Claude Skills by stanfish06

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

Integration with protocols.io API for managing scientific protocols. Use when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

Use when the user wants to spin up / create / launch / provision a DigitalOcean droplet (or "a remote dev box on DO") and connect to it from Codex as a remote SSH workspace.

Expert-thinking profile for Psycholinguist (experimental / neurolinguistic / computational psycholinguistics): Reasons from incremental parsing, lexical access, and prediction; designs SPR, eyetracking, VWP, and ERP studies with SUBTLEX/CELEX/MRC norms, maximal LMEMs, and OSF preregistration while treating list effects, SAT, spillover, and N400/P600 over-interpretation as first-class failure modes.

Expert-thinking profile for Psychophysicist (laboratory / psychophysics & perception): Reasons from psychometric functions, staircase/MLE threshold procedures, signal- detection theory, and calibrated display/audio transducers while treating timing jitter, adaptation, and criterion/sensitivity conflation as first-class failure modes.

Expert-thinking profile for Public Health Scientist (population health / surveillance / program evaluation / policy): Reasons from the 10 Essential Public Health Services, epidemiologic triad, and SDOH; runs outbreak field investigations, NSSP syndromic and NNDSS surveillance, BRFSS/WONDER complex-survey analysis, CDC Framework and RE-AIM program evaluation, PAF/PIF policy quantification, and Kass ethics review.

Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies. Triggers on "pubmed", "papers", "literature", "publications", "research on", "studies about".

Search PubMed for a gene name or disease term and generate a structured research briefing of the top recent English-language

PufferLib 2.x reinforcement learning workflows for the Dec 2024 API generation. Use when working with pufferlib>=2.0,<3.0, Puffer Ocean C environments, native PufferEnv/VecEnv-style vectorization, Gymnasium/PettingZoo compatibility wrappers, asynchronous sampling, or v2 training/evaluation migration from the deprecated v1 PuffeRL top-level API.

PufferLib 3.x reinforcement learning workflows for the Jun 2025 API generation. Use when working with pufferlib>=3.0,<4.0, the puffer CLI, pufferlib.pufferl training helpers, Ocean environments, PPO/PufferRL training, distributed torchrun runs, custom policies, vectorization, Gymnasium/PettingZoo wrappers, or migration from deprecated v1/v2 PufferLib code.

Expert-thinking profile for Pure Mathematician (proof-theoretic / theorem-proof / formal verification (Lean 4/mathlib, Coq, Isabelle) / MSC-classified): Reasons from definitions, axioms, and proved theorems through lemma-ladder proof strategies, computer algebra (SageMath, GAP, Magma) and proof assistants (Lean 4/mathlib, Coq, Isabelle/HOL) checked against MathSciNet/zbMATH and OEIS, while treating hidden hypotheses, circular reasoning, unjustified w.l.o.g. steps, and...

从逆向走到可用利用 (Working Exploit) 的全链路工程化方法。 适用场景：拿到了二进制 + 漏洞点 + 目标环境，需要写出一个能稳定打通的 exploit（不是只能本地复现一下、远程一打就崩的脚本）。 覆盖三大方向：栈溢出 / 堆利用 / 内核 pwn。强调"CTF 本地通 → 真实远程稳定打通"的工程差距：libc 版本错配、堆喷射时序、SMEP/SMAP/KASLR、栈对齐、远程缓冲。 核心工具链：pwntools + GEF/pwndbg + ROPgadget/Ropper + one_gadget + libc-database + qemu-system 内核调试。 触发关键词：pwn、栈溢出、堆溢出、ROP、ret2libc、ret2csu、one_gadget、libc-database、堆利用、tcache、fastbin、unsorted bin、kernel pwn、kROP、SMEP、SMAP、KASLR、modprobe_path、pwntools、GEF、pwndbg。

Python genomic interval arithmetic with BEDTools, complementing pysam, polars, and query for downstream tables. Use when intersecting, merging, subtracting, shuffling, finding closest features, computing coverage, or converting BED, GFF, GTF, VCF, BAM, and pandas DataFrames into interval operations.

Fast Python I/O for BigWig (continuous genome signal) and BigBed (interval annotation) files via libBigWig. Use for random-access signal queries at specific genomic coordinates (bw.values, bw.stats), computing per-region summary statistics (mean/max/coverage) over a BED file of regions, writing custom BigWig tracks from numpy arrays, and loading ChIP-seq/ATAC-seq/RNA-seq/methylation coverage tracks (e.g. produced by deeptools bamCoverage) into pandas/numpy for downstream analysis or ML featur...

Extend Pydantic AI agents with batteries-included capabilities from pydantic-ai-harness -- Code Mode (collapse many tool calls into one sandboxed Python execution), a filesystem and shell, sub-agents, planning, context compaction, and more. Use when the user mentions pydantic-ai-harness, CodeMode, Monty, code mode, or tool sandboxing, when they want first-party filesystem/shell/sub-agent/planning/compaction capabilities for a Pydantic AI agent, when they want an agent to run agent-written Pyt...

Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, ...

Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models (Transformer, RETAIN, GAMENet, SafeDrug, MICRON, StageNet, AdaCare, CNN/RNN/MLP), training with the PyHealth Trainer, computing clinical metrics, and using medical code utilities (ICD/ATC/NDC/RxNor...

Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand interactions. Do not use for docking, molecular dynamics, or sequence-only analysis.

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Continuously profile applications with Grafana Pyroscope and read the result as flame graphs. Covers three instrumentation paths — language SDK push (Go / Java / Python / Ruby / Node / .NET / Rust), Alloy eBPF auto-instrumentation (no code change, requires kernel 5.8+ with BTF), and SDK → Alloy receiver — plus ProfileQL queries, profile types (CPU / memory / allocations / goroutines / mutex), Grafana Cloud Profiles endpoint, and Span Profiles trace-to-profile linking. Use when adding profilin...

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

Testing Python code with pytest — fixtures, parametrization, markers, mocking, coverage, and configuration. Use when writing or running Python tests, setting up a test suite, debugging failing tests, adding fixtures or parametrized cases, measuring coverage, or configuring pytest in pyproject.toml. Pairs with test-driven-development for the workflow/methodology.

Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.

Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.

IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.

Expert-thinking profile for Quality / Six Sigma Engineer (DMAIC/DMADV / SPC & capability / measurement systems analysis / APQP-PPAP automotive / ISO 9001 auditing): Reasons from process variation, defect operational definitions, and customer-critical characteristics through Shewhart control charts, Gage R&R (%GRR, ndc), Cp/Cpk and Pp/Ppk capability, DMAIC tollgates, and AIAG PPAP/PFMEA in Minitab or JMP while treating Cpk on unstable processes, attribute data forced as normal...

Expert-thinking profile for Quantitative Biologist (computational / live-imaging / dynamical systems biology): Reasons from SBML/PEtab ODE models, structural and profile-likelihood identifiability, Bayesian inference (Stan/PyMC/AMICI), and live- cell pipelines (Cellpose/TrackMate/PhotoFiTT, REMBI); treats sloppiness, phototoxicity, and segmentation-tracking artifacts as first-class failure modes.

Expert-thinking profile for Quantum Chemist (computational / ab initio electronic structure theory): Reasons from the Schrödinger equation through HF, MP2/CCSD(T)/CBS, and multireference (CASSCF/CASPT2); uses ORCA/Psi4/Gaussian with GMTKN55/WTMAD-4 validation, T1/D1 diagnostics, Helgaker CBS extrapolation, and BSSE/spin-contamination checks while treating SCF near-degeneracy, intruder states, and global-vs-local...

Expert-thinking profile for Quantum Computing Scientist (experimental / computational / NISQ hardware & fault tolerance): Reasons from qubits as noisy open systems through T1/T2, gate fidelity, RB/GST/XEB, and quantum volume to surface-code QEC; compiles with Qiskit/Cirq, applies ZNE/PEC/readout mitigation, and treats crosstalk, transpilation depth, and calibration drift as first-class failure modes.

Expert-thinking profile for Quantum Information Scientist (theoretical / experimental QIS): Reasons from qubits as open systems, gate fidelities, and error correction while treating crosstalk and calibration drift as first-class failure modes.

Expert-thinking profile for Quantum Optics Scientist (optical bench / single-photon & squeezed-light / cavity QED / correlation & homodyne metrology): Reasons from field quadratures, atom-photon coupling (g, κ, γ), and heralding efficiency budgets through g⁽²⁾ Hanbury Brown-Twiss measurement, balanced homodyne tomography, HOM interference, and SNSPD/APD detector calibration while treating afterpulsing-faked antibunching, LO phase drift erasing squeezing, accidentals...

Expert-thinking profile for Quantum Physicist (theory / quantum information / open- system dynamics / device benchmarking / multi-platform hardware (superconducting, trapped-ion...): Reasons from Hilbert-space density operators, commutation relations, and Lindblad open-system dynamics through randomized benchmarking, gate-set and process tomography, Bell-CHSH tests, and Stim/PyMatching surface-code decoding while treating crosstalk, leakage, calibration drift, and measurement backaction as...

Expert-thinking profile for Quaternary Scientist (field geochronology / glacial geomorphology / multi-proxy paleoclimate / ice-core & tephra correlation): Reasons from dated landform-sediment-proxy associations, multi-method chronology, and ice-age cyclicity (MIS, orbital forcing) through radiocarbon/OSL/cosmogenic dating, Bayesian age models (OxCal, Bacon, IntCal20), tephrochronology, and GIA models while treating uncalibrated 14C years, incomplete OSL bleaching...

Query AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".

Query ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".

Query Ensembl for genomic data. Use when user asks about gene coordinates, genomic sequences, variants, gene structure, exons, transcripts, or species comparison. Triggers on "ensembl", "gene coordinates", "genomic location", "exon", "transcript", "variant location", "rsid", "rs number".

Query NCBI GEO for gene expression datasets. Use when user asks about RNA-seq datasets, microarray data, expression data, GEO accessions, or finding public datasets. Triggers on "geo", "gene expression omnibus", "expression dataset", "RNA-seq dataset", "microarray dataset", "GSE", "GDS".

Query KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Triggers on "kegg", "pathway", "metabolic pathway", "signaling pathway", "pathway genes".

Query STRING for protein-protein interactions. Use when user asks about protein interactions, interaction networks, binding partners, or interactome. Triggers on "string", "protein interaction", "interaction network", "binding partners", "interactome", "PPI".

Query UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".

Run SQL queries against the attached DuckDB database or ad-hoc against files. Accepts raw SQL or natural language questions. Uses DuckDB Friendly SQL idioms.

Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.

Use this skill whenever the user wants to analyze binaries with radare2/r2 from the command line, including reverse engineering, disassembly, function analysis, strings/import inspection, patching, binary diffing, hex inspection, or r2 scripting. Also use it when the user mentions PE/ELF/Mach-O/DEX/WASM files together with CLI analysis, `rabin2`, `rasm2`, `radiff2`, `r2pipe`, or asks for radare2 command help on Windows/Linux/macOS.

Expert-thinking profile for Radiation Oncology Physicist (clinical / research): Reasons from absorbed dose, fluence, beam geometry, and constraint-driven plan quality through TG-51/TRS-398 reference dosimetry, TPS engines (AAA, Acuros XB, Monte Carlo), DVH metrics, and gamma-based patient-specific QA while treating stale CT-to-density tables, couch-shift sign errors, MLC leaf-bank swaps, and...

Expert-thinking profile for Radio Astronomer (interferometry / uv-plane imaging / spectral-line & polarization / time-domain (pulsars, FRBs)): Expert profile for radio astronomer — see AGENTS.md for field-specific methods and failure modes.

Use for authorized RF/SDR security research including signal identification, replay feasibility study in shielded labs, and wireless protocol analysis outside classic Wi-Fi.

Expert-thinking profile for Radiochemist (tracer synthesis / radiopharmaceutical QC / cyclotron-generator production / dosimetry / GMP release (USP <823>, FDA 21 CFR 212)): Reasons from radionuclide half-life, specific activity, radiochemical purity, and dosimetry through analytical/prep HPLC with radiodetector, iTLC, HPGe γ-spectroscopy, OLINDA/MIRD, and USP <823>/EANM release specs while treating defluorination, transchelation of ⁶⁸Ga/⁸⁹Zr, ⁹⁹ᵐTc colloid and ⁶⁸Ge breakthrough as...