Claude Skills by stanfish06

Expert-thinking profile for Clinical Microbiologist (clinical diagnostic microbiology / bacteriology service line): Reasons from blood-culture volume and contamination criteria, staged Gram–ID–AST reporting, MALDI-TOF/VITEK/Phoenix and EUCAST RAST, CLSI M100 vs EUCAST breakpoint discipline, WHONET antibiograms, and NHSN MDRO alerts—treating contaminant vs pathogen and VME/ME as first-class failure modes.

Expert-thinking profile for Clinical Pharmacologist (clinical / translational pharmacometrics & regulatory PK/PD): Reasons from exposure–response, popPK (NONMEM), DDI (ICH M12), TDM/NTI windows, and renal/hepatic/allometric adjustment; aligns dose finding with ICH E4 and FDA clinical pharmacology labeling.

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.

Find clinical trials for a gene, variant, or condition from ClinicalTrials.gov + EUCTR, with FHIR R4 output

Expert-thinking profile for Clinical Trial Scientist (clinical operations / GCP trials): Reasons from protocol SAPs, ICH-GCP, randomization/blinding, and CDISC SDTM while treating protocol deviations and immortal time as first-class failure modes.

Classify germline variants from VCF/BCF files according to the ACMG/AMP 2015 28-criteria evidence framework and

Submit compact ClinicalTrials.gov API v2 requests for study search, metadata, enums, search areas, and field statistics. Use when a user wants concise ClinicalTrials.gov summaries

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug

Submit compact ClinVar Clinical Tables and NCBI Variation requests for search, VCV, RCV, SCV, and RefSNP lookups. Use when a user wants variant-level summaries or identifier mapping

Use for authorized cloud, container, and Kubernetes security assessment including metadata SSRF, IAM misconfig, container escape paths, and cluster RBAC review.

Create, restyle, compose, and export compact publication-ready scientific figures with the Python cnsplots library or its source-derived Cell/Nature/Science plotting patterns. Use for cnsplots code, journal-sized Matplotlib/Seaborn figures, editable vector output, semantic scientific color systems, statistical annotations, dense rasterized layers, and mixed-size multi-panel layouts with precise text, artist, padding, margin, and panel-label control. Pair with nature-figure or scientific-visua...

Expert-thinking profile for Coastal Engineer (field / computational / coastal structures & flood risk): Reasons from joint-probability surge and waves through CEM/EurOtop runup-overtopping, Van der Meer/Rock Manual armor, CERC–Van Rijn sediment budgets, and CMS/XBeach/ADCIRC–SWAN model selection while treating toe scour, armor breakage, datum mismatch (BFE vs MHHW), and downdrift impacts as first-class failure modes.

Use for authorized source-code security review and SAST workflows including Semgrep, CodeQL patterns, dangerous API hunting, and fix verification.

Conducts multi-axis code review. Use before merging any change. Use when reviewing code written by yourself, another agent, or a human. Use when you need to assess code quality across multiple dimensions before it enters the main branch.

Review the changes since a fixed point (commit, branch, tag, or merge-base) along two axes: Standards (does the code follow this repo's documented coding standards?) and Spec (does the code match what the originating issue/spec asked for?). Runs both reviews in parallel sub-agents and reports them side by side. Use when the user wants to review a branch, a PR, work-in-progress changes, or asks to \"review since X\".

Generates and writes new unit tests for any programming language — scaffolds test projects and configures coverage tooling (coverlet, pytest-cov, @vitest/coverage-v8) as part of test generation. Use when asked to generate tests, generate pytest tests, generate Vitest tests, write unit tests, add tests, improve coverage, comprehensive tests, or scaffold a new test project or suite for an app, service, library, REST API, blueprint, or package — including project-wide, multi-file test generation...

Provides file paths to language-specific extension files for the code-testing pipeline. Call this skill to discover available extension guidance files (e.g., dotnet.md for .NET, cpp.md for C++). Do not use directly — invoked by code-testing agents and skills that need language-specific references.

Expert-thinking profile for Cognitive Neuroscientist (human experimental / fMRI–EEG–MEG / behavioral cognitive neuroscience): Reasons from latent constructs through converging behavior, fMRI/M/EEG, TMS, and lesion evidence; designs factorial and dissociation contrasts, fMRIPrep/GLMsingle/MNE pipelines, MVPA/RSA, and COBIDAS reporting while treating pure insertion, reverse inference, motion confounds, and in- sample decoding as first-class...

Expert-thinking profile for Cognitive Scientist (behavioral experiments / computational modeling (DDM, ACT-R, Bayesian) / Marr levels / strong inference / preregistration): Reasons from Marr's levels of analysis, latent processes behind RT and accuracy, and strong inference through PsychoPy paradigms, signal-detection d-prime/criterion, sequential-sampling and ACT-R models, and crossed mixed-effects designs while treating speed-accuracy tradeoffs, criterion shifts, item confounds, and...

Fast AlphaFold2/ColabFold protein structure prediction. Use when predicting monomer or multimer protein structures from FASTA, running colabfold_batch, interpreting pLDDT/PAE, or preparing predicted structures for docking, molecular dynamics, or publication figures.

Expert-thinking profile for Colloid Chemist (wet-lab / dispersion formulation / DLS- zeta-SAXS characterization / interfacial rheology / nano & emulsion stability (ISO DLS, REACH)): Reasons from interfacial thermodynamics, DLVO and non-DLVO forces, zeta- potential, and rheology through orthogonal characterization (DLS, NTA, cryo-TEM, SAXS/SANS S(Q), pendant-drop tensiometry) and accelerated-aging stability tests while treating coalescence, Ostwald ripening, creaming, and flocculation crossing...

Expert-thinking profile for Combinatorialist (theoretical / computational discrete mathematics): Reasons from labelled vs unlabelled enumeration, EGF/OGF and species, bijective and probabilistic proofs, Turán/Ramsey/extremal bounds, and BIBD/OA design parameters through SageMath/GAP/nauty, OEIS, House of Graphs, and Colbourn–Dinitz tables while treating isomorphism double-counting, parity barriers, and OEIS false...

Expert-thinking profile for Combustion Engineer (experimental / combustion & propulsion): Reasons from stoichiometry, flame stability, emissions, and CFD-reacted flows while treating blow-off, flashback, and soot formation as first-class failure modes.

Expert-thinking profile for Communications Engineer (digital / wireless & wired PHY / link & system simulation): Reasons from Shannon capacity and matched-filter detection through OFDM/MIMO, 3GPP NR LDPC/polar (TS 38.212), TR 38.901 link budgets, Keysight 89600 VSA EVM, ns-3 SLS, and berconfint Monte Carlo while treating CFO/IQ/phase-noise coupling, pre- vs post-FEC BER, and AWGN-only optimism as first-class failure modes.

Expert-thinking profile for Community Ecologist (field / experimental / multivariate community assembly): Reasons from Vellend's four processes and Chesson stabilizing/equalizing coexistence through PERMANOVA/betadisper, betapart turnover–nestedness, Gotelli SIM9/C-score null models, and vegan/entropart/picante pipelines while treating compositional closure, dispersion heterogeneity, and pseudoreplicated quadrats as...

Build an industry comp sheet Excel model with deep operational KPIs

Expert-thinking profile for Comparative Medicine Researcher (clinical / research): Reasons from species biology, translational validity, and the 3Rs through model- validity frameworks, IACUC protocols, ARRIVE 2.0 reporting, and FELASA/AALAS health surveillance while treating substrain drift, subclinical colony infection (murine norovirus, pinworm, Mycoplasma), analgesia-pathway confounds, and...

Expert-thinking profile for Comparative Physiologist (integrative / respirometry / field & lab comparative biology): Reason from the Krogh principle and oxygen cascade through intermittent-flow respirometry, SMR/BMR/MMR scope, Q10 and heterothermy, hemoglobin P50, allometry and PGLS, while treating chamber drift, activity artifacts, phylogenetic pseudoreplication, and SMR definition mismatch as first-class failure modes.

End-to-end Proteina-Complexa design pipeline driver. Use when the user wants to "design a binder", "design binders for X", "run complexa design", "de novo binder", "PDL1 binder", "TrkA binder", "design proteins for target", "protein binder design", "ligand binder", "design a small-molecule binder", "ATP-binding protein", "AME motif scaffolding", "scaffold a motif near a ligand", "motif + ligand design", "enzyme scaffolding", "flow matching protein design", "beam-search binder", "FK steering",...

Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use when the user wants to "evaluate PDB files", "re-fold these designs", "compute interface pAE", "compute i_pLDDT for a folder", "run AF2 / RF3 / ESMFold on my designs", "score binder candidates", "designability of this folder", "scRMSD for designs", "motif RMSD for these PDBs", "complexa analysis", "complexa evaluate from a PDB directory", "evaluate from pdb dir", or to score third-party outputs (BindCraft, AlphaPro...

First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skill whenever the user says "set up complexa", "install complexa", "configure my environment file", "first-time setup", "what models do I have installed", "what's in my environment file", "download model weights", "download Complexa / AF2 / RF3 / ProteinMPNN / LigandMPNN / ESM2 / ESMFold checkpoints", "preflight my GPU", "verify environment", "complexa init", "complexa download", ...

Use when launching Proteina-Complexa jobs on a remote SLURM cluster, including binder search, LaProteina design or training, multi-node runs, sbatch, remote GPU jobs, Hydra sweeps, rsync-to-cluster workflows, `--on-cluster`, grizzly or polar, and singleton requeue chains.

Use this skill whenever the user wants to run a parameter sweep over a Proteina-Complexa design pipeline — cartesian-product hyperparameter scans, Pareto search over generation/reward/evaluation knobs, or any "compare configurations" workflow. Trigger phrases include "sweep beam width", "sweep nsteps", "hyperparameter sweep", "parameter scan", "scan beam_width and temperature", "compare configurations", "find the best generation params", "what's the optimal nsteps", "Pareto search for binder ...

Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME / enzyme scaffolding. Triggers include "add a target", "define a new target for binder design", "register a hotspot", "set up a PDL1 binder target", "ligand binder pocket", "SMILES target", "AME task", "enzyme motif", "M0024_1nzy", "complexa target add", "complexa target show", "configure target X", "what ta...

Expert-thinking profile for Composites Engineer (design / manufacturing / test / certification): Reasons from CLT/ABD laminate mechanics, Halpin–Tsai micromechanics, and CMH-17/NCAMP allowables through autoclave/OOA/RTM process control, ASTM D30 mechanical qualification, ultrasonic C-scan and CAI damage tolerance while treating fiber waviness, void content, under-cure, and quasi-isotropic strength traps as...

Trading comparables analysis with peer multiples and implied valuation

Expert-thinking profile for Computational Chemist (computational / dry / quantum chemistry & molecular simulation): Reasons from Kohn–Sham DFT, def2/D4 functional selection, and conformer ensembles through VASP/Gaussian/ORCA, AMBER/GROMACS MD, CREST/CENSO sampling, ONIOM/QM/MM electrostatic embedding, GMTKN55 validation, and SCF convergence escalation while treating B3LYP/6-31G*, BSSE, link-atom artifacts, and force-field mismatch...

Expert-thinking profile for Computational Linguist (computational / corpus & annotation / parsing & semantics): Reasons from UD/PTB formalisms, validate.py/eval.py (LAS/MLAS/ELAS), and evalb .prm settings through Stanza/UDPipe pipelines, PropBank/FrameNet/AMR/UMR layers, IAA (κ, Krippendorff α), CONDA contamination checks, and ARR reproducibility while treating tokenizer mismatch, oracle inflation, train–test leakage, and...

Expert-thinking profile for Computational Neuroscientist (computational / dry / modeling & neural data analysis): Reasons from encoding/decoding, GLM/LNP spike-train likelihood, mean-field E-I balance, and neural manifolds through NEST/Brian/NEURON/BMTK, GPFA/LFADS, Brain-Score alignment, and trained-RNN reverse engineering while treating spike-sorting contamination, model non-identifiability, nested-CV leakage, and...

Expert-thinking profile for Computational Physicist (computational / dry / HPC simulation): Reasons from governing equations, discretization, and HPC scaling through code/solution verification, DFT, MD, Monte Carlo, and FEM/FVM workflows (VASP, LAMMPS, COMSOL, OpenFOAM, QE).

Expert-thinking profile for Computational Scientist (computational / dry / simulation, UQ, and reproducible workflows): Reasons from Roache code/solution verification and ASME V&V 10/20/40 credibility through MMS/GCI, UQ ensembles, and Snakemake/Nextflow/CWL pipelines with conda-lock/Apptainer provenance while treating environment drift, workflow cache staleness, and validation-vs-calibration conflation as first-class failure modes.

Expert-thinking profile for Computational Social Scientist (digital-trace / network science / text-as-data / causal inference (DiD, IV, RDD) / field & survey experiments): Reasons from social mechanisms, measurement validity, and sampling frames through DAGs, fixed-effects and IV/DiD/RDD designs, ERGM/SAOM network models, and human-audited text classifiers while treating unobserved homophily, network interference and SUTVA violations, platform-driven selection, bot contamination, and...

Expert-thinking profile for Computer Architecture Researcher (computational / simulation / architecture evaluation): Reasons from ISA semantics, AMAT/CPI, MESI coherence, and branch prediction through gem5/SPEC/MLPerf evaluation, Amdahl and roofline discipline, TPU/GPU dataflow accelerators, DVFS/EDP, and Spectre/Meltdown mitigation overhead at ISCA/MICRO/HPCA rigor.

Expert-thinking profile for Computer Graphics Researcher (computational / offline & real-time rendering / neural graphics): Reasons from the rendering equation and Monte Carlo MIS through Mitsuba/Embree/Blender, Vulkan/DXR real-time stacks, BRDF/BSDF validation, SIGGRAPH/EG reporting, NeRF/3DGS pitfalls, OCIO color pipelines, OIDN denoising bias, and mesh/UV artifact diagnosis while treating train–display gamma errors and unequal-spp...

Expert-thinking profile for Computer Hardware Engineer (RTL / microarchitecture / physical design / verification): Reasons from CPI/AMAT and MESI/MOESI coherence through SystemVerilog RTL, PrimeTime/Design Compiler/Innovus signoff, PCIe LTSSM/TLP, SVA formal, and clock-gating power while treating CDC metastability, false-path abuse, X-optimism, and coherency traffic as first-class failure modes.

Expert-thinking profile for Computer Scientist (theory + systems / algorithms & complexity / distributed data / formal methods (TLA+, Coq) / security (STRIDE, OWASP ASVS)): Reasons from computational models, abstraction contracts, invariants, and measurable complexity through CLRS-grade algorithm analysis, impossibility results (FLP, CAP, NP-hardness), property-based and chaos testing, and formal tools (TLA+, Coq, Z3) while treating partial failure, race conditions, label leakage, and...

Expert-thinking profile for Computer Security Researcher (dry-computational / vulnerability, protocol, and empirical security research): Reasons from explicit threat models and CIA/STRIDE through AFL++/libFuzzer triage, ASan/KASAN oracles, ProVerif/Tamarin proofs, CVE/CWE/CAPEC taxonomies, CyberGym dual-execution benchmarks, Menlo/CVD ethics, and USENIX open-science artifact norms.

Expert-thinking profile for Computer Vision Scientist (computational / detection, segmentation, pose & 3D vision): Reasons from calibration, augmentations, and domain shift through COCO/LVIS/KITTI metrics (mAP, IoU, mask AP), convnets vs ViTs, OpenCV/PyTorch/MMDetection stacks, COLMAP/NeRF 3D, and CVPR/ICCV/ECCV eval discipline while treating label noise, train-test leakage, and resolution mismatch as first-class failure modes.

Reproducible Conda/Mamba/micromamba environment management for bioinformatics, with correct Bioconda channel setup, environment files, version pinning, and lockfiles. Use when installing bioinformatics tools (samtools, bwa, GATK, STAR, etc.), creating or sharing reproducible environments, resolving "PackagesNotFound"/slow-solver issues, or when a project has an environment.yml. For pure-Python projects without compiled bio tools, prefer uv (see modern-python).

Expert-thinking profile for Condensed Matter Physicist (experimental / computational / quantum materials): Reasons from Bloch bands, quasiparticles, and symmetry through ARPES/STM/neutron/transport workflows, VASP/QE/Wannier90/DMFT, and Materials Project/ICSD/MPDS while treating matrix-element artifacts, Mott vs. DFT gaps, pseudogap vs. SC gap, and Planckian bad-metal transport as first-class failure modes.