Skill UI

The ESM skill provides comprehensive tools for computational biology, leveraging ESM3 and ESM-C models. It enables sophisticated protein sequence generation, structure prediction (sequence to 3D structure), inverse folding (structure to sequence design), and generating function-conditioned proteins. Use it for de novo protein design, feature embedding, and advanced structural analysis in bioinformatics workflows.

FluidSim is an object-oriented Python framework for high-performance Computational Fluid Dynamics (CFD) simulations. It provides specialized solvers for complex equations like 2D/3D Navier-Stokes, shallow water, and stratified flows. Utilizing pseudospectral methods with FFT, the framework supports parallel computing (MPI) and offers a complete workflow, including parameter configuration, simulation execution, and advanced post-processing and visualization.

A comprehensive toolkit for advanced geospatial analysis. It covers remote sensing (Sentinel, Landsat), GIS operations (vector/raster/point cloud), spatial statistics, and Machine Learning for Earth Observation. Supports cloud-native workflows, multiple data types, and 8 programming languages, making it ideal for complex scientific research and commercial spatial projects.

This skill proactively detects and reports comprehensive system resources, including CPU cores, GPU types (NVIDIA, AMD, Apple Silicon), available memory, and disk space. It generates a detailed JSON report with strategic, context-aware recommendations for optimizing scientific computing workflows, such as recommending parallel processing libraries (Dask, joblib), out-of-core methods (Zarr), or appropriate GPU acceleration backends (Metal, ROCm). Use this before any large-scale data analysis, model training, or computationally intensive simulation to make informed architectural decisions.

gget is a comprehensive command-line tool and Python package offering unified access to over 20 genomic databases. It facilitates quick lookups for gene information, sequence analysis (BLAST), protein structures, and expression data, supporting both interactive CLI use and advanced programmatic Python workflows for biological research.

Ginkgo Cloud Lab provides remote access to an advanced autonomous lab infrastructure, enabling users to submit and manage complex molecular biology protocols. It supports diverse applications including protein expression and purification (cell-free, E. coli, Pichia), quantitative assays (HiBiT, A280, LabChip), nucleic acid synthesis (IVT mRNA/circRNA), and characterization techniques (Thermal Shift, Echo-MS, SPR). The platform features an AI agent (EstiMate) for custom workflow feasibility and pricing.

Histolab is a specialized Python library for digital pathology research, enabling robust processing of Whole Slide Images (WSI). It automates complex workflows including tissue detection, sophisticated segmentation, and flexible tile extraction from various formats (SVS, TIFF). This tool is crucial for preparing structured, high-quality datasets required for deep learning models and advanced computational pathology analysis.

A systematic tool for scientific inquiry, guiding users through the entire research process. It helps formulate testable, mechanistic hypotheses from raw observations or preliminary data, following the established scientific method. The workflow includes comprehensive literature review, evidence synthesis, generating competing explanations, and designing experiments, all while mandating the creation of scientific schematics for visualization.

This skill provides comprehensive integration with the LabArchives Electronic Lab Notebook (ELN) platform via its REST API. It allows users to programmatically manage notebooks, retrieve user data, automate entry creation, upload diverse attachments (PDF, CSV, images), perform full notebook backups, and generate detailed usage reports. Ideal for automating scientific workflows and integrating ELN data with tools like Jupyter or REDCap.

LaminDB is an open-source, lineage-native lakehouse specifically designed for complex biological datasets and models. It provides unified capabilities for querying, tracking data lineage, validating schemas, and ensuring FAIR compliance across diverse data types (e.g., AnnData, Parquet, Zarr). Use this skill when managing multi-modal genomic data, tracking computational workflows (like Nextflow/Snakemake), or building robust, reproducible data infrastructure in bioinformatics.

Latch is a robust Python framework designed for building, deploying, and managing complex, scalable bioinformatics workflows as serverless pipelines. It supports integrating multiple analysis tools (like Nextflow/Snakemake) and handles cloud data management (LatchFile/LatchDir) and detailed resource configuration (GPU, CPU, memory). Ideal for running large-scale analyses such as RNA-seq, AlphaFold, and single-cell analysis in a reproducible, production-ready environment.

Molfeat is a comprehensive Python library designed for molecular featurization. It converts chemical structures (SMILES/RDKit) into numerical feature vectors, supporting over 100 featurizers like ECFP, MACCS, and deep embeddings (ChemBERTa). It unifies featurization pipelines, making it ideal for QSAR modeling, virtual screening, and integrating into deep learning ML workflows.