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Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling (dipcall/PAV) to two-step .snf cohort merging to Truvari benchmarking - chaining ONT and PacBio HiFi runs while handing the SV signal mechanism off to the component skills. Use when running a long-read SV workflow from reads to a benchmarked callset, choosing the minimap2 preset and SV caller by platform and goal, deciding when long reads are worth it for the insertions and repeat-mediated SVs short reads physically miss, building a joint-genotyped cohort with the two-step .snf design, or parameterizing a Truvari benchmark against GIAB HG002 Tier 1 plus CMRG. Not for the SV signal mechanism itself (see variant-calling/structural-variant-calling) or short-read SV.

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Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose ORA vs GSEA, convert gene IDs per method, run enrichGO/enrichKEGG/enrichPathway/enrichWP or gseGO/gseKEGG (clusterProfiler, ReactomePA, rWikiPathways), and visualize. Use when a DESeq2/edgeR/limma result must become enriched GO terms, KEGG/Reactome/WikiPathways pathways, or a GSEA leading edge; when the input is a full ranking for all genes (GSEA, named decreasing vector) or only a pre-selected list (ORA plus a defensible background universe); or when assembling DE-to-pathway end to end. The DE list and ranking statistic come from differential-expression/de-results; per-method nuance lives in the pathway-analysis skills.

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Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researchers, or regulatory work.

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Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.

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Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, calibration (Platt, isotonic), feature importance (SHAP, atomic attribution), and prospective validation. Use when building target-specific predictive models from in-house bioassay data, ADMET endpoints, or selectivity profiles.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

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Place contracts and behavior across authority, prediction, presentation, localization, and assembly boundaries.

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Design SS14 components as serialized state in the correct assembly.

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Prove repository ownership, module ownership, assembly boundaries, edit-marker rules, extension points, and test placement.

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Build hybrid search systems combining semantic and keyword. TRIGGERS - Use when user needs help with ai-hybrid-search related tasks.

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Extract property, owner, legal description, liens, mortgages, easements, and tax status from title search reports.

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Extract timekeeper entries, disbursements, matter references, and billing summaries from law firm invoices.

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Gets a custom map into CARLA on UE 5.8 — the four distinct routes and which one to pick — via Util/Tools/Import.py for FBX+OpenDRIVE assets into a source build, CARLA_MAPS_TO_COOK to ship a map inside a package, or client.generate_opendrive_world() for an OpenDRIVE-only map at runtime with no build at all. Covers where imported assets land, why an imported map cannot be loaded from a package by name, and the four capabilities the UE4 skill has that ue58 lacks — standalone asset packages, their installer, semantic-material tagging, and a pedestrian navmesh that is generated but silently skipped. Use when the user asks to "import a map", "add a custom map", "load my .xodr", "package my own town", or "create a standalone map package".

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Spawns and attaches sensors on a running CARLA server — cameras (rgb/depth/semantic/instance/optical-flow/normals), lidar, radar, IMU, GNSS, collision/lane-invasion/obstacle — to the ego or any actor, with a mount transform and blueprint attributes (resolution, fov, sensor_tick, lidar range/points, …). Also sets up native ROS 2 publishing (--ros to enable_for_ros, --ros-name/--ros-frame-id topic and TF naming) and prints the topics the sensor will publish. Use when the user asks to "add a camera/lidar/sensor", "put a dashcam on the ego", "attach a depth camera", "mount a sensor", or "publish a sensor to ROS". Prints the sensor id; read its data with the read-sensor skill.

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Queries the live CARLA world and resolves an entity description into a concrete actor id — find actors by type, role, or colour, or the single one nearest a point/actor; read the world snapshot; get static level bounding boxes by label; cast rays for semantic points; project a point to the ground; or (ros-topics) list the native ROS 2 topics each actor should be publishing and why any is silent. Identifies by stable attributes, not by any rank/order. Use when the user asks "what actors are here", "find the red prius", "the vehicle nearest the ego", "list the pedestrians", or needs a specific actor id for another skill.

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Writes a new ScenarioRunner scenario — a Python class deriving from BasicScenario with its behaviour tree assembled from srunner atomic behaviours and criteria, plus the XML config that gives it a town, ego spawn and parameters — and registers it so `--scenario MyScenario_1` works. Also covers adding a scenario to a route via --additionalScenario. Generates a working skeleton and validates it without a simulator. Use when the user asks to "create/write a new scenario", "add a custom scenario", "make my own traffic situation", or wants to extend the scenario library.

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Imports FBX meshes into a CARLA source build as spawnable static.prop.* blueprints — pass a directory whose subdirectories name the semantic tags, or a single FBX with its tag, and the props are imported into content, registered, added to the prop factory and verified by spawning. Use when the user asks to "add a prop to CARLA", "import an FBX as a prop", "add street furniture/benches/signs", or needs a custom mesh spawnable from the Python API.

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Imports an FBX vehicle into a CARLA source build as a spawnable vehicle.<make>.<model> — checks the FBX carries CARLA's 4-wheel bone rig, imports the mesh, then assembles the vehicle through CarlaTools' VehicleAuthoringLibrary (physics asset with kinematic wheel bodies, retargeted anim blueprint, four configured wheel blueprints, the vehicle blueprint), registers it in VehicleFactory through CARLA's own add_vehicle_to_vehicle_factory.py, and verifies it spawns, drives and steers. Use when the user asks to "add a car/truck/van to CARLA", "import a vehicle FBX", or needs a custom drivable vehicle spawnable from the Python API.

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Listens to a CARLA sensor and either saves its data to files, shows it live in a window, prints a one-shot summary, or (ros-info) reports the native ROS 2 topics, QoS and enabled-for-ROS state so you can echo it from ROS instead. Cameras save as PNG (depth/semantic auto-colourised) and display in a pygame window; lidar saves as .ply and shows as a top-down scatter; IMU/GNSS/radar/collision stream to JSONL or the console. Use when the user asks to "show/view the camera", "display the lidar", "save the sensor data / capture a dataset", or "what is this sensor reading". Select the sensor by id, type, or the actor it's attached to.

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MUST USE for building FastAPI/REST API applications with Aerospike database (aerospike-py Rust/PyO3 async client). Covers AsyncClient lifespan management, FastAPI Depends injection, aerospike_py exception-to-HTTP-status mapping (RecordNotFound→404, RecordExistsError→409, BackpressureError→503, AerospikeTimeoutError→504), POLICY_EXISTS_CREATE_ONLY/UPDATE_ONLY for CRUD semantics, NamedTuple attribute access (record.bins not tuple unpacking), client.ping() readiness probe, batch_read returning dict, batch_write with in_doubt retry signal, and global AerospikeError handler. Triggers on: FastAPI + Aerospike, REST API + aerospike-py, CRUD API with Aerospike, client.ping() health probe, batch_read/batch_write endpoint, web server/HTTP service backed by Aerospike NoSQL, uvicorn + Aerospike.

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Build WCAG 2.1 AA compliant web applications for University of Sheffield. Covers semantic HTML, ARIA patterns, form accessibility, keyboard navigation, color contrast, alt text, captions, and automated testing. Use when creating websites, web apps, forms, interactive components, or auditing accessibility for WCAG compliance, screen readers, keyboard access, or inclusive design.

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Accessibility testing toolkit using Selenium WebDriver 4+ with Java 21+ and axe-core engine. Use when asked to validate WCAG 2.1/2.2 compliance, scan pages or components for a11y violations, test keyboard navigation, audit color contrast, check ARIA semantics, generate accessibility reports, filter axe rules, debug screen reader issues, or implement POUR principles (perceivable, operable, understandable, robust).

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Design, audit, and improve accessibility and inclusive user experiences. Use when Codex is asked about WCAG, keyboard navigation, focus states, screen readers, ARIA, contrast, captions, reduced motion, forms, semantic HTML, accessible UI, game accessibility, inclusive design, accessibility QA, or compliance-sensitive accessibility work.

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