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Manages work transitions between team members or agents by creating structured handoff documents, summarizing project status, documenting key decisions, blockers, and open questions, and generating onboarding briefs. Use when someone needs to hand off, hand over, or transition a project; pass work to another person or agent; brief a colleague taking over; prepare a shift change summary; or onboard someone mid-task. Produces ready-to-use handoff documents covering current status, next steps, known issues, technical context, and communication templates for both planned and unplanned transfers.

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Use when strengthening AAMAS reproducibility evidence for interaction claims, including proofs and game definitions, opponent and population sets, self-play protocols, random seeds, compute, uncertainty on strategic outcomes, baselines, and consistency between what the paper claims about agents and what the artifact can actually show.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.

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Apply modern Swift language patterns and idioms for non-concurrency, non-SwiftUI code. Covers if/switch expressions (Swift 5.9+), typed throws (Swift 6+), result builders, property wrappers, opaque and existential types (some vs any), guard patterns, Never type, Regex builders (Swift 5.7+), basic Codable shaping (CodingKeys, custom decoding, nested containers), modern collection APIs (count(where:), contains(where:), replacing()), basic FormatStyle usage, and string interpolation patterns. Use when writing core Swift code involving generics, protocols, enums, closures, or modern language features; route deep Codable to swift-codable, detailed formatting/localization to swift-formatstyle, and API naming to swift-api-design-guidelines.

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Smart triggered RF capture on NI USRP radios with Wireless Testbench — record only when a signal of interest appears, not continuously (triggered spectrum sensing). Use energy detection to capture when signal power rises above the noise floor, or preamble detection to cross-correlate against a known sequence (WLAN L-LTF, 5G NR PSS/SSS, LTE PSS, Zadoff-Chu, custom protocols) and capture only when that protocol's preamble is detected. Use when implementing triggered (wake-on-signal) capture or spectrum sensing, capturing protocol-based signals via cross-correlation, calibrating detection thresholds (plotDetectionSignals / plotThreshold), scanning frequency bands for activity, or building transmit-then-detect workflows.

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Use when setting up vehicle network communication in MATLAB using Vehicle Network Toolbox. Covers CAN/CAN FD (fully implemented), with architecture for J1939, XCP, and future protocols. Handles hardware discovery, channel creation, bus configuration, message exchange, signal encoding/decoding, and analysis across all supported vendors. (Vector, Kvaser, PEAK-System, NI, SocketCAN, MathWorks Virtual).

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Design multi-agent orchestration with workflow DAGs, routing, handoff protocols, and state management. Use when building pipelines of specialized agents, designing fan-out/fan-in patterns, or implementing fault-tolerant workflows.

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Design AI agent communication protocols: MCP tool schemas, A2A, function calling, and inter- agent messaging. Use when building multi-agent systems, defining tool interfaces, or implementing agent-to-agent communication.

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Select and configure a structured discussion protocol matched to the purpose, topic, and group readiness. Use when planning classroom discussions, Socratic seminars, or structured debate.

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Generate a coaching conversation guide with questions, protocols, and follow-up actions for a teaching focus. Use when preparing for coaching sessions, mentoring, or peer feedback conversations.

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Analyze digital and analog captures from Saleae Logic MSO devices. Decode protocols like UART, SPI, I2C from exported binary files. Use when analyzing logic analyzer captures for CTF challenges, hardware reverse engineering, or protocol decoding.

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Generate protocol/interface test suites that any implementation must pass. Define the contract once, test every implementation. Use when designing protocols or swapping implementations.

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Use for authorized reverse engineering of custom binary protocols, Protobuf/gRPC, WebSocket frames, and PCAP-driven protocol recovery.

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Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for [intervention]", or when developing FDA submission documentation for investigational products.

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Tool safety protocols, adversarial output validation, error recovery patterns, and I/O contracts for research operations

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Cross-agent collaboration protocols, workflow handoff patterns, and commit message formats for TDD/Mikado/refactoring workflows

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Enforce universal security protocols for safe, resilient software. Use when implementing authentication, encryption, authorization, input validation, secret management, or any security-sensitive feature across any language or framework.

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Guide incident response from detection to post-mortem using SRE principles, severity classification, on-call management, blameless culture, and communication protocols. Use when setting up incident processes, designing escalation policies, or conducting post-mortems.

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Build .NET AI agents, harnesses, and multi-agent workflows with Microsoft Agent Framework using the right agent type, sessions, tools, workflows, hosting protocols, and enterprise guardrails. USE FOR: building or reviewing .NET code that uses Microsoft.Agents.*, Microsoft.Extensions.AI, AIAgent, HarnessAgent, AgentSession, or Agent Framework hosting packages; choosing agent, harness, workflow, and hosting shapes. DO NOT USE FOR: unrelated stacks; generic tasks that do not need this specific guidance. INVOKES: inspect the repository context, edit targeted files, and run relevant build, test, lint, or validation commands when changes are made.

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Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for [intervention]", or when developing FDA submission documentation for investigational products.

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Use when building, backtesting, operating, or scaling automated trading on prediction markets (Kalshi or similar) — evidence-gated methodology, live-execution safety rails, and falsification protocols distilled from a real live-money campaign

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Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows.

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Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

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