129 件 ・ 関連度順
概要と使いどころ
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
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Nature-style chemistry manuscript reviewer skill for testing synthesis, catalysis, chemical biology, molecular/materials chemistry and analytical claims against identity, purity, controls, selectivity, mechanism, scope, reproducibility and quantitative comparison.
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Comprehensive scientific research toolkit with 139 specialized skills for biology, chemistry, medicine, data science, and computational research. Transforms Claude into an AI research assistant with access to scientific databases, analysis tools, and domain-specific workflows.
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Design an acoustic levitation system that uses standing waves to trap and suspend small objects at pressure nodes. Covers ultrasonic transducer selection, standing wave formation between a transducer and reflector, node spacing and trapping position calculation, acoustic radiation pressure analysis, and phased array configurations for multi-axis manipulation. Use when designing contactless sample handling for chemistry, biology, materials science, or demonstration purposes.
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Analyze a tensegrity system by identifying compression struts and tension cables, classifying type (class 1/2, biological/architectural), computing prestress equilibrium, verifying stability via Maxwell's rigidity criterion, and mapping biological tensegrity (microtubules, actin, intermediate filaments). Use when evaluating tensegrity in architecture, robotics, cell biology, or any system with isolated compression in continuous tension.
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Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz, Chai, ESMFold), protein, binder, and de novo design (RFdiffusion, ProteinMPNN, BoltzGen), antibody and nanobody design and developability, protein-ligand docking (DiffDock, Autodock Vina), binding-affinity prediction, MSA generation, and molecular dynamics. Use when the user mentions Tamarind or tamarind.bio, wants to run any of these open-source tools in the cloud, references app.tamarind.bio/api or the x-api-key header, or needs to submit batches of sequences for structural or biophysical characterization.
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Score a PhD applicant's profile and rank candidate advisors using a connection-first 4.0-scale scoring system. Best-supported for physics / HEP and materials science (MSE), with the scoring engine extensible to chemistry, biology, CS, math, EE, ChemE, earth science (each with field-specific caveats — see references/journal_tiers.md). Use when the user wants to evaluate their PhD application chances, find matching advisors at top US programs, score a CV for graduate school, or compare candidate professors. Also triggers when the user mentions phdtaketaketake or its connection-first philosophy of valuing advisor network over h-index.
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Use when a task needs the judgment of a Biochemist — determining enzyme kinetics (Km/Vmax, inhibition mechanism) from rate data, choosing a structural-biology method (X-ray crystallography, cryo-EM, or NMR) for a target, designing or interpreting a binding assay (ITC, SPR, fluorescence polarization), or selecting a protein-purification strategy and diagnosing why a prep failed.
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Use when a task needs the judgment of a Bioinformatics Scientist — designing a differential-expression or GWAS analysis with correct multiple-testing correction, calling and triaging variants from NGS data using genotype-likelihood confidence rather than raw allele counts, interpreting a BLAST/DIAMOND homology search, choosing or building a genomics pipeline (aligner, caller, normalization method) for a specific data-generating process, or judging whether a computational-biology analysis's statistical design actually supports the biological claim being made. Distinct from a bioinformatics-technician (executes and QC-gates an established pipeline someone else designed) and a data-scientist (general product/experimentation judgment, not genomics-specific statistics) — this role owns which method and statistical model a genomics question requires, and why.
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Statistical methods for biology and medicine — study design, hypothesis testing, regression, and survival analysis.
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Expert in evolutionary biology, ecological systems, biodiversity, and conservation
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Designs and analyzes in vivo CRISPR screens in animal tumor models, organoids, and immune-cell adoptive transfers. Covers bottleneck math (250x cells/sgRNA requires ~25M cells implanted; impossible for most syngeneic models, forcing focused libraries), focused library design (Manguso 2017 Nature 547:413 immune screen; Chen 2015 tumor screens), CRISPR-StAR intrinsic-control screening (Uijttewaal 2025 Nat Biotechnol 43:1848), clonal-dynamics-limited detection, tumor-explant DNA recovery, syngeneic vs xenograft vs PDX considerations, and the relationship to downstream MAGeCK / drugZ analysis. Use when designing in vivo CRISPR screens for tumor / immune / metastasis biology, choosing focused vs genome-wide for animal models, addressing bottleneck-induced clonal collapse, picking the syngeneic / xenograft / PDX model, integrating in vivo with in vitro results, or applying CRISPR-StAR for animal experiments.
日本語の概要は準備中です。原文の説明を表示しています。
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
日本語の概要は準備中です。原文の説明を表示しています。
Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields
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Expert-level immunology covering innate and adaptive immunity, antibody structure and function, T cell biology, immune evasion, vaccines, autoimmunity, and immunotherapy.
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Expert-level ecology covering population ecology, community ecology, ecosystem ecology, food webs, energy flow, nutrient cycling, biodiversity, and conservation biology.
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Expert-level genetics covering Mendelian inheritance, molecular genetics, mutations, linkage analysis, population genetics, epigenetics, and GWAS. Covers classical and modern approaches from Mendel to CRISPR.
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Search and retrieve preprints from arXiv via the Atom API. Use this skill when searching for papers in physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, or economics by keywords, authors, arXiv IDs, date ranges, or categories.
日本語の概要は準備中です。原文の説明を表示しています。
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
日本語の概要は準備中です。原文の説明を表示しています。
Solve quantitative problems in biophysics — pharmacokinetics (PK volume of distribution, clearance, half-life), epidemiology (R0, attack rate), toxicology (LD50, NOAEL), population genetics (Hardy-Weinberg, Fst), enzyme kinetics (Michaelis-Menten), thermodynamics. Use for first-principles quantitative biology calculations, dose calculations, exposure assessment, and biophysical-property estimation.
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Explains ML predictions on omics data with SHAP, LIME, and permutation importance, handling the correlated-feature trap, the conditional-vs-interventional Shapley choice, and the attribution-is-not-causation boundary. Use when interpreting an omics classifier, debugging shortcut/batch learning, or deciding whether an attribution ranking can be trusted as biology. For validated feature selection see machine-learning/biomarker-discovery; explanations are not a selection method.
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ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square, correlation, power), tooluniverse-image-analysis (microscopy, colony, fluorescence, dose-response, .tif — including ANOVA / Dunnett / power-analysis on image-derived measurements), tooluniverse-epigenomics (DNA methylation, CpG, m6A, MeRIP-seq, bisulfite, ChIP-seq, chromatin), tooluniverse-sequence-analysis (FASTQ, Trimmomatic, BWA, samtools, coverage), tooluniverse-variant-analysis (VCF, VAF, SNP, mutation), tooluniverse-phylogenetics (treeness, PhyKIT, parsimony), tooluniverse-single-cell (scRNA, h5ad, scanpy), tooluniverse-crispr-screen-analysis (MAGeCK, sgRNA), tooluniverse-proteomics-analysis (mass spec, TMT). Use for CSV/Excel/VCF/FASTA/h5ad and any biology/chemistry/medicine analysis question.
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Small molecule identification, characterization, and procurement — PubChem, ChEMBL, BindingDB, ADMET-AI, SwissADME, eMolecules, Enamine. Covers compound name to structure to activity to ADMET properties to commercial sourcing. Use for chemical biology, lead identification, probe selection, and the full small-molecule discovery pipeline.
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Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers, distinct from steady-state pool profiling. Covers tracer choice, isotopologue vs isotopomer, mass-isotopomer distributions (MID), fractional enrichment, the mandatory natural-abundance + tracer-purity correction (IsoCor, AccuCor), and the metabolic/isotopic steady-state vs non-stationary (INST-MFA) distinction. Use when feeding a labeled tracer and interpreting labeling patterns, correcting raw isotopologue intensities, computing or plotting an MID, or deciding tracing vs abundance profiling. For absolute pool concentration and MRM mechanics see metabolomics/targeted-analysis; for constraint-based genome-scale flux (FBA, not empirical tracing) see systems-biology/flux-balance-analysis; for feature detection see metabolomics/xcms-preprocessing; for pathway enrichment that ignores the pool-vs-flux caveat see metabolomics/pathway-mapping.
日本語の概要は準備中です。原文の説明を表示しています。