Skill UI

Conducts STRIDE-A threat modeling on repositories or systems, running either a full single-pass analysis with architectures, DFDs, prioritized findings, and executive assessments, or an incremental update that compares a baseline report to the current code and highlights deltas.

This guide enforces a mandatory, multi-stage process for debugging complex software issues. It moves developers beyond merely patching symptoms by forcing them through Root Cause Investigation, Pattern Analysis, Hypothesis Validation, and proper Implementation with testing. It is crucial for solving production bugs, failed tests, and performance issues in a structured manner.

Utilize advanced media intelligence to analyze audio, image, video, and text for synthetic manipulation and AI-generated content. This skill detects deepfakes, traces the original AI synthesis source, applies and detects watermarks, verifies speaker identity, and provides comprehensive media provenance analysis, ensuring media authenticity claims are rigorously supported.

A comprehensive, adaptive mathematics tutor covering K-12 topics from arithmetic through calculus. This skill utilizes proven pedagogical strategies—such as Socratic questioning, CPA approach, and error analysis—to ensure students build deep mathematical understanding rather than just procedural fluency. It adapts to multiple global curricula (SAT, A-Level, Gaokao) and tracks progress to target weak spots.

This skill provides integration with the Adaptyv Bio Foundry API, enabling the automated design, submission, and analysis of protein experiments. Users can submit amino acid sequences for various high-throughput assays, including binding kinetics (BLI/SPR), thermostability, and expression yield. It guides the entire research workflow, from sequence input to final results retrieval, accelerating biopharma discovery.

Aeon is a comprehensive, scikit-learn compatible Python toolkit designed for advanced time series analysis. It supports a wide range of temporal machine learning tasks, including classification, regression, clustering, forecasting, anomaly detection, and similarity search. Use this skill when working with sequential patterns, time-indexed observations, or complex temporal data that requires specialized algorithms.

AnnData is a specialized Python package designed for managing and analyzing annotated matrices, particularly crucial in single-cell genomics and bioinformatics. It efficiently stores experimental measurements (X) alongside comprehensive metadata (obs, var, obsm, etc.). This skill allows users to read, write, subset, and concatenate large, complex datasets in formats like .h5ad and .zarr, making it essential for scRNA-seq analysis workflows and integration with the scverse ecosystem.

Arboreto is a powerful Python library designed to infer Gene Regulatory Networks (GRNs) from various gene expression datasets, including bulk and single-cell RNA-seq. It employs scalable algorithms like GRNBoost2 and GENIE3 to identify critical transcription factor-target gene relationships. Featuring support for Dask distributed computing, Arboreto is optimized for large-scale, high-throughput transcriptomic analysis.

Biopython is a robust, comprehensive toolkit for computational molecular biology written in Python. It enables users to manipulate biological sequences (DNA, RNA, protein), parse standard formats (FASTA, GenBank, PDB, etc.), and programmatically access major bioinformatics databases like NCBI via Entrez. This skill is ideal for developing complex bioinformatics pipelines, including sequence alignment, structural analysis, and phylogenetic tree construction.

A comprehensive Python package providing a unified interface to over 40 major bioinformatics web services and databases. Use it for complex biological workflows, including cross-database querying (e.g., UniProt, KEGG, ChEMBL), identifier mapping, protein sequence retrieval, pathway analysis, and running sequence similarity searches like BLAST. It streamlines data integration from multiple life science resources into consistent Python code.

COBRApy is a powerful Python library for Constraint-Based Reconstruction and Analysis (COBRA). It enables deep dives into cellular metabolism, allowing users to build, simulate, and analyze complex metabolic models (e.g., genome-scale models). Core functionalities include Flux Balance Analysis (FBA), Flux Variability Analysis (FVA), performing gene/reaction knockouts, and optimizing growth media. It supports standard metabolic model formats like SBML, JSON, and YAML.

An autonomous research agent that plans complex investigations using Directed Acyclic Graphs (DAGs). It executes sub-questions in parallel, performs gap analysis, and iteratively refines findings before synthesizing a comprehensive, structured report. Ideal for deep market analysis, academic literature reviews, or complex problem-solving requiring multiple data sources.