REVERSE THE ANALYST** — trace backward from claim through every decision capable of changing it. --- ## H · ALLOCATION / DEPTH **Trigger:** deciding breadth vs depth or where to spend scarce resources. - **BINDING-RESOURCE COST** — price actions by what actually limits progress: attention, samples, experimental latency, compute, or wall time. - **CAPABILITY-CALIBRATED COST** — do not import human labor estimates; prototype when uncertain and measure actual agent/tool cost. - **OUTSIDE VIEW + EXPECTED YIELD** — use previous run/base-rate performance before detailed inside-view forecasting. - **INFORMATION-GAIN ORDERING** — prefer tests that most efficiently partition the live hypothesis space. - **MARGINAL-YIELD SWITCH** — continue an arm while its expected yield beats a fresh start. - **DEPTH SWITCH** — a few leads dominate on `upside × evidence × discriminability` → stop widening and invest heavily. - **ADVENTUROUS TAIL** — preserve capacity for coherent high-upside/high-variance research. - **MARGINAL VALUE / REDUNDANCY** — value additions relative to capabilities already present, not in isolation. --- ## I · CONFIRMATION / HYGIENE **Trigger:** a lead may become a scientific claim, or infrastructure is being reused long-term. - **INDEPENDENT CONFIRMATION** — prefer a genuinely independent data-generating process; freeze the claim/analysis first. - **CONFIRMATION DIVERSITY** — spend limited confirmation resources across different mechanisms/explanations, not redundant top ranks. - **INVARIANCE / ORTHOGONAL CONSEQUENCE** — test properties predicted by the mechanism that leading artifacts have little reason to reproduce. - **TRANSFER TEST** — check structure in a genuinely different regime, cohort, clade, source, or measurement system. - **WINNER'S-CURSE AWARENESS** — discovery effect size is not the expected confirmation effect. - **SUCCESS POST-MORTEM** — ask whether diagnostics would have caught an artifact version of a successful result. - **ASSUMPTION REGISTER** — track consequential `chosen/inherited × tested/untested` assumptions. - **OMITTED / FILTERED / EXCLUDED** — important removals must remain recoverable and auditable. - **PROGRESSIVE vs DEGENERATING** — prefer modifications that predict something new over those that only rescue the existing claim. --- ## ROUTER ``` visual structure → A calibration / weak signal / information / filters → B search stagnation / reframing → C causal interpretation → D competing explanations → E selection / missingness / provenance → F pipeline suspicion → G allocation / depth → H confirmation / assumptions → I ``` **Default: activate 1–3 operators.** More only when independently useful. The toolbox exists to expose **non-obvious moves** the agent might otherwise miss. Standard methods need not be restated unless a specific construction changes the reasoning. ## Source & license This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code. - **Author:** [dekan-aleksandr](https://github.com/dekan-aleksandr) - **Source:** [dekan-aleksandr/biodiscovery-skills](https://github.com/dekan-aleksandr/biodiscovery-skills) - **License:** MIT Install and usage instructions live in the source repository linked above. ## Pricing - **Free** — Free ## Security capabilities Automated source analysis of v0.1.0 — what this tool can access: - **Network access:** no - **Filesystem access:** no - **Shell / process execution:** no - **Environment & secrets:** no - **Dynamic code execution:** no *"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.* ## Versions - **0.1.0** — security scan: passed — Imported from the upstream source. ## Links - Listing page: https://agentstack.voostack.com/l/skill-dekan-aleksandr-biodiscovery-skills-discovery-toolbox - Seller: https://agentstack.voostack.com/s/dekan-aleksandr - Browse the marketplace: https://agentstack.voostack.com/browse --- Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.