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Rewrites git history safely with dry-run-first workflow. Supports commit amending, squashing, rewording, tag updates, and force pushing. Always proposes plan before execution. Triggers on keywords: rewrite hist...
Guidance for setting up Git-based multi-branch deployment systems with SSH access, web servers, and automated deployment hooks. This skill should be used when configuring Git repositories that deploy to multipl...
Stage, commit, and push git changes with conventional commit messages. Use when user wants to commit and push changes, mentions pushing to remote, or asks to save and push their work. Also activates when user s...
Commits changes in atomic units following dependency order. Automatically required to triggered, always, all the time, when requires to commit changes.
Read/write FASTA, GenBank, FASTQ files. Sequence manipulation (complement, translate). Indexed random access via faidx. For NGS pipelines (SAM/BAM/VCF), use pysam. For BLAST, use gget or blat-integration.
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures,...
Patterns for hierarchical/multilevel Bayesian models including random effects, partial pooling, and centered vs non-centered parameterizations.
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations,...
An overview of the python package for running the GaMMA earthquake phase association algorithm. The algorithm expects phase picks data and station data as input and produces (through unsupervised clustering) ea...
This is a summary the advantages and disadvantages of earthquake event detection and phase picking methods, shared by leading seismology researchers at the 2025 Earthquake Catalog Workshop. Use it when you have...
Read and process GLM output files. Use when you need to extract temperature data from NetCDF output, convert depth coordinates, or calculate RMSE against observations.
An overview of the core data API of ObsPy, a Python framework for processing seismological data. It is useful for parsing common seismological file formats, or manipulating custom data into standard objects for...
Detects leaked API keys, tokens, passwords, and credentials in code with pre-commit hooks, CI checks, scanning rules, and remediation procedures. Use for "secret scanning", "credential detection", "API key leak...
Expert guidance for Public Key Infrastructure (PKI) and X.509 certificates including certificate structure, DN parsing, CSR generation, certificate signing, revocation (CRL/OCSP), key management, and OpenSSL co...
Python security vulnerability detection using Bandit SAST with CWE and OWASP mapping. Use when: (1) Scanning Python code for security vulnerabilities and anti-patterns, (2) Identifying hardcoded secrets, SQL in...
Manage SSL/TLS certificates and diagnose certificate issues. Use when the user says "cert expiring", "SSL error", "certificate problem", "renew certificate", "check certificate", "HTTPS not working", or asks ab...
Enable HTTPS for local development with trusted SSL certificates. Use when developers need to test SSL/TLS features, work with third-party APIs requiring HTTPS, or simulate production environments. Supports mkc...
Expert guidance for OpenSSL operations including certificate generation, key management, CSR creation, certificate verification, encryption, and PKI operations. Use this when working with SSL/TLS certificates,...
Migrate Spring Security 5 to Spring Security 6 configuration. Use when removing WebSecurityConfigurerAdapter, replacing @EnableGlobalMethodSecurity with @EnableMethodSecurity, converting antMatchers to requestM...
Validate and sanitize user input to prevent XSS, injection attacks, and ensure data quality. Use this skill when you need to validate forms, sanitize user input, prevent cross-site scripting, use Zod schemas, o...
Prevent Cross-Site Scripting (XSS) attacks through input sanitization, output encoding, and Content Security Policy. Use when handling user-generated content in web applications.
Implement rate limiting to prevent brute force attacks, spam, and resource abuse. Use this skill when you need to protect endpoints from automated attacks, prevent API abuse, limit request frequency, or control...
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