3. Data, Science & AI

Executes direct PostgreSQL queries for debugging, performance analysis, and SQL optimization using read-only connections.

Executes direct ClickHouse queries for analytics, metrics, and event data exploration with read-only access.

Provides read-only administrative access to Meilisearch index status, health, tasks, and configuration for debugging and monitoring search operations.

Integrates with protocols.io API for managing scientific protocols, including creation, updates, steps, materials, and collaborative features in research workflows.

Offers AI-ready drug discovery datasets including ADME, toxicity, and DTI benchmarks with molecular oracles for therapeutic ML and pharmacological prediction.

ETE toolkit for phylogenetic tree manipulation, evolutionary event detection, orthology/paralogy analysis, and visualization in phylogenomics research.

Toolkit for microbiome analysis with sequence alignment, phylogenetic trees, diversity metrics, and statistical tests like PERMANOVA.

Queries NCBI ClinVar for variant clinical significance, enabling gene/position searches, pathogenicity interpretation, and VCF annotation in genomic medicine.

Queries Ensembl REST API for genomic data including gene lookups, sequence retrieval, and variant analysis across 250+ species.

Performs differential gene expression analysis on RNA-seq data using DESeq2 in Python, including Wald tests, FDR correction, and volcano/MA plots.

Provides the anndata data structure for handling annotated single-cell omics data in .h5ad format, foundational for scverse tools.

Python framework for discrete-event simulation, modeling processes, queues, and time-based events in systems such as manufacturing and logistics.

Interactive visualization library for creating web-based charts with hover, zoom, and pan features, ideal for data dashboards and exploratory analysis.

Cheminformatics toolkit for molecular data processing including SMILES/SDF parsing, descriptors, and substructure search.

Organizes PyTorch code into LightningModules for scalable neural network training with distributed strategies and integrated logging.

Python library for geospatial vector data analysis, spatial operations, and map visualization with support for common formats and tools.

Provides PyTorch-native graph neural network tools for developing custom models in drug discovery, protein modeling, and knowledge graph reasoning.

Enables supervised and unsupervised machine learning, model evaluation, hyperparameter tuning, and pipeline building in Python.

Provides access to ZINC database for drug discovery, enabling compound searches by ID, SMILES, and similarity with 3D structures for docking and virtual screening.

Enables programmatic access, management, and backup of electronic lab notebooks (ELNs) with integrations for scientific workflows including Jupyter and REDCap.

Builds and deploys bioinformatics pipelines using Latch SDK with Nextflow/Snakemake integration for scientific data processing.

Provides machine learning tools for genomic interval data (BED files), including region embeddings and scATAC-seq analysis.

Toolkit for processing, analyzing, and visualizing spreadsheet data with formula support and formatting capabilities.

Applies drug-likeness rules (Lipinski, Veber), PAINS filters, and structural alerts to prioritize compounds and filter chemical libraries.