Skill UI

The ETE Toolkit is a powerful Python library designed for analyzing, manipulating, comparing, and visualizing phylogenetic trees stored in Newick or Nexus formats. It allows users to perform topology edits, calculate phylogenetic distances (e.g., Robinson-Foulds), detect evolutionary events, and query external taxonomic databases like NCBI/GTDB. Note that this tool analyzes existing trees; it is not used for inferring trees from raw sequences.

FlowIO is a specialized, low-level library designed for reading, inspecting, and writing Flow Cytometry Standard (FCS) files (versions 2.0, 3.0, and 3.1). It allows users to extract event data as NumPy arrays, inspect detailed metadata (HEADER, TEXT, ANALYSIS), and handle multi-dataset structures. It is crucial for data preparation, format conversion, and foundational metadata management in bioinformatics pipelines, but does not perform complex analysis like gating or compensation.

A comprehensive framework for planning, configuring, executing, and analyzing complex Computational Fluid Dynamics (CFD) simulations using pseudospectral methods. It enforces a rigorous, multi-stage workflow, guiding users from defining state equations and boundary conditions to generating resource estimates, running dry-runs, and preparing site-specific MPI jobs. Designed for high-fidelity scientific computing and reproducibility.

Geniml provides a robust framework for running machine learning and statistical workflows over genomic interval sets. It treats coordinates, assemblies, and model artifacts as explicit contracts, enabling users to validate data structures (like BED files) and plan complex runs (such as Region2Vec or scEmbed) locally. The tool emphasizes reproducibility, adherence to biological data standards, and running without unnecessary network calls.

This tool provides a conservative, resource-aware snapshot of the current process's environment, including CPU, memory, disk, and accelerator limits. It helps users plan workloads accurately by providing clear boundary constraints (cgroup, scheduler, host limits) without performing stressful tests or making assumptions about usability.

gget is a comprehensive command-line and Python package providing unified access to over 20 major bioinformatics databases. Users can perform deep analyses across genomics, proteomics, and disease associations. Key functions include gene information lookups, sequence alignment (BLAST), structural prediction (AlphaFold), single-cell analysis, and enrichment studies, supporting both interactive queries and automated pipelines.

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.

This skill provides comprehensive tools for analyzing and engineering protein glycosylation patterns. It scans sequences for canonical N-glycosylation sequons (N-X-S/T), predicts O-glycosylation hotspots, and supports rational modification. It is essential for optimizing therapeutic antibodies, improving protein stability, or designing complex vaccine antigens.

Gtars is a robust toolkit providing native Rust implementations and Python bindings for advanced genomic interval modeling. It supports core bioinformatic tasks including set algebra, coverage calculation, tokenization, and fragment processing. The library emphasizes data integrity by enforcing strict genomic data contracts, ensuring correct handling of coordinates, assemblies, and reference sequences across complex computational pipelines.

This skill analyzes the implementation gap by comparing approved feature requirements against the existing codebase, architecture, and context. It helps identify missing capabilities, potential integration challenges, and necessary technical research areas. The output provides multiple viable implementation options and a comprehensive analysis report, guiding the transition from requirements definition to technical design.

LaminDB is an open-source, lineage-native lakehouse designed for managing complex biological datasets and computational workflows. It makes diverse scientific data (like scRNA-seq, AnnData) queryable, traceable, and compliant with FAIR principles. Core capabilities include robust data lineage tracking, schema validation, ontology-backed annotation (Bionty), and unified querying across multiple cloud/local storage systems. It is essential for bioinformatics research and building reproducible data infrastructure.

This skill provides a comprehensive framework for building, registering, debugging, and operating complex bioinformatics workflows on the Latch platform. It supports multiple industry-standard pipelines (Nextflow, Snakemake) and utilizes the Python SDK, CLI, and Latch Data/Registry. Use this when developing, deploying, or managing robust, data-intensive computational pipelines in a controlled environment.