DevOps & Infra

cyberstrikeus Skill

Ensure 'Cross Region Restore' is set to 'Enabled' on Recovery Services vaults

cyberstrikeus Skill

Ensure 'Cross Subscription Restore' is set to 'Disabled' or 'Permanently Disabled' on Recovery Services vaults

holobiomicslab Skill

Use when after converting or downloading a pre-trained Keras model to HDF5 TensorFlow 2.3.0 format, particularly when integrating the model into a fixed-interface pipeline (e.g., NP Classifier) that expects specific named input/output layers.

holobiomicslab Skill

Use when when you have Thermo Fisher Scientific .raw files from an Orbitrap instrument and need to identify the m/z value and corresponding intensity of the most abundant ion in each MS1 scan for quality control, method optimization, or feature extraction in a modular R-based proteomics pipeline.

holobiomicslab Skill

Use when deploying the ipbhalle/metfragweb container and you need to supply custom MetFrag settings (ChemSpider tokens, proxy servers, local database connections) without modifying the container image.

holobiomicslab Skill

Use when when designing or integrating a file parser for mass spectrometry formats (.raw Thermo RAW format, .mzml XML-based format) in a metabolomics processing pipeline, or when reading legacy or heterogeneous instrument output where file integrity cannot be guaranteed.

holobiomicslab Skill

Use when when deploying an OpenMS streamlit application that must support both local development (offline mode with multiprocessing) and production cloud/HPC environments (online mode with Redis + RQ task queue), and you need to transparently route workflow job submissions to the correct backend.

holobiomicslab Skill

Use when you have raw mass spectrometry quantification tables (feature abundance matrices), sample metadata tables, and spectral data files (e.g., from the omsw_pleurotus dataset) that must be ingested into the msFeaST pipeline;

holobiomicslab Skill

Use when when you have cloned or obtained a Python package repository and need to confirm that the codebase's tests pass before integration, contribution, or deployment. Particularly relevant when the repository advertises a Tests badge linked to a CI/CD workflow (e.

holobiomicslab Skill

Use when when implementing or extending file format parsers in a spectral data pipeline, you need unit tests to ensure that format-specific parsers correctly instantiate spectrum objects with expected m/z arrays, intensity arrays, and metadata attributes before releasing to users or integrating.

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 a traditional peak extraction pipeline (e.g., XCMS) has generated a feature table from LC-MS data but fails to detect known or suspected compounds present in your sample. Specifically, when you have a suspect database (e.

holobiomicslab Skill

Use when when you have raw LC-HRMS metabolomics data in .mzML or .

holobiomicslab Skill

Use when when your untargeted LC-MS pipeline must support multiple peak-picking backends and you need to let users specify which algorithm to use (via configuration file or parameter) without hard-coding algorithm dependencies.

holobiomicslab Skill

Use when when reproducing or auditing FIDDLE's formula prediction pipeline, or when implementing the TCN encoder in your own codebase and need to confirm that the precursor m/z (env[:, 0]) has been removed from the feature vector to avoid leakage of mass information into the model's learned.

holobiomicslab Skill

Use when your annotation pipeline depends on multiple external web converters and you need to diagnose why annotation jobs are failing, slow, or incomplete. Use it if you observe missing metadata fields in output .

holobiomicslab Skill

Use when after rewriting or refactoring a Python module (such as calculate_feature_overlap.py in a metabolomics pipeline) to improve performance, maintainability, or functionality, you need to confirm that the new implementation does not introduce regressions.

holobiomicslab Skill

Use when when you need to coordinate multiple bioinformatics tools (quality control, alignment, quantification, normalization, batch correction) across diverse compute environments (HPC, cloud, local) while ensuring reproducibility and parameter traceability.

holobiomicslab Skill

Use when after deploying a containerized web application (e.g., via `docker run`), before proceeding to functional testing or integration. Use this skill to confirm the application server (Tomcat, etc.) has fully initialized and the web service is listening on the mapped port and URL path.

holobiomicslab Bundle

Use when you have untargeted LC-MS/MS data (mzML) and want an annotated feature table — preprocessing, blank/QC filtering, feature-based molecular networking, spectral library matching, SIRIUS de novo annotation, optional taxonomy-aware re-weighting, and a fused master table. This is the canonical metabopipe-style annotation pipeline.

holobiomicslab Skill

Use when when initializing an mWISE annotation pipeline with a new or custom KEGG database, or when you need to reconstruct the Cpd.Add matching table with modified adduct/fragment specifications (e.g., subset to instrument-specific adducts or adjust frequency thresholds).

holobiomicslab Skill

Use when a mass spectrometry analysis pipeline must accept data from multiple sources with different identifier schemes (GNPS Task ID, Universal Spectrum Identifiers, or Feature-Based Molecular Networking task IDs), and you need to transparently route each to the correct loader without requiring.

holobiomicslab Skill

Use when after Casanovo has generated ranked peptide sequence predictions from MS/MS spectra and you need to persist, share, or integrate the results into a proteomics data management or visualization pipeline.

holobiomicslab Skill

Use when when you have a fragment peak list (m/z values and intensities) from MS/MS data and need to assign candidate chemical subformulae to each peak as part of a de novo chemical formula inference pipeline.

holobiomicslab Skill

Use when when reproducing or validating a tandem mass spectrometry denoising pipeline on mzML files with known feature precursor m/z and RT coordinates, compare pre- and post-filter counts of spectra and fragments at each major step (TIC cutoff, intra-spectrum grouping, frequency-based labeling).

holobiomicslab Skill

Use when when you have MS/MS spectral data (raw or intermediate format) that must be fed into the Mass2SMILES Docker container or similar deep learning models for MS/MS-to-structure inference.

holobiomicslab Skill

Use when after executing a Nextflow-based MS-DIAL workflow on .mzML LC-HRMS metabolomics data using Docker or Singularity container backends.

holobiomicslab Skill

Use when when you have domain-specific functionality (e.g., spectral similarity scoring, peak detection algorithms) implemented in one language (Python) but need to make it callable and composable within an R-based analytical pipeline (Spectra objects);

holobiomicslab Skill

Use when when deploying a multi-service microarchitecture (such as MAGMa's four distinct subprojects: magmaweb, joblauncher, job, and pubchem) via Docker Compose and you need to ensure that service startup order respects true readiness rather than container existence—particularly when services have.

holobiomicslab Skill

Use when you are building a Docker image for a .NET Framework 4.8 application (like AirdPro) that must run on both Windows native containers and Linux+Wine environments, and you need to reduce build time and image size while maintaining separate targets for GUI, CLI, and development modes.

holobiomicslab Skill

Use when after completing dereplication and cosine similarity clustering in the MolNotator pipeline, when you have merged deduplicated molecular predictions and ion annotations and need to construct the final network representation for visualization and compound identification.

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 after executing feature detection and quantification on raw LC-MS data (mzML or NetCDF format) using an automated pipeline such as MetaboAnalystR 4.0, and before proceeding to downstream normalization, scaling, or functional analysis.

holobiomicslab Skill

Use when when implementing new scoring components (inchikey score, neighbourhood score, or similar structural/spectral similarity metrics) that are integrated into an MS/MS candidate re-ranking pipeline.

holobiomicslab Bundle

Use when running the Workflow4Metabolomics LC-MS pipeline end to end on a Galaxy instance — MSnbase import, xcms peak detection, correspondence, alignment and gap filling, CAMERA annotation, three-table conformance, batch correction, statistics — in the stage order the wrappers' datatypes enforce.