DevOps & Infra

holobiomicslab Skill

Use when after converting or loading a Keras model to HDF5 TensorFlow 2.3.0 format, especially when the model will be served through a pipeline (e.g., NP Classifier) that expects specific input/output layer names.

holobiomicslab Skill

Use when you need to containerize a C# application (e.g., AirdPro) that targets .NET Framework 4.8 and must run on Linux hosts via Docker, but the application was originally built for Windows. Use this skill when you are building multi-stage Docker images from a Ubuntu 22.

holobiomicslab Skill

Use when when releasing or archiving a computational workflow (e.g., an R or Python-based normalization pipeline) and you need to ensure that future users or reviewers can re-run the analysis in an identical computational environment.

holobiomicslab Skill

Use when after computing molecular descriptors (RDKit, mordred) or featurizing chromatographic parameters (column metadata, gradient slopes, pH, additives), you have a NumPy array or list of arrays in memory that must be persisted for reproducibility, shared across pipeline stages, or archived.

holobiomicslab Skill

Use when when selecting a spectrum processing library for high-throughput proteomics or metabolomics workflows, or when optimizing an existing pipeline for computational efficiency. Apply this skill when you have access to representative raw MS data (e.

holobiomicslab Skill

Use when you have cloned a scientific Python project (e.g., scverse/scanpy) and need to verify that your local development environment matches the CI specification before submitting contributions, or when auditing whether the published test suite executes without failures on a fresh checkout.

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 you are setting up HiC-Pro or a similar multi-tool pipeline for the first time, or you need to validate that all required dependencies are installed and discoverable.

holobiomicslab Skill

Use when you have translated or raw SMILES strings from a chemical structure curation pipeline and need to remove invalid chemical structures, resolve sanitization errors (e.

holobiomicslab Skill

Use when you have trained or pre-trained ML models (Keras, TensorFlow) that need to be exposed as HTTP endpoints for programmatic classification or inference, require reproducible deployment across environments, or need to coordinate multiple services (e.

holobiomicslab Skill

Use when you have executed an end-to-end SnapATAC2 pipeline on the pbmc10k_multiome dataset (or a similar single-cell ATAC-seq dataset with a published reference) and need to validate that spectral embedding, Leiden clustering, and UMAP layout have converged to expected cluster identities and.

holobiomicslab Skill

Use when you are deploying a Windows .NET application (e.g., AirdPro CLI) inside a Docker container on a non-Windows host and need to understand whether Wine initialization completes, how long it takes (documented as >30 minutes), whether .

holobiomicslab Skill

Use when you have built multiple Docker image variants (e.g., cli, dev, linux, windows) from a multi-stage Dockerfile and need to verify that their uncompressed and compressed storage footprints fall within documented acceptable ranges (e.

holobiomicslab Skill

Use when before launching any MetaboDirect pipeline run on a new system or environment. Trigger conditions: (1) first-time setup on a target OS (Windows, Linux, or macOS); (2) environment lacks Python 3.5+, R 4.0+, or Cytoscape 3.8+;

holobiomicslab Skill

Use when after starting a TensorFlow Serving instance (e.g., via docker-compose) and before attempting classification tasks, to confirm that input layers are named 'input_2048' and 'input_4096' and the output layer is named 'output'.

holobiomicslab Skill

Use when after running a non-targeted preprocessing (NPP) pipeline (e.g., XCMS, MZmine 2, OpenMS) on the same set of centroided mzML files that were used to generate a validated benchmark dataset.

holobiomicslab Skill

Use when you have a Windows-only C# GUI application (e.g., AirdPro) built for .NET Framework 4.8 that needs to run on non-Windows hosts (macOS or Linux), and you are using a multi-stage Docker build where the runtime stage includes Wine and Windows compatibility libraries.

holobiomicslab Skill

Use when you have raw mass spectrometry data converted to MS1 format and need to predict peptide features (charge, isotope count, retention time) without installing complex dependencies or configuring GPU/Python environments locally.

holobiomicslab Skill

Use when after deploying a web service in a Docker container with port mapping (e.g., -p 8888:8080), verify that the application is running and responding to HTTP requests at the mapped endpoint.

holobiomicslab Skill

Use when when building a mass spectrometry analysis pipeline that requires exact mass lookups, molecular formula validation, or isotope abundance predictions. Specifically: (1) you are constructing a MolecularFormula class that needs to validate element symbols against known isotopes;

holobiomicslab Skill

Use when your metabolomics analysis pipeline requires CCS value prediction for ion-mobility mass spectrometry data, you have access to a curated training set of known metabolites with experimentally validated CCS values, and you plan to predict CCS values on target datasets containing 10,000+.

holobiomicslab Skill

Use when when ingesting raw mass spectrometry data from multiple instrument vendors or file formats into a metabolomics processing pipeline, and you need to expose spectral and chromatographic metadata through a single, consistent interface regardless of the source format's internal structure.

holobiomicslab Skill

Use when you have executed a structure annotation pipeline (like BAM) on a validation dataset for which ground-truth molecular structure annotations exist, and you need to assess whether the pipeline's predictions match the reference annotations at the required sensitivity and specificity.

holobiomicslab Skill

Use when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all required tools are installed, executable, meet version requirements (e.g., samtools ≥1.

holobiomicslab Skill

Use when after cloning or installing a peak-calling or genomic analysis tool from a repository, before using it on production data.

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 you need to verify whether a GitHub Actions workflow badge (e.g., main.yml) accurately reports the CI pipeline's true pass/fail status.

holobiomicslab Skill

Use when when accepting a file path as input in an MSI data processing pipeline and you need to determine which data reader module to instantiate before calling get_image_data() or load_pixels(). This arises when building a multi-vendor instrument workflow (e.

holobiomicslab Skill

Use when you have a raw .xlsx or tabular file listing candidate compounds with theoretical or measured m/z values, expected retention times, and ionization polarities, and you need to feed this into TARDIS or another targeted LC–MS analysis pipeline.

holobiomicslab Skill

Use when you have raw metabolomics data (e.g., in standard bioinformatics formats supported by maplet) and need to initialize an analytical pipeline that will integrate multiple processing and analysis steps.

holobiomicslab Skill

Use when ingesting heterogeneous raw chemical structures from external datasets, publications, or user submissions into a retention time or molecular property prediction pipeline.

holobiomicslab Skill

Use when when you have documented pinned package versions for a Python-based scientific implementation (e.g., from a README or project documentation) and need to distribute a reproducible computational environment to other users or CI/CD systems.

holobiomicslab Skill

Use when you need to embed CYP450 metabolite prediction directly into a larger Java software pipeline or require dynamic toggling of the CypReact filter module based on experimental parameters.

holobiomicslab Skill

Use when building a Streamlit application that must support both cloud deployments (with Redis task queuing) and local/offline execution (with multiprocessing), and you need to automatically select the execution path without requiring separate code paths or manual configuration switches at runtime.

holobiomicslab Skill

Use when you have FT-ICR MS peak abundance data in Formularity .

holobiomicslab Skill

Use when after peak clustering in a GCIMS preprocessing pipeline, when the peak table matrix contains NA values corresponding to peaks detected in some samples but not others, and you have computed cluster statistics that characterize each peak cluster's properties.