Git & Version Control

Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.

Production-ready PDF processing with forms, tables, OCR, validation, and batch operations. Use when working with complex PDF workflows in production environments, processing large volumes of PDFs, or requiring robust error handling and validation.

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.

PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

Comprehensive fullstack development skill for building complete web applications with React, Next.js, Node.js, GraphQL, and PostgreSQL. Includes project scaffolding, code quality analysis, architecture patterns, and complete tech stack guidance. Use when building new projects, analyzing code quality, implementing design patterns, or setting up development workflows.

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.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Intelligently organizes your files and folders across your computer by understanding context, finding duplicates, suggesting better structures, and automating cleanup tasks. Reduces cognitive load and keeps your digital workspace tidy without manual effort.

Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets, for PyTorch-based ML on molecules, proteins, and biomedical graphs.

Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.

Comprehensive security engineering skill for application security, penetration testing, security architecture, and compliance auditing. Includes security assessment tools, threat modeling, crypto implementation, and security automation. Use when designing security architecture, conducting penetration tests, implementing cryptography, or performing security audits.

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Comprehensive SecOps skill for application security, vulnerability management, compliance, and secure development practices. Includes security scanning, vulnerability assessment, compliance checking, and security automation. Use when implementing security controls, conducting security audits, responding to vulnerabilities, or ensuring compliance requirements.

Automatically creates user-facing changelogs from git commits by analyzing commit history, categorizing changes, and transforming technical commits into clear, customer-friendly release notes. Turns hours of manual changelog writing into minutes of automated generation.

Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).

Manage issues, projects & team workflows in Linear. Use when the user wants to read, create or updates tickets in Linear.