数据与 AI技能

Turn small-molecule structures into numerical features for similarity searches and models that predict activity or properties. Using Molfeat, the skill covers representation choices, invalid inputs, alignment with experimental labels, and saving feature-generation settings for reuse.

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• Prepare molecular features for activity or property prediction
• Choose molecular representations for similarity searches
• Keep experimental labels aligned after rejecting invalid molecules

Helps build and review NeuroKit2 research workflows for physiological recordings such as ECG, respiration, and skin conductance. Covers preprocessing, time alignment, event analysis, heart rate variability, and complexity measures, while recording methods and checking data quality.

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• Inspect physiological recordings before preprocessing
• Analyze ECG and heart rate variability for research
• Plan event windows and baseline correction

Prepare and analyze genomic intervals, regions defined by chromosome coordinates, with Gtars. Validate BED files, compare overlaps and coverage, combine region sets, and plan tokenization or reference storage while tracking data provenance and resource limits.

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• Validating BED coordinates and reference assemblies
• Counting overlaps and comparing genomic region sets
• Converting genomic intervals into token IDs

Work with geographic points, lines, and areas in Python using GeoPandas. Guidance and local audit tools help check coordinate systems, geometry validity, spatial join matches, and export settings before trusting or sharing analysis results.

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• Checking geographic data before analysis
• Reviewing coordinate systems and transformations
• Auditing matches between points and areas

Process satellite imagery and map data for geospatial research. Helps align coordinate systems and image grids, calculate vegetation and terrain measures, summarize data by area, and analyze road networks while preserving masks and source information.

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• Align coordinate systems and raster grids
• Calculate vegetation indices from satellite imagery
• Analyze slope and aspect from elevation data

Build and operate bioinformatics workflows on Latch using Python, Nextflow, or Snakemake. Configure computing resources and input forms, move data, connect Registry records, and register, debug, launch, and monitor analysis runs.

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• Create and register Python analysis workflows
• Package Nextflow or Snakemake pipelines for Latch
• Connect Latch Data and Registry records

Prepare small image tiles from whole-slide histology scans with Histolab. Inspect tissue regions, choose random, grid, or score-based extraction, standardize H&E staining, and organize tile datasets with patient-level splits and visual checks.

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• Extracting training tiles from whole-slide histology scans
• Previewing tissue masks and tile locations
• Standardizing H&E stain appearance

Build, analyze, and visualize relationship data in Python with NetworkX. Find shortest routes, identify important nodes and groups, generate networks for simulations, and exchange graph data through tables and common file formats.

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• Finding important people and groups in social networks
• Calculating shortest routes in transportation networks
• Visualizing relationships between research papers

Process calibrated one-dimensional NMR signals into spectra, candidate peaks, and signed integration results. Supports manual phase adjustment, baseline correction, and recorded processing settings so results can be reviewed and reproduced.

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• Convert raw one-dimensional NMR signals into spectra
• Check peak positions against reference signals
• Review phase and baseline corrections

Find scientific datasets, AI models, methodology posts, and interactive demos through the Hugging Science catalog. Compare candidates for a research task and verify their licenses, input formats, access requirements, and supported ways to run them.

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• Finding models for protein or genome analysis
• Selecting datasets for scientific machine learning
• Comparing resource licenses and runtime requirements

Analyze Neuropixels neural recordings with SpikeInterface, from loading and preprocessing to motion correction and spike sorting, which separates signals by neuron. Calculate quality metrics, review candidate units, and export plots and data for further inspection.

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• Inspect and preprocess SpikeGLX, Open Ephys, or NWB recordings
• Check and correct movement-related drift before spike sorting
• Evaluate and select units using quality metrics

Helps organize biological datasets and models in LaminDB. Covers data registration, table validation, annotation with standardized biological terms, metadata searches, and tracking analysis inputs and outputs so researchers can preserve the context needed to repeat their work.

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• Register and organize biological datasets
• Validate DataFrame or AnnData metadata
• Standardize annotations with biological vocabularies

Convert single-plane, single-channel two-photon TIFF images and timestamped behavioral position CSV files into NWB, a neuroscience data format. Preserve metadata, check clock alignment against acquisition evidence, and report format validation findings and source-to-output comparisons.

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• Converting two-photon TIFF images to NWB
• Combining imaging and behavioral position records
• Checking clock alignment using synchronization pulses

Match scientific labels to ontology identifiers, standardized IDs for concepts such as tissues, cell types, and diseases. Checks existing IDs, labels, obsolete terms, and prefixes to support metadata annotation, submission preparation, and table audits.

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• Annotating tissue, cell type, or disease fields with standard IDs
• Auditing metadata tables for incorrect IDs and labels
• Checking obsolete terms and available replacements

Measure fluid velocity from pairs of particle images with OpenPIV. The skill covers image preparation, velocity calculation, correction of unreliable vectors, plotting, and calculation of vorticity and strain rate to examine flow patterns.

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• Measure velocity fields from experimental image pairs
• Detect and replace unreliable velocity vectors
• Calculate vorticity and strain rate

Query public single-cell and spatial gene expression data by tissue, disease, or cell type. Retrieve selected expression values, cell metadata, and summary counts for analysis and comparisons across datasets without first downloading entire collections.

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• Explore cell types within a tissue
• Retrieve expression values for selected marker genes
• Compare cells across tissues and datasets

Process DNA, RNA, and protein sequences with Biopython, convert biological files, and retrieve NCBI records. Supports batch workflows for sequence comparison, searches for similar sequences, protein structure analysis, and evolutionary trees.

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• Convert GenBank files to FASTA
• Calculate sequence length and GC content in batches
• Retrieve sequences and publication records from NCBI

Organize repeated experiments to improve models, prompts, or agent systems against measurable goals. The skill records hypotheses and lessons in a persistent tree, isolates trials, and compares promising candidates using evaluation data kept separate from development.

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• Compare repeated experiments to improve model training
• Improve an agent system's measured success rate
• Test prompt changes against a fixed evaluator

Estimate intracellular reaction rates from steady-state carbon-13 tracing measurements. Validate carbon atom mappings and measurement inputs, simulate labeling, fit constrained fluxes, and diagnose which pathway rates the data can meaningfully constrain.

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• Estimate metabolic fluxes from carbon-13 labeling
• Validate atom mappings and measurement inputs
• Simulate labeling for proposed reaction rates

Process molecular datasets in Python through a simpler interface to RDKit, a chemistry toolkit. Convert and standardize structures, calculate molecular properties, compare and cluster compounds, generate 3D conformations, and visualize results for drug discovery workflows.

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• Load and standardize molecular datasets
• Calculate molecular properties and similarities
• Cluster compounds and select diverse subsets

Prepare bulk RNA-seq sequencing files or quantification outputs for gene-level comparisons. Check sample information and data quality, configure processing workflows, and assemble validated count tables and metadata for downstream differential expression analysis with PyDESeq2.

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• Preparing gene count tables from FASTQ files
• Configuring an nf-core/rnaseq workflow
• Combining Salmon, STAR, or featureCounts outputs

Rank possible gene regulatory relationships from bulk or single-cell expression data using GRNBoost2 or GENIE3. The skill guides input preparation, compatible execution, method comparison, and stability checks to help prioritize candidates for further biological investigation.

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• Rank candidate regulator–target gene relationships
• Compare GRNBoost2 and GENIE3 results
• Check network stability across seeds and resampled data

Prepare genomic interval data for machine learning by checking BED files, reference genome consistency, and model compatibility. Plan Region2Vec or scEmbed workflows and assess shared reference regions using local validation and planning helpers.

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• Check BED coordinates and reference genome consistency
• Plan Region2Vec or scEmbed training
• Inspect model and tokenizer compatibility

Retrieve and combine protein annotations, biological pathways, and chemical identifiers from services such as UniProt, KEGG, and UniChem using Python. Supports cross-database lookups and batch identifier conversion while preserving multiple matches and failed requests.

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• Collect protein sequences and functional annotations
• Retrieve pathway information for genes
• Match compound identifiers across databases