「sci」の検索結果

Use when a notebook run fails on a missing package (ImportError, ModuleNotFoundError, "there is no package called"), when you need to inspect an installed package version, or when you need to install, add, or manage Python or R packages for the notebook runtime. Covers inspect_packages, routing Python vs R through manage_packages, why in-cell %pip/!pip/install.packages() and OS installers are forbidden, restarting the kernel after an install, and when to stop and ask the user.

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Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted track delta.

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Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source AlphaFold3 alternative with optional binding-affinity prediction.

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Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab). Reach for this skill to predict an antibody-antigen or protein-ligand complex from a single FASTA, to re-fold designed binders as an AlphaFold-multimer alternative, or to drive co-folding from Python for batched campaigns on a GPU.

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Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.

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Use when the user wants to create or manage a Specialist agent or create, revise, publish, or delete a Skill through the conversational `/Customize` entry. Routes Skill work to the internal skill-creator and handles Specialist work through the JavaScript host.agents SDK.

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Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks. For probabilistic single-cell models (scVI etc.), use the scvi-tools library.

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Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequence embeddings for downstream ML, (2) Masked-LM likelihood / mutation effect scoring, (3) Contact prediction from a sequence.

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Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.

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Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified residues. FoldBench Ab-Ag 50-55%, PPI 70-77% DockQ-pass. Also covers the ESMC-{300M,600M,6B} protein language models from the same release: masked-LM logits, hidden states, mutation scoring, contact prediction, and the SAE interpretability head. MIT-licensed weights on HuggingFace org `biohub`. Use this skill when: (1) Predicting complex structures with single-sequence input, (2) Validating designed binders with ESMFold2-Fast, (3) Running ESMFold2 with MSA input, (4) Getting ESMC embeddings or per-residue mutation scores, (5) Choosing kernel backend and sampling-step settings for paper-faithful throughput.

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Judge and reshape the story told by an entire paper figure deck. Use when writing or revising a paper to derive a grounded brief from the manuscript and captions, review the full deck as a handling editor, and hand an ordered figure arc to `figure-composer`.

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Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1) Computing per-nucleotide or per-sequence likelihoods for variant effect scoring, (2) Embedding genomic windows for downstream classification, (3) Generating DNA conditioned on a prefix, (4) Scoring regulatory or coding regions across species.

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Compose one publication-grade multi-panel figure. Start from a one-line claim plus immutable data Artifact Version references, or inspect an existing figure and draft its outline directly. Plan a 12-column panel outline, delegate one worker per panel, compose and inspect the result, then run at most three adversarial review rounds while regenerating only affected panels. For a standalone plot use `figure-style`; for whole-paper figure ordering use `paper-narrative`.

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Polishes academic English paragraph by paragraph, reviewing grammar, word choice, voice, coherence, and sentence structure. Outputs revision suggestions alongside polished text. Triggered by phrases like 'polish this paragraph,' 'check the grammar,' 'rewrite in academic English,' or keywords like manuscript editing, SCI polishing, and journal submission editing.

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Diverga v12.0 setup wizard. 4-step researcher profile setup. Captures discipline, experience, tools, database access, and Agent Teams + VS Arena preference. Triggers: setup, configure, 설정, install

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Agent D4 - Measurement Instrument Developer - Scale construction and psychometric validation. Covers item development, validity evidence, and reliability testing for social science research.

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Diverga Dashboard - Live configuration status and feature overview. 24 specialized agents across 9 categories for social science research. VS methodology prevents mode collapse. Human checkpoints enforce human-in-the-loop decisions. Triggers: /diverga, diverga dashboard, diverga status

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Review research code for reproducibility and quality, extract the paper's main empirical claims, compare paper to code, and write a constructive markdown report. Designed for social science / economics projects with LaTeX papers and Stata, R, or Python code.

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Interactive setup wizard that configures a new project for the social-science-research plugin. Asks the user questions about their field, institution, journals, datasets, key researchers, and R color palette, then writes the answers into references/domain-profile.md and CLAUDE.md. Make sure to use this skill first whenever a user is starting fresh or wants to configure the plugin. Triggers include: "set up my project", "configure the plugin", "run setup", "initialize this project", "I just installed the plugin", "set my field", "set my institution", "configure my domain profile", or any request to personalize the plugin for a specific research context.

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APSA style checker for Quarto (.qmd) files. Checks numbers, capitalization, abbreviations, italics, in-text citations, titles of works, neutral and unbiased language, and APSA-specific terminology against the APSA Style Manual for Political Science (2018, updated 2023). Produces a structured markdown report organized by document section — never modifies the source file. Use when asked to check APSA style, fix citations, review capitalization, check number formatting, or flag biased language in a .qmd document. For grammar, spelling, and punctuation, use the proofread skill instead. Supports an optional output-file argument and an optional @sec-label argument to restrict checking to one section.

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This skill covers Bayesian estimation and inference in quantitative social science. Use when the user is specifying priors, running MCMC, diagnosing chain convergence, or reporting posterior summaries — including hierarchical models, Bayesian structural models, and small-sample settings where priors regularize. Triggers on "Bayesian estimation", "Bayesian inference", "MCMC", "Markov chain Monte Carlo", "Stan", "PyMC", "NumPyro", "prior", "posterior", "credible interval", "Bayesian structural", "Bayesian BLP", "Bayesian DSGE", "hierarchical model", "random effects Bayesian", "posterior predictive check", "Bayes factor", "prior predictive check", "NUTS", "HMC", "Hamiltonian Monte Carlo", "R-hat", "rhat", "effective sample size", "ESS", "Bayesian calibration", "posterior distribution", "prior elicitation", "weakly informative prior", "brms", "rstanarm", "cmdstanpy", "pymc", "arviz".

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This skill covers causal machine learning methods in applied economics and quantitative social science. Use when implementing or choosing between modern ML-based causal estimators — including double machine learning, DML, partially linear models, interactive regression models, cross-fitting, Neyman orthogonality, debiased ML, causal forests, generalized random forest, GRF, honest causal trees, AIPW with machine learning, doubly robust with machine learning, DR-Learner, T-Learner, S-Learner, X-Learner, meta-learners, heterogeneous treatment effects, conditional average treatment effect, CATE, HTE, high-dimensional controls, LASSO controls, post-LASSO, post-double selection, Belloni-Chernozhukov-Hansen, Riesz representer, Chernozhukov, sample splitting, econml, DoubleML package, or any combination of machine learning and causal inference.

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PubMed search with keyword optimization, result parsing, and metadata extraction

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Evaluate a paper's contribution novelty, identify best-fit SSCI journal fields and ABS star rating, and recommend 20 target journals. Trigger when user says "paper submission" / "paper-submission" / "投稿评估" / "期刊推荐" / "target journal" / "选刊".

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