DevOps & Infra

holobiomicslab Skill

Use when when you have raw PubChem compound records or other public chemical structure databases and need to supply candidate metabolite structures to a mass spectrometry annotation workflow like MAGMa.

holobiomicslab Skill

Use when after msFeaST pipeline execution has produced a dashboard_data.json file containing quantification, metadata, and spectral matrices, or when you need to validate that preprocessing steps correctly loaded and rendered ms/ms feature data before downstream statistical or network analysis.

holobiomicslab Skill

Use when when you have vendor-format LC-MS acquisition files (Thermo .raw, Bruker .d, Sciex .ms, Agilent, Waters formats) that need to be ingested into a quality control or data processing pipeline that requires open, standardized spectral formats.

holobiomicslab Skill

Use when when preparing to process raw LC-HRMS metabolomics data (.mzML or .abf files) with MS-DIAL within a Nextflow pipeline, before executing peak detection and chromatogram alignment.

holobiomicslab Skill

Use when you need to assess whether a newly developed FT-ICR MS pipeline (e.

holobiomicslab Skill

Use when when a repository displays a GitHub Actions workflow badge (e.

holobiomicslab Skill

Use when you are evaluating a new or existing data analysis pipeline (e.g., MetaboDirect) and need to produce a transparent, evidence-based feature matrix showing which analyses it supports—particularly when the pipeline is positioned as an alternative to or improvement over established tools.

holobiomicslab Skill

Use when when preparing to apply LDA to a new MS/MS spectral dataset in bag-of-fragments format, before running the full modeling pipeline.

holobiomicslab Skill

Use when when you need to quantify and document the computational cost of a multi-stage analysis pipeline (such as MetaboDirect) across varying input sizes (e.

holobiomicslab Skill

Use when you have prepared metabolomics input files (feature quantification table, MS/MS spectra in MGF format, sample metadata) and are about to execute the TIMA taxonomically informed annotation pipeline, or after pipeline execution to verify all outputs were generated correctly.

holobiomicslab Skill

Use when when invoking Asari to process centroid mzML files for the first time in a PCPFM experiment, or when RT and m/z accuracy characteristics of your LC-MS instrument differ from the pipeline defaults (e.

holobiomicslab Skill

Use when you have executed multiple database search pipelines (Dereplicator, VarQuest, and/or Dereplicator+) on centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) against a chemical structure database of known natural products, and you need to: (1) identify which pipeline(s).

holobiomicslab Skill

Use when you are preparing to run the MetaboDirect pipeline for the first time on a new machine, or you need to reproduce a published benchmark or analysis on a different OS (Windows, Linux, MacOS) and want to guarantee that all six pipeline steps (data pre-processing, diagnostics, exploration.

holobiomicslab Skill

Use when you have one or more vendor mass spectrometry raw files (Thermo .raw, Agilent .d, Sciex .wiff2, or other MSConvert-supported formats) that must be converted to Aird format for batch processing, cloud deployment, or integration with downstream analysis tools.

holobiomicslab Skill

Use when when you have a .msp mass spectra file with incomplete or missing chemical metadata fields (SMILES, InChI, CAS number, formula, InChIKey, IUPAC name) and need to populate those fields by querying multiple external chemical identifier services and local cheminformatics tools in parallel.

holobiomicslab Skill

Use when when you have access to source code or algorithmic documentation of a metabolite generation pipeline (such as MAGMa's job subproject) and need to understand, validate, or reconstruct the transformations that convert a parent compound into enumerated metabolite candidates.

holobiomicslab Skill

Use when you have developed new scoring logic (e.g., average inchikey score, neighbourhood score) for an MS/MS spectral analogue search tool and need to embed these components into an existing production pipeline that uses a random forest to combine multiple features for candidate re-ranking.

holobiomicslab Skill

Use when you have a vendor mass spectrometry raw file (e.g., .raw format) that requires conversion to Aird format using AirdPro CLI, and you are running on macOS or Linux.

tools-only Bundle

Provides AWS CloudFormation patterns for IAM users, roles, policies, and managed policies. Use when creating IAM resources with CloudFormation, implementing least privilege access, configuring cross-account access, setting up identity centers, managing permissions boundaries, and organizing template structure with Parameters, Outputs, Mappings, Conditions for secure infrastructure deployments.

tools-only Bundle

Provides AWS RDS (Relational Database Service) management patterns using AWS SDK for Java 2.x. Use when creating, modifying, monitoring, or managing Amazon RDS database instances, snapshots, parameter groups, and configurations.

tools-only Bundle

End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2. Use when processing 16S/ITS amplicon data.

tools-only Bundle

End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR editing experiments for gene knockout, correction, or tagging.

tools-only Bundle

End-to-end time-course analysis from expression matrix to temporal patterns and enrichment. Covers temporal DE, Mfuzz soft clustering, optional rhythm detection, GAM trajectory fitting, and per-cluster pathway enrichment. Use when analyzing bulk time-series expression experiments from any omics platform.

tools-only Bundle

Comprehensive DAG failure diagnosis and root cause analysis. Use for complex debugging requests requiring deep investigation like "diagnose and fix the pipeline", "full root cause analysis", "why is this failing and how to prevent it". For simple debugging ("why did dag fail", "show logs"), the airflow entrypoint skill handles it directly. This skill provides structured investigation and prevention recommendations.

tools-only Bundle

Generates Azure and technical architecture diagrams (PNG via Python diagrams) from requirements or IaC, including topology, process flow, ERD, and wireframe visuals.

tools-only Bundle

End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac. Use when analyzing joint scRNA+scATAC data.

tools-only Bundle

Creates Azure Architecture Decision Records (ADRs) with WAF mapping, alternatives, consequences, and implementation guidance; use for architecture decision documentation requests.

tools-only Bundle

End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.

tools-only Bundle

Manages Apache Airflow operations including listing, testing, running, and debugging DAGs, viewing task logs, checking connections and variables, and monitoring system health. Use when working with Airflow DAGs, pipelines, workflows, or tasks, or when the user mentions testing dags, running pipelines, debugging workflows, dag failures, task errors, dag status, pipeline status, list dags, show connections, check variables, or airflow health.

tools-only Bundle

Comprehensive technical diagramming toolkit for solutions architects, presales, and developers. Creates Azure architecture diagrams (700+ official Microsoft icons), business process flows, ERD diagrams, project timelines, UI wireframes, and network topology diagrams. Also generates diagrams from Bicep, Terraform, and ARM templates. **Output format**: PNG images via Python diagrams library (mingrammer/diagrams).

tools-only Bundle

End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.

tools-only Bundle

AWS CloudFormation patterns for Amazon S3. Use when creating S3 buckets, policies, versioning, lifecycle rules, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.

tools-only Bundle

AWS Lambda patterns using AWS SDK for Java 2.x. Use when invoking Lambda functions, creating/updating functions, managing function configurations, working with Lambda layers, or integrating Lambda with Spring Boot applications.

tools-only Bundle

End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods. Use when analyzing pooled CRISPR screens from count data to hit calling.

tools-only Bundle

Executes Azure deployments using generated Bicep templates. Runs deploy.ps1 scripts, performs what-if analysis, and manages deployment lifecycle. Step 6 of the 7-step agentic workflow.

tools-only Bundle

Executes Azure deployments using generated Bicep templates. Runs deploy.ps1 scripts, performs what-if analysis, and manages deployment lifecycle. Step 6 of the 7-step agentic workflow.