Results for “bio”

Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.

Query 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome) with a unified Python interface for cross-database analysis, identifier mapping, and sequence analysis.

Discovers and executes bioinformatics tools from the Galaxy ecosystem via natural language, with multi-signal scoring, workflow templates, and reproducibility bundles.

Manages biological datasets and models with LaminDB, covering setup, artifact registration, querying, lineage tracking, validation, ontology annotation, collections, branches, storage, and workflow integrations.

Manage biological datasets and models with LaminDB, an open-source lineage-native lakehouse. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation, collections, branches, storage, and workflow integrations.

Perform high-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames, including overlap, nearest, merge, coverage, complement, subtract, and reading/writing BED, VCF, BAM, GFF, FASTA, and FASTQ formats with streaming and cloud-native support.

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

Build and deploy bioinformatics workflows as serverless pipelines on the Latch platform using Python decorators, cloud data management, and GPU support.

Queries 20+ bioinformatics databases from the command line or Python for gene info, sequences, BLAST/BLAT, protein structures, viral data, and expression metrics.

Query 20+ bioinformatics databases from the command line or Python for gene information, sequences, protein structures, enrichment analysis, and more.

Performs constraint-based metabolic modeling with COBRApy: FBA, FVA, gene knockouts, flux sampling, and SBML model handling for systems biology and metabolic engineering.

Queries and displays Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via labstepPy, with an offline demo mode using synthetic biology data.

Automates sequencing quality control by running FastQC and MultiQC, extracting quality metrics, and generating publication-ready visualizations via a CLI or MCP stdio server.

Fetches Instagram user profile metadata including bio, follower count, following count, post count, and verification status using the internal REST API via browser automation.

Perform constraint-based metabolic modeling with COBRApy: run FBA, FVA, gene knockouts, flux sampling, and manage SBML models for systems biology and metabolic engineering.

Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus structured JSON for downstream chaining.

Generate professional clinical decision support documents for pharmaceutical and clinical research, including biomarker-stratified cohort analyses and evidence-based treatment recommendation reports with GRADE grading, statistical analysis, and publication-ready LaTeX/PDF output.

Processes and analyzes multiple physiological signals (ECG, respiration, EDA, EMG, PPG, EOG) together using NeuroKit2, including cross-signal features like RSA and event-related analysis.

Compile SOUL.md character profiles into synthetic diploid genomes (.genome.json) via trait-to-allele mapping.

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

Process and analyze physiological signals including ECG, EEG, EDA, RSP, PPG, EMG, and EOG using Python.

Query documented public database APIs with explicit endpoints, filters, pagination, and provenance for reproducible retrieval of scientific, regulatory, or financial facts.

Index local folders and search documents with BM25, vector, or hybrid queries, plus AI answers with citations and a web UI.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.

Downloads genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

Organize, query, validate, and convert neuroscience and biomedical data using the Brain Imaging Data Structure (BIDS) standard.

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

Computes phylogenetic distance matrices and trees from genomic VCF or FASTA data using the fastreeR hybrid Java/Python toolkit.

Annotates VCF variants using Ensembl VEP, ClinVar, and gnomAD, ranks them by predicted impact, and generates a reproducible report.

Performs HLA allele genotyping from WGS/WES VCF data, producing a structured markdown report and machine-readable JSON results.