DevOps & Infra

holobiomicslab Skill

Use when you have a shallow decision tree trained on ChemEcho feature vectors (peak or neutral loss formulas) and need to deploy it as an executable query against tandem mass spectrometry data.

holobiomicslab Skill

Use when you have mass-spectrometry raw data files from multiple vendors (e.g., Thermo, Waters, Bruker, Sciex) and/or mixed standard formats (mzML, mzXML) that must be processed by a single analysis pipeline.

holobiomicslab Skill

Use when when you need to capture a snapshot of a research software project's health metrics from multiple CI/CD and repository services (Travis CI, Landscape.

holobiomicslab Skill

Use when when you need to confirm that a published Docker image (e.g., hosted on Docker Hub) can be pulled and instantiated successfully, and when the target tool has a defined entry point or CLI interface.

holobiomicslab Skill

Use when when you have a partially documented or undocumented MS analysis pipeline and need to verify its correctness, trace data provenance through multiple processing stages, integrate tools via unified parameter handling (CTD scheme), or ensure the workflow adheres to community standards for.

holobiomicslab Skill

Use when when you have a containerized scientific tool available on Docker Hub (e.

holobiomicslab Skill

Use when after implementing or modifying the scoring module that computes average InChIKey scores and neighbourhood scores for candidate matches, or when integrating new scoring logic into an existing MS2Query pipeline.

holobiomicslab Skill

Use when after training a decision tree classifier on ChemEcho sparse feature vectors (representing tandem mass spectra fragmentation patterns), especially when the goal is to deploy predictions as executable queries or to validate that learned splits correspond to chemically meaningful.

holobiomicslab Skill

Use when you have raw LC-MS/MS spectral data in vendor formats or unvalidated .mgf files before feeding them into the specXplore importing pipeline.

holobiomicslab Skill

Use when when you need to deploy SAND for 1D NMR spectrum deconvolution on a new machine or cluster, or when testing code changes before merging into production.

holobiomicslab Skill

Use when you need to verify that a GitHub Actions workflow (such as a Build and Publish pipeline) executes successfully on a specific branch (e.g., release branch) and produces a passing build status.

holobiomicslab Skill

Use when when you need to verify that a continuous integration pipeline for a scientific software project (e.g., mzmine) completes successfully, produces expected build artifacts, or fails in a reproducible manner.

holobiomicslab Skill

Use when you need to validate that a software project's release branch is stable and ready for distribution. Specifically, use it when: (1) a release tag has been created or code pushed to a release branch; (2) you need to confirm that CI/CD pipelines execute without failures;

holobiomicslab Skill

Use when you need to validate that a scientific software project's continuous integration pipeline is functional and producing reproducible builds—particularly before releasing new versions, after merging changes to release branches, or when troubleshooting build failures that block distribution of.

holobiomicslab Skill

Use when when you have a metadata table with taxonomic annotations (species, genus, family columns) that may contain outdated, misspelled, or non-canonical taxon names, and you need to integrate these samples into a natural products analysis pipeline that requires standardized taxonomy (e.

holobiomicslab Skill

Use when when you have deposited mass spectrometry imaging data in NetCDF (CDF) format paired with MATLAB workspace files (.

holobiomicslab Skill

Use when when you have obtained source code for a Maven-based Java project and need to determine whether your local build environment can successfully compile it, or when preparing to reproduce a published CI/CD build workflow from a GitHub Actions or similar pipeline configuration.

holobiomicslab Skill

Use when you need to automate testing and quality checks on code changes—specifically when pull requests or commits are made to a repository and you want to verify that builds succeed, test suites pass, and code quality metrics meet project standards before merging.

holobiomicslab Skill

Use when after feature clustering and drift correction (Gravity and Blueshift outputs) are complete and you need to produce a final, validated feature table ready for storage, archival, or downstream analysis.

holobiomicslab Skill

Use when when you have loaded (un)targeted metabolite data into a Metaboprep object and need to exclude samples with excessive missing values before quality control or statistical analysis. This is typically applied early in the QC pipeline when sample-level data completeness is a concern (e.

holobiomicslab Skill

Use when after you have processed raw LC-MS/MS spectral data through the specXplore importing pipeline in a Jupyter notebook and produced an in-memory specXplore session data object containing t-SNE embeddings (based on ms2deepscore similarity scores) and associated spectral metadata.

cyberstrikeus Skill

Ensure that the --service-account-lookup argument is set to true (Manual)

cyberstrikeus Skill

Ensure that the --service-account-key-file argument is set (Manual)

cyberstrikeus Skill

Ensure that the --etcd-certfile and --etcd-keyfile arguments are set (Manual)

cyberstrikeus Skill

Ensure that the --tls-cert-file and --tls-private-key-file arguments are set (Manual)

cyberstrikeus Skill

Ensure that the --tls-ca-file argument is set (Manual)

cyberstrikeus Skill

Ensure that the --etcd-cafile argument is set (Manual)

cyberstrikeus Skill

Ensure that encryption providers are appropriately configured (Manual)

cyberstrikeus Skill

Ensure that the API Server only makes use of Strong Cryptographic Ciphers (Manual)

cyberstrikeus Skill

Ensure that unsupported configuration overrides are not used (Manual)

cyberstrikeus Skill

Ensure that the kubelet configuration file ownership is set to root:root (Automated)

cyberstrikeus Skill

Ensure that the --rotate-certificates argument is not set to false (Manual)

cyberstrikeus Skill

Verify that the RotateKubeletServerCertificate argument is set to true (Manual)

cyberstrikeus Skill

Ensure that the Kubelet only makes use of Strong Cryptographic Ciphers (Manual)

cyberstrikeus Skill

Minimize access to privileged Security Context Constraints (Manual)

cyberstrikeus Skill

Minimize access to the approval sub-resource of certificatesigningrequests objects (Manual)