DevOps & Infra

holobiomicslab Skill

Use when after running the ENCODE Hi-C uniform processing pipeline or Juicer on FASTQ input data and generating a .hic output file.

holobiomicslab Skill

Use when you have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating domains, or annotate other structural features without re-running the full alignment and contact matrix construction.

holobiomicslab Skill

Use when when you need to verify the current operational status of a software project across multiple dimensions (CI/CD, code quality, test coverage, containerization, archival) and those status indicators are exposed as badge endpoints in the project's README.

holobiomicslab Skill

Use when you need to validate that a repository's automated build and publish pipeline is functioning correctly on a release or target branch, particularly when assessing the reliability of release artifacts or the health of a CI/CD workflow.

holobiomicslab Skill

Use when after implementing or modifying an mzML parser module that converts mzML files into MS-DIAL's internal data model, and before integrating the parser into the production analysis pipeline.

holobiomicslab Skill

Use when when you have a metabolomics dataset loaded into a SummarizedExperiment and need to apply a sequence of analysis steps (data loading, annotation, statistical analysis, visualization, reporting) in a reproducible, self-contained pipeline where each function's output becomes the next.

holobiomicslab Skill

Use when you have raw MS data files directly from a vendor instrument (Thermo .raw, Agilent .d, Waters .ms, etc.) and need to process them through AriumMS or any other metabolomics pipeline that accepts only .mzXML or .mzML formats.

holobiomicslab Skill

Use when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) and need to feed it into a CNN-based metabolite annotation pipeline.

holobiomicslab Skill

Use when after modifying a FIDDLE configuration file to add or remove instrument types from the allowlist (e.g., adding 'ftms' to gnps_orbitrap), run the full preprocessing pipeline and validate that the resulting training and test set sizes match documented targets.

holobiomicslab Skill

Use when when processing large-scale mass spectrometry datasets (>1 million spectra) where CPU-based clustering runtime would exceed minutes to hours, and when the analysis pipeline includes: (1) encoding raw spectra into high-dimensional binary vectors, (2) computing pairwise distance matrices.

holobiomicslab Skill

Use when you have a published predictive model with known coefficients and feature requirements (e.g., MetaboAge from a peer-reviewed study), a target R package with an established data pipeline (e.

holobiomicslab Skill

Use when you have fingerprint or spectrum data that requires compound-class annotation but prefer not to run SIRIUS locally, or need to integrate predictions into an automated analysis pipeline.

holobiomicslab Skill

Use when you have configured a GitHub Actions workflow that executes build, test, and quality checks, and you want to embed a machine-readable, auto-updating badge in your repository README to signal pipeline status at a glance.

holobiomicslab Skill

Use when you need to build a web-based data ingestion layer that accepts raw MS files (.raw, .mzML, .mzXML) from users, validates them before storage, and tracks their processing status through a data management pipeline.

holobiomicslab Skill

Use when you have raw GCIMS sample files (from a GC–IMS instrument) and an annotations table (Excel, CSV, or TSV) with sample metadata, and you need to begin the GCIMS preprocessing pipeline.

holobiomicslab Skill

Use when when receiving raw MS data files of unknown or mixed acquisition modalities and needing to route each to its corresponding analysis pipeline. Specifically, apply this skill when: (1) input files arrive without documented instrument type or chromatographic/mobility dimensionality;

holobiomicslab Skill

Use when transitioning feature intensity data between pipeline stages (e.

holobiomicslab Skill

Use when you have raw LC-HRMS metabolomics data in mzML or ABF format that needs to be processed through a reproducible pipeline. Use this skill when: (1) you have public or proprietary .mzML LC-MS datasets (e.g. from MetaboLights, MassIVE, or PRIDE);

holobiomicslab Skill

Use when you have Thermo Orbitrap .raw files and need to access raw spectral data (individual MS1 or MS2 scans, base-peak values, chromatogram traces, retention times, or scan-level metadata) for custom analysis, visualization, or integration into an R-based pipeline.

holobiomicslab Skill

Use when after applying a configuration fix (e.g., adding an instrument type to an allowlist, updating filtering thresholds) to a dataset preprocessing pipeline, you need to confirm that the change produces the documented training/test split counts.

holobiomicslab Skill

Use when you have raw 1D NMR spectra (FID or processed spectrum files) and need to extract peak parameters (chemical shift, intensity, linewidth) in a tabular format for downstream metabolomic or structural analysis.

holobiomicslab Skill

Use when after executing the Juicer pipeline on raw Hi-C FASTQ files, to confirm that the pipeline has generated the expected .hic output artifact and that the contact matrix construction and normalization steps completed without error.

holobiomicslab Skill

Use when when you have obtained or are considering use of the tima Docker image (adafede/tima-r) and need to confirm that the containerized environment is operational before proceeding with metabolite annotation workflows. This is a smoke test to catch environment or registry issues early.

holobiomicslab Skill

Use when you need to launch a pre-built Docker image of a scientific tool (e.

holobiomicslab Skill

Use when when you have raw Agilent MassHunter (.d) or UIMF IM-MS data files from drift tube (DT) or structure for lossless ion manipulations (SLIM) instruments and need to ingest them into a preprocessing pipeline that requires standardized in-memory or intermediate representations for.

holobiomicslab Skill

Use when you have constructed molecular graphs with atom features (atomic number, degree, formal charge, hybridization) and bond features (bond type, aromaticity) from SMILES or MOL files using RDKit, and need to feed them into a PyTorch-based GNN training pipeline without memory overhead or I/O.

holobiomicslab Skill

Use when before launching the DaDIA metabolomics pipeline or any analysis that requires specific R package versions. Apply this skill when you have access to an R environment and need to verify that R ≥4.0, XCMS ≥3.11.4, and metaMS ≥1.25.1 are installed and compatible.

holobiomicslab Skill

Use when you have a complete R package (e.g., pmartR) implementing a multi-step omics analysis pipeline (upload → transform → filter → normalize → test → visualize), and you want to make those steps accessible to scientists who lack R expertise.

holobiomicslab Skill

Use when after completing data merging, cleanup, and batch correction steps in the FBMN-STATS pipeline, when you have a processed feature quantification table combined with sample metadata in memory (R data frame or Python pandas DataFrame) and need to preserve it for multivariate statistical.

holobiomicslab Skill

Use when when developing or validating a DNA methylation array analysis pipeline using ChAMP, you need an independent ground-truth dataset to confirm that DMR detection is working correctly.

holobiomicslab Skill

Use when when you have .mzML or .abf LC-HRMS raw data files that require MS-DIAL-based feature detection, chromatogram alignment, and metabolite identification, and you need to ensure reproducibility across local machines, cloud, and HPC systems without manual tool installation and dependency.

holobiomicslab Skill

Use when when you need to verify that a GitHub Actions workflow (such as a development build or release pipeline) executes without fatal errors and produces expected artifacts. Use this skill when the workflow is already configured in a repository (e.g., a .yml file in .

holobiomicslab Skill

Use when you need to confirm that a documented web service URL is live and reachable before attempting to submit analysis jobs, download results, or integrate the service into an automated pipeline. Use it as a prerequisite check when the service documentation claims academic or public availability.

holobiomicslab Skill

Use when when you need to verify that a Java project's automated build pipeline (GitHub Actions workflow) executes without errors and generates distributable artifacts (e.g., .deb installers, portable binaries, or .jar files).

holobiomicslab Skill

Use when when deploying a containerized application (e.g., ipbhalle/metfragweb) with injected configuration files via Docker volume mounts, and you need to confirm that the container accepted the mounted file and applied its settings before proceeding with downstream analysis or services.

holobiomicslab Skill

Use when when building a platform that must accept raw MS data files (e.g., .raw, .mzML, .mzXML) from instrument runs or external sources as the first stage of an automated omics workflow.