Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+...
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm...
Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or...
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory...
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing...
Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game...
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure,...
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information,...
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference...
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and...
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For...
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.