Git & Version Control

Generate descriptive commit messages by analyzing git diffs. Use when the user asks for help writing commit messages or reviewing staged changes.

Comprehensive frontend development skill for building modern, performant web applications using ReactJS, NextJS, TypeScript, Tailwind CSS. Includes component scaffolding, performance optimization, bundle analysis, and UI best practices. Use when developing frontend features, optimizing performance, implementing UI/UX designs, managing state, or reviewing frontend code.

Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

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.

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

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.

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

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.

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.

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.

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

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.

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

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

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).

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.

Help address review/issue comments on the open GitHub PR for the current branch using gh CLI; verify gh auth first and prompt the user to authenticate if not logged in.

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.