K-Dense

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.

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

Organize ISO evidence for medical devices and laboratories, including controlled documents, risk records, corrective actions, and supplier controls. Produce structured gap reports for authorized human review while keeping certification, accreditation, and regulatory processes distinct.

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• Organize controlled documents and implementation records
• Check links in medical-device risk and design records
• Review corrective-action and supplier-control evidence

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

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.

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

Inspect CPU, memory, disk, and accelerator information alongside container and scheduler limits. Produce a JSON snapshot with identifying details removed and conservative worker and memory estimates for planning local workloads, without running stress tests.

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• Choosing worker counts before a large local job
• Checking CPU and memory limits inside a container
• Comparing resource snapshots before and after changes

Helps build LabArchives connections for electronic lab notebooks and laboratory inventory. Guides endpoint selection, request signing for authentication, and user authorization, with local tools to inspect container files and prepare redacted request plans before remote operations.

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• Plan an electronic lab notebook API connection
• Check authentication for laboratory inventory requests
• Inspect an LA container file locally

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

Extract text and its page coordinates locally from PDFs, Office documents, and images. Use OCR to read scans, export structured JSON or Markdown, process document folders, and render pages as PNG images for agents that analyze visual content.

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• Extracting text from scanned PDFs and images
• Preparing document text and coordinates for retrieval-based AI answers
• Batch-processing folders of research papers

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.

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

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

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.

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

Plan and write literature reviews using multiple scholarly databases. Document searches, screen papers, synthesize findings, and check citations, then prepare Markdown or PDF reports with transparent selection counts, evidence limitations, and reproducible search records.

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• Prepare a literature review for a thesis or research paper
• Record reproducible searches across scholarly databases
• Track screening decisions and exclusion reasons

Analyze pooled CRISPR screens from FASTQ reads or guide-count tables using MAGeCK. Validate inputs, assess library and replicate quality, and rank enriched or depleted genes with effect sizes and false discovery rates, which estimate false-positive proportions.

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• Counting guide reads from FASTQ files
• Checking library representation and replicate consistency
• Comparing treatment and control screens

Turn observations or preliminary findings into testable research plans. The skill separates candidate hypotheses from evidence, develops competing explanations and distinguishing predictions, and helps specify measurements and analysis plans for preregistration, a research plan recorded before testing.

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• Turn an observation into testable research hypotheses
• Compare competing explanations and distinguishing predictions
• Define measurements and review an analysis plan

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 experiments for Ginkgo Cloud Lab by choosing a protocol, organizing required inputs, checking configured pricing, and navigating browser ordering. Covers protein expression, RNA synthesis, stability assays, and setup of measurement methods.

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• Choosing a protein expression and purification protocol
• Preparing inputs for mRNA or circRNA synthesis
• Reviewing stability assays and measurement method setup

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

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.

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

Prepare and launch nf-core/pacsomatic workflows for matched tumor and normal PacBio HiFi samples. Generate sample sheets and launch files from unaligned BAM inputs, run local checks, submit cluster launchers, and troubleshoot startup failures.

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• Prepare sample sheets for matched tumor and normal samples
• Review generated launch files with a dry run
• Submit a Nextflow launcher to a computing cluster

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.

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

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.

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

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.

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

Look up genes, sequences, protein structures, expression patterns, and disease associations across more than 20 bioinformatics resources using command-line tools or Python. Useful for interactive exploration, with results that can be saved for further analysis.

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• Looking up gene details and sequences
• Exploring protein structures and residue annotations
• Comparing tissue expression and disease associations

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.

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