Claude Skills by stanfish06

Neo4j Visualization Library (NVL) — framework-agnostic graph rendering for the browser.

Diagnoses and fixes slow Neo4j Cypher queries by reading execution plans, identifying

Programmatic security management in Neo4j — RBAC/ABAC, user lifecycle (CREATE/ALTER/DROP USER),

Run Neo4j Graph Analytics algorithms (PageRank, Louvain, WCC, Dijkstra, KNN,

Use when reading from or writing to Neo4j with Apache Spark or Databricks using the

Use when building Spring Boot applications with Neo4j using Spring Data Neo4j (SDN 7.x/8.x) —

Create and manage Neo4j vector indexes, run vector similarity search (ANN/kNN),

Guide for using the Netlify CLI and deploying sites. Use when installing the CLI, linking sites, deploying (Git-based or manual), managing environment variables, or running local development. Covers netlify dev, netlify deploy, Git vs non-Git workflows, and environment variable management.

Use when the task involves authentication, user signups, logins, password recovery, OAuth providers, role-based access control, or protecting routes and functions. Use `@netlify/identity`. Never use `netlify-identity-widget` or `gotrue-js` — they are deprecated.

Expert-thinking profile for Network Engineer (operations / design — campus, WAN, datacenter fabric): Reasons from OSI layering, control vs. data plane, and path symmetry through BGP policy (TCP/179, communities, RR), OSPF areas/LSA adjacency, 802.1Q VLAN/trunk design, spine-leaf Clos/VXLAN-EVPN fabrics, and L1→L7 troubleshooting while treating asymmetric routing, MTU black holes, native-VLAN mismatch, and BGP...

Expert-thinking profile for Network Scientist (graph theory / community detection / generative models (SBM, ERGM) / network dynamics / null-model inference): Reasons from adjacency structure, generative models, and null hypotheses through configuration- model and SBM/ERGM nulls, CSN power-law fitting with log-normal Vuong tests, and multi-algorithm community detection (Louvain, Leiden, Infomap, graph-tool) while treating artifactual scale-free tails from correlation...

Expert-thinking profile for Neuroanatomist (wet-lab histology / tract tracing + computational atlas registration): Stereotaxic targeting and skull leveling, Paxinos/Allen atlases, anterograde/retrograde tracing, Nissl vs IHC, BrainGlobe/QuickNII registration, and injection-spread or fibers-of-passage artifacts.

Expert-thinking profile for Neuroendocrinologist (wet-lab / in vivo physiology + translational neuroendocrine): Reasons from hypothalamic–pituitary portal axes (HPA, HPG, HPT), KNDy/GnRH pulsatility, SCN circadian gating, and SON/PVN neuropeptide release; uses HypoMap/HYPOMAP, stereotaxics with opto/chemogenetics, validated ELISA/RIA/FCM and LC-MS/MS, CoAL/CAR reporting, while treating bleed-stress corticosterone, pulse...

Expert-thinking profile for Neuroengineer (wet-lab / neural interfaces / chronic electrophysiology / translational regulatory): Reasons from electrode–electrolyte charge-density limits and foreign-body gliosis through Utah/Neuropixels chronic recording, EIS impedance spectroscopy, Kilosort3/MountainSort validation, FDA IDE pathways, and explant histology (GFAP/Iba1) while treating impedance drift, unvalidated auto-sort inflation, and...

Expert-thinking profile for Neuroimaging Scientist (clinical / research): Reasons from k-space acquisition physics, BOLD hemodynamics, and per-voxel statistical models through fMRIPrep/QSIPrep BIDS pipelines, FSL/SPM/nilearn analysis, neuroCombat harmonization, and TFCE/permutation inference while treating head motion, partial- volume and reference-region errors in PET, global-signal...

Expert-thinking profile for Neuroinformatician (data standards / BIDS-NWB / reproducible pipelines / archive federation (DANDI, OpenNeuro) / atlas registration): Reasons from FAIR schema, provenance, and pinned software environments through BIDS, NWB, ontologies, versioned Snakemake/Nextflow pipelines, and bids- validator/nwbinspector checks while treating silent metadata failures like wrong NWB units, colliding multi-site subject IDs, unsynced event onsets, and atlas-version...

Expert-thinking profile for Neurologist (clinical / research): Reasons from anatomic localization, time course, and phenomenology through NIHSS/ASPECTS stroke triage, ILAE 2025 seizure classification, McDonald 2017 and AQP4/MOG cell-based assays, EEG and EMG/NCS, and SNOOP4 red flags, while treating CT-negative early ischemia, ~50%-sensitive routine EEG, MS-versus-NMOSD/MOGAD...

Expert-thinking profile for Neuropharmacologist (wet-lab / in vitro pharmacology + in vivo behavioral PK/PD + translational imaging): Reasons from Kp,uu,brain and receptor occupancy, radioligand binding with depletion-aware Ki, biased GPCR/allosteric signaling, PDSP/GtoPdb panels, microdialysis and PET RO, and operant self- administration while treating Cheng-Prusoff error, P-gp efflux, FST validity limits, and patch-clamp Rs artifacts as first-class...

Expert-thinking profile for Neurophysiologist (wet-lab / intracellular & extracellular electrophysiology + spike sorting): Reasons from membrane biophysics, patch clamp Rs/seal quality, Neuropixels AP/LF streams, LFP referencing and spike contamination, Kilosort4/Phy curation, and stimulation-artifact suppression.

Expert-thinking profile for Neuroscientist (integrative / multiscale circuits / in vivo electrophysiology + optogenetics / translational (ARRIVE, BIDS/NWB)): Expert profile for neuroscientist — see AGENTS.md for field-specific methods and failure modes.

Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or ...

Next.js App Router expert guidance. Use when building, debugging, or architecting Next.js applications — routing, Server Components, Server Actions, Cache Components, layouts, middleware/proxy, data fetching, rendering strategies, and deployment on Vercel.

Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt.

Route BCL, FASTQ, BAM/CRAM, count-matrix, or VCF sequencing requests to the right public NGS analysis skill and ask only the missing assay-specific setup questions.

Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows.

Validate Illumina BCL run folders and sample sheets, plan demultiplexing, review index/UMI/lane choices, run BCL-to-FASTQ conversion, and interpret demux metrics while surfacing license/download boundaries.

Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.

Run or plan bulk RNA-seq differential-expression analysis from count matrices with replicate, design formula, contrast, batch, normalization, QC plot, and result-table checks.

Dispatch bulk RNA-seq requests to FASTQ-to-count QC or count-matrix differential-expression skills using nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC, and R/Bioconductor workflows.

Run or plan ChIP-seq, CUT&RUN, or CUT&Tag QC, control handling, spike-in, peak calling, broad-vs-narrow target selection, replicate, bigWig, and differential binding workflows.

The core command-line NGS workhorses for going from raw reads to variants — bwa-mem2/minimap2/bowtie2 (alignment), samtools (BAM sort/index/stats/view), bcftools (VCF call/filter/normalize/query), GATK4 (BQSR, HaplotypeCaller, best practices), and plink2 (genotype QC, PCA, GWAS). Use for read alignment, BAM/CRAM manipulation, variant calling and VCF wrangling on the command line. For Python-native BAM/VCF access use pysam; for full managed pipelines use the nf-core wrappers.

Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks.

Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks.

Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.

Dispatch WGS, WES, or targeted DNA variant requests to germline, somatic, or UMI-panel skills, then plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows.

Dispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows.

Validate FASTQ inputs, run local FastQC/MultiQC QC, interpret QC signals, and optionally execute fastp or Cutadapt trimming branches without overwriting raw reads.

Check whether public NGS tools and packages already exist before downloading, installing, or running a sequencing pipeline.

Route single-cell or single-nucleus RNA-seq FASTQs to public count-generation workflows and defer post-count matrix QC, annotation, clustering, and UMAP analysis to the embedded scrna-seq-qc skill.

Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.

Choose and apply automatic layout strategies for node-link diagrams and connected-node visuals. Use when the user asks how to auto-arrange nodes, reduce line crossings, route edges, avoid overlaps, stabilize layout, or choose graph-layout algorithms for network diagrams, dependency graphs, database schema diagrams, ERDs, state machines, decision trees, flow diagrams, box-and-line editors, or other line-connected nodes.

Expert-thinking profile for Nonlinear Dynamics & Chaos Scientist (theoretical / computational / experimental dynamical systems): Reasons from flows, maps, bifurcations, and invariant sets; continues with MatCont/AUTO/COCO, validates chaos with IAAFT surrogates and embedding convergence, and treats spurious Lyapunov exponents, stiff integrator artifacts, and colored-noise confounds as first-class failure modes.

Capture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking.

Prepare meeting materials with Notion context and Codex research; use when gathering context, drafting agendas/pre-reads, and tailoring materials to attendees.

Research across Notion and synthesize into structured documentation; use when gathering info from multiple Notion sources to produce briefs, comparisons, or reports with citations.

Turn Notion specs into implementation plans, tasks, and progress tracking; use when implementing PRDs/feature specs and creating Notion plans + tasks from them.

Expert-thinking profile for Nuclear Chemist (clinical / research): Reasons from decay- corrected activity ledgers, decay modes and cross sections, and ALARA dose control through Bateman/ORIGEN modeling, extraction-chromatography separations (TRU/Sr/TEVA resins), and HPGe/alpha/LSC spectroscopy while treating daughter ingrowth, generator breakthrough, spectral pile-up and sum peaks...

Expert-thinking profile for Nuclear Engineer (reactor physics / thermal hydraulics / safety & licensing): Reasons from k_eff, DNBR/CHF margins, xenon transients, and defense-in-depth; couples SCALE/MCNP, PARCS, TRACE/RELAP, and MELCOR to 10 CFR and PRA; treats nodalization, nuclear-data, and CHF-correlation uncertainties as first- class failure modes.

Expert-thinking profile for Nuclear Medicine Scientist (clinical / research): Reasons from radioactive decay, biodistribution kinetics, and detector physics through HPLC/TLC radiochemical-purity QC, dose-calibrator cross-calibration, OSEM/PSF reconstruction, and MIRD/OLINDA dosimetry while treating partial-volume effects, attenuation mismatch, 68Ge breakthrough and other radionuclidic impurity...

Expert-thinking profile for Nuclear Physicist (experimental / theoretical / nuclear data & applications): Reasons from shell and collective structure, reaction mechanisms, and ENDF/EXFOR data; matches FRIB–CEBAF–RHIC science to R-matrix, Hauser- Feshbach, chiral ab initio, and GEANT4 tools; treats dead time, normalization, and evaluation covariances as first-class failure modes.