scientific-pkg-gget
ゲノムデータベースへのクイック検索、配列検索、BLAST スタイルの検索、エンリッチメントチェック、および再現可能なバイオインフォマティクス証拠ログのための gget CLI および Python ワークフロー。
Sprache des Skill-Inhalts: Japanisch
Agent Skills für wissenschaftliche Simulationen, Berechnungsforschung und Data Science durchsuchen
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9.852 Ergebnisse
ゲノムデータベースへのクイック検索、配列検索、BLAST スタイルの検索、エンリッチメントチェック、および再現可能なバイオインフォマティクス証拠ログのための gget CLI および Python ワークフロー。
Sprache des Skill-Inhalts: Japanisch
gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs. Use when a task needs quick bioinformatics lookup across genomic reference databases with the gget CLI or Python package.
Sprache des Skill-Inhalts: Englisch
SAM: zero-shot image segmentation via points, boxes, masks.
Sprache des Skill-Inhalts: Englisch
Investigate whether structured datasets and query results are trustworthy enough to use. Use for underlying data-quality risks such as freshness, grain, missingness, duplicates, broken joins, schema drift, and conflicting source results.
Sprache des Skill-Inhalts: Englisch
Processes and analyzes data with resident-kernel engines (DuckDB, Polars) and one-shot tools. Use for CSV/parquet/JSON analysis, group-by/join/aggregation, time series, distributions, cleaning, or plotting a dataset.
Sprache des Skill-Inhalts: Englisch
Deletes memories by search query or memory ID with confirmation before removal. Use when removing outdated information, incorrect memories, sensitive data, or cleaning up after experiments.
Sprache des Skill-Inhalts: Englisch
Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom molecular-biology pipelines, BLAST automation, structure analysis, and motif analysis.
Sprache des Skill-Inhalts: Englisch
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Sprache des Skill-Inhalts: Englisch
Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evidence, and preparing NetNGlyc, NetOGlyc and GlycoSHIELD workflows. Use for glycoprotein engineering, antibody Fc glycosylation, glycan shielding, and site-specific glycoproteomics interpretation.
Sprache des Skill-Inhalts: Englisch
Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting scientific ML resources in biology, chemistry, genomics, materials, climate, physics, astronomy, medicine, mathematics, protein design, single-cell analysis, or PDE modeling, and when checking their actual datasets, Transformers, native-runtime, Inference Providers, or Gradio interfaces.
Sprache des Skill-Inhalts: Englisch
Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired total alkalinity, dissolved inorganic carbon, pH, or seawater pCO2/fCO2 measurements; carbonate speciation; aragonite and calcite saturation; Revelle factors; lab-to-in-situ temperature and pressure corrections; and measurement uncertainty propagation. Applies to carbonate-system calculations, not general aqueous speciation or air-sea gas-flux estimation.
Sprache des Skill-Inhalts: Englisch
Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks. Use pyopenms instead for LC-MS feature detection or proteomics pipelines.
Sprache des Skill-Inhalts: Englisch
Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry sensitivity, electronic-structure I/O, and bounded Materials Project queries.
Sprache des Skill-Inhalts: Englisch
Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.
Sprache des Skill-Inhalts: Englisch
Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
Sprache des Skill-Inhalts: Englisch
Builds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches, error mitigation, and Qiskit ecosystem packages.
Sprache des Skill-Inhalts: Englisch
Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event scheduling, resource queues, interrupts, monitoring, independent replications, warm-up, and reproducible output analysis.
Sprache des Skill-Inhalts: Englisch
Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned visualizations, and file conversion. Use for larger-than-RAM HDF5, Arrow, CSV, or Parquet analysis, virtual feature engineering, or Vaex ML preprocessing; distinguishes these operations from estimators and conversions that materialize data.
Sprache des Skill-Inhalts: Englisch
Create or extract one SPF playback-engine behavior. Use for a new atomic responsibility with signals, lifecycle, cleanup, composition, and tests.
Sprache des Skill-Inhalts: Englisch
Detects sophisticated cyber-physical attacks that follow the Stuxnet pattern of modifying PLC logic while spoofing sensor readings to hide the manipulation, using PLC logic integrity monitoring (Claroty xDome, Nozomi Guardian) and physics-based process anomaly detection. Use when hunting for IT-to-OT lateral movement or discrepancies between PLC program state and physical process behavior in ICS/SCADA environments.
Sprache des Skill-Inhalts: Englisch
Detect process injection techniques (T1055) - including DLL injection, process hollowing, and APC injection - by analyzing Sysmon Event IDs 1, 7, 8, 10, and 25 for cross-process memory operations, remote thread creation, and anomalous DLL loads. Use when hunting defense-evasion activity that hides code inside legitimate processes, investigating an EDR alert on suspicious cross-process access, or validating Sysmon coverage for injection detection.
Sprache des Skill-Inhalts: Englisch
Systematically investigate all persistence mechanisms on Windows and Linux systems to identify how malware survives reboots and maintains access.
Sprache des Skill-Inhalts: Englisch
Performs static analysis of Windows PE malware samples using PEStudio to examine file headers, imports, strings, and resources without executing the binary, identifying packing, anti-analysis tricks, and malicious imports. Use for pre-execution triage of a suspicious Windows executable before sandbox detonation.
Sprache des Skill-Inhalts: Englisch
Expert data scientist for advanced analytics, machine learning, and statistical modeling. Handles complex data analysis, predictive modeling, and business intelligence.
Sprache des Skill-Inhalts: Englisch
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
Sprache des Skill-Inhalts: Englisch
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Sprache des Skill-Inhalts: Englisch
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Sprache des Skill-Inhalts: Englisch
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Sprache des Skill-Inhalts: Englisch
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
Sprache des Skill-Inhalts: Englisch
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
Sprache des Skill-Inhalts: Englisch
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
Sprache des Skill-Inhalts: Englisch
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
Sprache des Skill-Inhalts: Englisch
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
Sprache des Skill-Inhalts: Englisch
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
Sprache des Skill-Inhalts: Englisch
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
Sprache des Skill-Inhalts: Englisch
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
Sprache des Skill-Inhalts: Englisch
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.
Sprache des Skill-Inhalts: Englisch
Use when designing a prospective clinical study: choosing primary and secondary endpoints, estimating sample size and power, or scoring feasibility before submission. Runs endpoint_selector.py, sample_size_estimator.py and phase_gate_scorer.py; outputs are estimates for a biostatistician to confirm.
Sprache des Skill-Inhalts: Englisch
Generate realistic dummy datasets for testing with customizable columns, constraints, and output formats (CSV, JSON, SQL, Python script). Use when creating test data, building mock datasets, or generating sample data for development and demos.
Sprache des Skill-Inhalts: Englisch
Evolutionary explanation-discovery engine for hard-to-vary causal theories of unknown phenomena. USE WHEN develop a new theory, explain a mystery, solve an explanatory gap, discover a mechanism, consciousness, origin, or scientific breakthrough. Also use for multi-cycle creative exploration. NOT FOR a single-pass divergent brainstorm (use BeCreative) or delivery validation alone (use Assay).
Sprache des Skill-Inhalts: Englisch
Python simulation lifecycle (MjSpec, MjModel, MjData), simulation stepping (mj_step, mj_step1, mj_step2, mj_forward), named access (data.body, model.geom), bind(), multi-threaded CPU batch simulation (mujoco.batch.Batch, mujoco.rollout), optimization and system ID (mujoco.minimize, mujoco.sysid, mjd_transitionFD), contact and touch sensors, sensordata, keyframe resets, integrators, mju_ spatial math (quaternions, poses), energy diagnostics. Use for Python physics simulation, state access, CPU batching, stepping loops, sensors. Do NOT use for model building/editing (mujoco-spec-editing), headless rendering (mujoco-rendering), GPU/TPU (mujoco-accelerated), cross-engine parity debugging (mujoco-parity), or GUI/viewers (mujoco-gui, mujoco-studio).
Sprache des Skill-Inhalts: Englisch
Validate a COBRApy genome-scale metabolic model for mass/charge balance, stoichiometric consistency, biomass producibility, dead-end metabolites, thermodynamic loops, and GPR rule formatting. Outputs a structured validation report with errors and warnings.
Sprache des Skill-Inhalts: Englisch
Parse and interpret Z3 output for human consumption. Handles models, unsat cores, proofs, statistics, and error messages. Translates solver internals into plain-language explanations.
Sprache des Skill-Inhalts: Englisch
Submit compact NCBI Datasets v2 requests for assembly, genome, taxonomy, and related metadata endpoints. Use when a user wants concise NCBI Datasets summaries; save raw JSON or text only on request.
Sprache des Skill-Inhalts: Englisch
Submit compact ProteomeXchange PROXI requests for datasets, libraries, peptidoforms, proteins, PSMs, spectra, and USI examples. Use when a user wants concise PROXI summaries
Sprache des Skill-Inhalts: Englisch
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
Sprache des Skill-Inhalts: Englisch
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
Sprache des Skill-Inhalts: Englisch
Data science methodology for Python research: EDA, validation, causal inference (IV, DiD, RD, synthetic control), clustering/PCA/UMAP, supervised ML, geospatial, visualization. Method selection guidance. For syntax, load tool-specific skills.
Sprache des Skill-Inhalts: Englisch