Claude Skills by stanfish06

Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.

Structures Benchmark and Evaluation papers using the five-pillar framework (Research Gap, Construction Pipeline, Evaluation Framework, Empirical Findings, optional Companion Method). Returns a completeness audit, a six-part Introduction logic chain, a Section 2-7 skeleton, and a pre-submission checklist. Use when writing a benchmark paper, structuring a benchmark paper, checking whether a benchmark idea is substantive, drafting a benchmark Introduction, or planning the data-construction pipel...

Auto-instrument an application's HTTP / gRPC / DB traffic with Grafana Beyla eBPF — no code changes, no SDK, no restart. Covers requirements (Linux 5.8+ with BTF, CAP_SYS_ADMIN, host PID), language matrix (Go / Java / Python / Ruby / Node / .NET / Rust / C++ / PHP), Docker + Helm + DaemonSet install, port- / process- / Kubernetes-metadata discovery, OTLP traces + Prometheus metrics export, routes decorator (cardinality control), trace sampling, and Grafana Cloud via Alloy. Use when adding obs...

Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.

跨版本符号迁移与二进制差分。当你有旧版本的符号/逆向结果，需要快速迁移到新版本时使用。 适用场景：内核缺 PDB 用旧版符号推导、程序更新后批量迁移函数名、应用更新后快速定位新偏移。 核心方法：用 LLM 做结构化差异比对，程序化输入输出，成本极低（200 函数 ~1 元）。 触发关键词：符号迁移、bindiff、跨版本、PDB 缺失、函数偏移迁移、symbol migration、binary diff、版本对比。

Submit compact BindingDB REST API requests for ligand-target binding lookups by PDB, UniProt, or similarity search. Use when a user wants concise BindingDB summaries; save raw payloads only on request.

Analyze MSBuild binary logs to diagnose build failures. USE FOR: build errors that are unclear from console output, diagnosing cascading failures across multi-project builds, tracing MSBuild target execution order, and generally any MSBuild build issues. Requires an existing .binlog file. DO NOT USE FOR: generating binlogs (use binlog-generation), non-MSBuild build systems.

Step 5 of the bio-manuscript pipeline: design the analysis-method system. Use when planning which analyses, tools, and biological validations support each figure and task, mapping analyses to BioClaw-compatible tools or fallbacks, and connecting analyses to figure panels.

Step 3 of the bio-manuscript pipeline: find and match public datasets to manuscript tasks. Use when extracting datasets from related papers or searching repositories (e.g. GEO), normalizing dataset metadata, and mapping datasets to the task system.

Step 6 of the bio-manuscript pipeline: design manuscript figures panel by panel. Use when planning figure logic, panel content, supplementary figures, and draft captions, keeping figure logic synchronized with manuscript claims.

Phase 2.6 of the bio-manuscript pipeline: human review checkpoint. Use when presenting a refined proposal to a human reviewer, collecting explicit feedback, recording approval or requested changes, and routing the workflow back to the correct phase.

Step 1 of the bio-manuscript pipeline: assess research-idea novelty. Use when expanding a topic into variants/synonyms, searching PubMed/bioRxiv/arXiv q-bio, de-duplicating related papers, assigning a novelty level, and suggesting how to sharpen or reposition the idea.

End-to-end bio-manuscript planning pipeline orchestrator: turn structured research input into a full manuscript plan. Use to run the multi-step workflow (innovation check, task/dataset/metric/analysis design, figure design, drafting, refinement) phase by phase using the sibling bio-* skills and bio-manuscript-common templates.

Refinement loop for the bio-manuscript pipeline: three-reviewer iterative optimization (editor, computational, biological). Use when reviewing a manuscript plan, producing structured review comments, revising round by round, and tracking score and revision history toward a target journal.

Step 7 of the bio-manuscript pipeline: draft the main manuscript text. Use when writing the Introduction, Results (around the figure logic), Discussion, and a Methods skeleton from the figure plan, metric system, and analysis system.

Step 4 of the bio-manuscript pipeline: design the evaluation-metric system. Use when extracting quantitative and qualitative metrics from literature or adjacent fields, organizing them into groups, and explaining what each metric measures and how to compute it.

Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis

Generate a presentation package from a finalized bio-manuscript proposal. Use when producing a 10-15 slide, Markdown-first presentation outline (group-meeting / 组会 style) from FINAL_PROPOSAL.md plus demo or validation results.

Step 2 of the bio-manuscript pipeline: design the task system. Use when identifying the dominant task taxonomy in a field and organizing it into a staged Level 1-4 difficulty ladder to prepare for downstream dataset and metric design.

Biology research tools reference. Always available inside agent containers.

Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant

Expert-thinking profile for Biochemist (wet-lab / biophysical characterization / metabolism): Reasons from thermodynamics, enzyme mechanisms, and binding energetics; designs orthogonal purification and assay readouts while controlling oxidation, aggregation, coupled assays, and activity-vs-abundance confounds.

Expert-thinking profile for Biogeochemist (field / lab / soil-sediment biogeochemistry / process modeling): Reasons from coupled C/N/P/S redox cycles through TEAP zonation, porewater Rhizon-peeper sampling, δ13C/δ15N/δ34S tracers, chamber and eddy-covariance fluxes, and Century/DayCent SOM modeling while treating porewater O2 contamination and nitrification-denitrification coupling errors as first-class failure modes.

Expert-thinking profile for Biogeographer (field / GIS / phylogenetics / spatial modeling): Reasons from Wallace's ecological vs historical split through GBIF occurrence curation, blockCV spatial cross-validation, MaxEnt/biomod2 SDMs with MESS extrapolation flags, BioGeoBEARS vicariance/dispersal tests, and phylogeographic coalescence while treating random-CV AUC inflation, background bias, and...

Expert-thinking profile for Bioinformatician (dry-lab / computational genomics): Reference-build discipline (GRCh38/GENCODE/Ensembl, MANE), batch-as-covariate DE (DESeq2/edgeR), index hopping/UDI, GATK/BQSR/PLINK GWAS multiplicity, nf-core reproducibility, and scRNA-seq ambient-RNA/doublet artifacts.

Expert-thinking profile for Bioinformatics Engineer (dry-lab / pipeline engineering / production genomics): Builds production genomics DAGs in Nextflow/nf-core, Snakemake, and WDL/Cromwell with digest-pinned containers, GIAB regression CI (nf-test, pytest), QC-gated MultiQC runbooks, and CLIA-grade provenance—distinct from analyst-focused bioinformatician DE/GWAS reasoning.

Expert-thinking profile for Biological Oceanographer (sea-going / plankton ecology / production & export rates / omics + microscopy / fisheries oceanography): Reasons from light-nutrient-grazing coupling, the microbial loop, and size-structured export through CTD/MOCNESS sampling, 14C and O2/Ar production with 234Th export flux, imaging and flow cytometry enumeration, and SILVA/PR2 metabarcoding while treating spatial patchiness, diel-migration tow aliasing, CDOM-biased...

Expert-thinking profile for Biomaterials Scientist (device R&D / implants, scaffolds, drug delivery / biocompatibility (ISO 10993) / degradation & leachables / regulatory (510(k), PMA, ISO...): Reasons from material-biology interfaces, degradation-product toxicity, and mechanical mismatch to host tissue through ISO 10993 biological evaluation plans, ISO 10993-12 extract conditions, GPC/ICP/SEM characterization, and sterilization validation while treating endotoxin contamination, pH shift from...

Expert-thinking profile for Biomedical Engineer (device R&D / implants / biomechanics / regulatory (510(k), ISO 10993)): Reasons from ISO 14971 risk management, ISO 10993 biocompatibility matrices, ASTM F/ISO 14242 mechanical and wear testing, and FDA 510(k) substantial equivalence; treats stress shielding, UHMWPE osteolysis, F2129 corrosion artifacts, and predicate/material mismatches as first-class failure modes.

Expert-thinking profile for Biomedical Imaging Scientist (clinical / research): Reasons from contrast mechanisms, the resolution-SNR-scan-time triangle, and measurement reliability through DICOM/BIDS pipelines, QIBA profiles, phantom QC (ACR, NEMA IQ, Catphan), and blinded central reads (RECIST, RANO, PERCIST) while treating motion, partial volume effects, and cross-scanner harmonization drift as...

Expert-thinking profile for Biophysical Chemist (wet-lab / biophysics / calorimetry & surface methods / single-molecule / binding thermodynamics & kinetics): Reasons from free energy landscapes, binding equilibria (K_d, ΔG = ΔH − TΔS), and probe–system coupling through ITC, SPR/BLI, smFRET, AUC, and global fitting (KinTek, SEDFIT) while treating probe perturbation, mass-transport-limited kon, aggregation-driven avidity, and two-state melting violations as first-class...

Expert-thinking profile for Biophysicist (single-molecule biophysics / force spectroscopy / electrophysiology / structural (cryo-EM, NMR) / MD simulation): Reasons from energy landscapes, kT-scale thermodynamics, conformational ensembles, and the equilibrium-versus-kinetics distinction through smFRET, optical/magnetic tweezers, patch clamp, cryo-EM, and MD with force-field validation while treating photobleaching and blinking, FRET crosstalk, tether and series-resistance...

Expert-thinking profile for Bioprocess Engineer (wet-lab / integrated biologics USP–DSP, scale-up & GMP validation): Reasons from QTPP–CPP–CQA QbD, CHO fed- batch/perfusion scale-up (P/V, kLa, mixing), platform mAb DSP (Protein A, low-pH viral hold, IEX polish, UF/DF), tech transfer and PPQ lifecycle; treats transport-limited scale-up, harvest fouling, on-column aggregation, SUB leachables, and arbitrary three- batch PPQ as...

Expert-thinking profile for Bioprocess Microbiologist (wet-lab / industrial microbial fermentation & GMP biomanufacturing): Reasons from kLa/OTR–OUR balance, fed-batch μ control, off-gas RQ, van't Riet scale-up, and contamination (phage, bioburden, adventitious agents); treats antifoam kLa penalty, exponential-feed open-loop risk, and SUB vs stainless transfer as first-class failure modes.

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

Expert-thinking profile for Biostatistician (clinical / computational / trial and omics biostatistics): Reasons from estimands, SAPs, and error budgets; aligns ICH E9(R1), CONSORT/STROBE, multiplicity, MMRM, Cox survival, causal DAGs, and GWAS FDR while treating immortal time, ICEs, and batch confounding as first-class failure modes.

Expert-thinking profile for Biosystems & Agricultural Process Engineer (postharvest / grain drying & storage / heat-mass transfer / ag bioprocessing / ASABE standards (D245.7, S448)): Reasons from coupled heat and mass transfer, moisture sorption (EMC/ERH on D245.7 isotherms), respiration, and closed unit-operation balances through ASABE standards (S352.2 oven moisture, S448 Page thin-layer kinetics, D272.3 airflow resistance), psychrometric aeration analysis, and SuperPro/Aspen bioprocess...

Boltz job status and result recovery. Use when listing jobs, checking progress, resuming downloads, recovering results, or downloading an existing job ID. Not for starting new jobs.

Boltz CLI setup and auth. Use when installing, updating, verifying, or authenticating `boltz-api`, or fixing missing CLI, PATH, sandbox, browser login, or auth errors.

Design new protein binders with Boltz. Use when generating protein, peptide, antibody, nanobody, or custom binder candidates for a target. Not for screening existing proteins or small molecules.

Screen existing protein binders with Boltz. Use when ranking a supplied protein, peptide, antibody, nanobody, or binder library against a target. Not for designing new proteins or screening small molecules.

Predict Tier-1 ADME/ADMET for small molecules with Boltz from bare SMILES — no target, no docking. Use when the user wants solubility, permeability, or lipophilicity/logD for a molecule or list of molecules. Not for ranking molecules against a protein target (use boltz-small-molecule-screen, which already returns ADME free).

Design new small-molecule binders with Boltz. Use when generating novel ligands or hits for a target without a fixed compound library. Not for screening existing molecules or one-off docking.

Screen existing small-molecule libraries with Boltz. Use when docking, scoring, or ranking a supplied SMILES or compound library against a target; also returns free Tier-1 ADME/ADMET (solubility, permeability, lipophilicity/logD) per molecule. Not for de novo molecule design, one-off docking, or ADME on bare SMILES with no target (use boltz-small-molecule-adme).

Predict structures and binding for one defined complex with Boltz. Use when folding a protein, RNA, DNA, or ligand complex, docking one ligand, predicting an interface, or scoring binding. Not for screening libraries or design.

Use Boltz2 NIM for biomolecular structure prediction and binding affinity. Invoke for Boltz2, protein structures, protein-ligand/DNA/RNA complexes, SMILES or CCD ligands, pIC50/IC50 affinity scoring, mmCIF output, hosted NVIDIA API calls, or local Docker deployment.

Expert-thinking profile for Botanist (field / herbarium / lab / computational plant science): Reasons from morphology, floras (FNA/Jepson/eFlora), voucher herbarium specimens (Darwin Core, Index Herbariorum), nomenclature (IPNI/POWO/Madrid Code), APG IV phylogeny, DNA barcoding (rbcL/matK/ITS2), community ecology (vegan adonis2/betadisper, TRY traits), and CITES/ABS ethics; treats vegetative mis-ID...

Build and troubleshoot Box integrations for uploads, folders, folder listings, downloads and previews, shared links, collaborations, search, metadata, event-driven automations, and Box AI retrieval flows. Use when Codex needs to add Box APIs or SDKs to an app, wire Box-backed document workflows, organize or share content, react to new files, or fetch Box content for search, summarization, extraction, or question-answering.

Expert-thinking profile for Brain–Computer Interface Engineer (EEG/ECoG/intracortical acquisition, real-time signal processing, and clinical BCI systems): Reasons from modality–paradigm fit (EEG, ECoG, Utah arrays), CSP/Riemannian decoding (pyriemann, MOABB), BCI2000/OpenBCI pipelines, and charge-density stimulation safety; validates within- vs cross-session claims and treats muscle ICA, impedance drift, and IDE/IRB gates as first-class failure modes.