K-Dense

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.

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

Clean and compare tandem mass spectra, measurements used to study molecular fragments, with matchms. Standardize metadata, filter peaks, search reference libraries, and export ranked candidate matches with similarity scores and matched-peak counts.

• Clean MS/MS spectra and standardize metadata
• Search reference libraries for compound candidates
• Compare spectra using similarity scores and matched peaks

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.

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

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.

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

Build, run, and troubleshoot data processing pipelines with Nextflow and nf-core. The skill guides modular workflow development, input preparation, testing, cached restarts, and configuration for local computers, computing clusters, or cloud environments.

• Run an nf-core workflow with a samplesheet
• Build and test reusable DSL2 modules
• Investigate failed runs and restart with cached results

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.

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

Plan and audit HypoGeniC workflows that use language models to propose patterns from labeled text. Check configurations, dataset splits, cost limits, and saved predictions while keeping candidate hypotheses separate from scientific confirmation.

• Reviewing task settings before a HypoGeniC run
• Checking duplicates across training and test data
• Estimating token and cost limits before model calls

Calculate seawater carbonate chemistry from two independent measurements using PyCO2SYS. Produce pH, carbonate species, and mineral saturation results, convert laboratory conditions to ocean conditions, and propagate measurement uncertainty while recording calculation assumptions.

• Calculate carbonate chemistry from paired seawater measurements
• Assess aragonite and calcite saturation
• Convert laboratory results to ocean temperature and pressure

Turn supplied data or optional research into infographic drafts for reports, presentations, or social posts. Choose layouts and visual styles, generate PNG images, and use automated reviews to guide revisions while retaining review logs.

• Turning report statistics into an infographic
• Creating a timeline of project milestones
• Comparing product features visually

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.

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

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.

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

Analyze candidate sites where sugars may attach to proteins, review experimental evidence, and prepare prediction or structural shielding workflows. Supports mutation planning, antibody glycan comparisons, and interpretation of site-specific measurements while distinguishing candidates from confirmed modifications.

• Find candidate glycosylation sites in protein sequences
• Plan mutations and rescan altered sequences
• Compare antibody Fc glycoforms

Find and download public cancer imaging data from NCI Imaging Data Commons. Select CT, MR, PET, or pathology datasets using metadata, view images in a browser, and check licenses and citations before using the data.

• Find cancer images by disease, modality, or anatomical site
• Download selected DICOM image series
• View radiology and pathology images in a browser

Build and review numerical workflows for MATLAB or GNU Octave, including arrays, tables, graphics, tests, and MAT files. Helps plan release migrations, reproducible projects, and Python integration while checking runtime, compatibility, and license requirements.

• Reviewing array operations and numerical tolerances
• Planning MATLAB release migrations and compatibility checks
• Preparing reproducible projects and unit test scaffolds

Look up biomedical relationships in ARAX using explicit entity types and tightly bounded paths. Inspect direct links or paths through one intermediate entity, along with returned publications and source records, to identify candidates for further research.

• Checking recorded drug–gene relationships
• Exploring paths between a drug and a disease
• Inspecting publications and original data sources

Create market research reports that connect claims to sources, compare competitors, and estimate market size. Build alternative forecasts with explicit assumptions, so readers can review the calculations, uncertainties, and evidence behind each conclusion.

• Preparing a market report for a new business
• Comparing market size estimates and their assumptions
• Building competitor comparisons with traceable sources

Build Python workloads on Modal for cloud execution, including GPU model training and inference, web APIs, scheduled jobs, and parallel batch processing. Configure container environments, persistent storage, and automatic scaling through the Modal SDK.

• Serving an AI model through a web API
• Running model training or fine-tuning on cloud GPUs
• Processing independent batch inputs in parallel

Search biomedical papers, regulatory documents, clinical trials, and protein records through GXL Paperclip. Extract comparable information across documents, inspect figures, and organize findings with citations linked to the source lines that support them.

• Finding biomedical papers on a topic
• Comparing methods and results across papers
• Reviewing regulatory documents and clinical trials

Screen compound libraries for drug discovery using drug-likeness guidelines, structural alerts that flag patterns for review, and molecular complexity measures. Combine criteria to shortlist candidates and retain filtering results with reasons for further assessment.

• Screen compound libraries with drug-likeness rules
• Flag PAINS and other structures for review
• Combine property, structure, and complexity filters

Create Markdown research notes, reports, and guides with Mermaid diagrams, which describe relationships as editable text. Choose suitable diagrams for workflows, timelines, or schemas, add accessible descriptions, and check rendering in the intended destination.

• Writing research notes with workflow diagrams
• Diagramming data structures and relationships
• Creating project timelines

Finds papers, preprints, citation links, and openly available full text through 18 scholarly APIs. Selects databases for the task and returns relevant records with search parameters, identifiers, and access dates so the retrieval can be repeated.

• Find papers and preprints on a research topic
• Look up a paper by DOI, PMID, or arXiv ID
• Find openly available full text or PDFs

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.

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

Prepare and run molecular dynamics simulations with OpenMM, then analyze molecular motion with MDAnalysis. Examine protein flexibility, structural changes, and protein–ligand contacts through calculations and plots of simulated trajectories.

• Investigating protein stability after a mutation
• Measuring structural changes and flexibility
• Tracking protein–ligand contacts

Search the 1000 Genomes Project’s 3,202 participants for genetic variants and their carriers. Filter by frequency or annotations, inspect variants in selected individuals, and check relatedness between two participants.

• Find participants carrying variants that match specified criteria
• Inspect genetic variants carried by selected participants
• Identify participants with two reference copies at a position