Web & Frontend

holobiomicslab Skill

Use when when you need to inventory a collection of related web applications or tools distributed across multiple repositories, discover their live deployment URLs, trace their associated publications, and verify accessibility and metadata completeness.

holobiomicslab Skill

Use when you have raw GC-MS output exported as CSV (containing columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.

holobiomicslab Skill

Use when when deploying Galaxy-M or similar multi-component metabolomics platforms that depend on heterogeneous runtime environments (Python, R, MATLAB, WINE) across multiple operating systems (Ubuntu 14.

holobiomicslab Skill

Use when after computing deviations for both motif and kmer annotations on the same chromVAR dataset, when you need to determine whether kmers and motifs are redundant predictors of chromatin accessibility variability or provide complementary information for downstream clustering, annotation, or.

holobiomicslab Skill

Use when you have aligned ATAC-seq BAM files from Tn5-based chromatin accessibility assays and need to perform footprinting analysis.

holobiomicslab Skill

Use when you have access to the source code of a webservice component (Python, configuration files, route definitions) and need to produce machine-readable API documentation (OpenAPI 3.

holobiomicslab Skill

Use when when you have source code access to a webservice component (such as the MAGMa joblauncher) and need to enumerate all exposed HTTP endpoints, their methods (GET, POST, etc.), URL patterns, parameter names, request/response payload structures, and authentication requirements in order to.

holobiomicslab Skill

Use when when you have a Python package with docstrings in the source code and need to generate comprehensive, browsable HTML API documentation.

holobiomicslab Skill

Use when you are loading index.html locally in a browser and WebWorker or WebAssembly components fail to initialize with cross-origin or file-access policy errors. This occurs when the default browser file-access policy blocks local resource sharing required by these technologies.

holobiomicslab Skill

Use when when you need to deploy the NP Classifier locally with TensorFlow Serving backend and nginx frontend on the same host, and you want to avoid manual container lifecycle management and inter-container networking configuration.

holobiomicslab Skill

Use when preparing ion image data for contrastive learning in mass spectrometry imaging (MSI), specifically when you need to augment single ion images into pairs of variants for encoder training in COL mode (co-localized ions) or as a base component of ISO mode (isotope ions).

holobiomicslab Skill

Use when when you have raw GC-MS output (CSV with columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.

holobiomicslab Skill

Use when when you have MS/MS-annotated features from a natural extract (via SIRIUS, CANOPUS, or ISDB) and need to compute the Literature Component or Class Component of a priority rank—i.

holobiomicslab Skill

Use when you need to run a web application locally (by opening index.html directly in the browser) and the application uses WebWorker or WebAssembly modules that fail to load with cross-origin policy or file-access errors.

holobiomicslab Skill

Use when you have executed batch searches against one or more domain-specific MASST tools and received multiple output files (_microbe.html, _plant.html, _tissue.html, _microbiome.html, _food.html, _matches.tsv, _library.tsv, _datasets.tsv, _count_*.

holobiomicslab Skill

Use when you have instantiated a learned component (embedding layer, encoder, or transformer submodule) from a published codebase and need to verify that its forward pass produces outputs matching the original paper's implementation before integrating it into a downstream analysis pipeline.

holobiomicslab Skill

Use when when you need to understand the modular structure of a multi-component research software project—particularly when integrating, documenting, or extending a system whose architecture is not immediately obvious from high-level descriptions.

holobiomicslab Skill

Use when you have an existing R package with statistical or data-processing functions and need to expose its functionality through an interactive web interface where end users (non-R programmers) can upload datasets, configure analysis parameters (e.

holobiomicslab Skill

Use when raw GC-MS data (netCDF or mzML format) contains overlapping chromatographic peaks with co-eluting ions that cannot be resolved by retention time alone.

holobiomicslab Skill

Use when analyzing GC-MS data containing overlapped peaks where two or more components co-elute within the same retention time window, making direct spectral assignment impossible.

holobiomicslab Skill

Use when a webservice component (like MAGMa's joblauncher) lacks formal API documentation but the source code is accessible, and downstream consumers (web applications, external services) need to understand available HTTP endpoints, parameter schemas, and response formats without manual.

holobiomicslab Skill

Use when when deploying a multi-component research application (e.g., MAGMa's four subproject services) as containerized microservices that need to communicate internally—specifically when you have identified service interdependencies (e.

holobiomicslab Skill

Use when you have a log2-transformed metabolite abundance matrix and need to visualize sample clustering patterns, batch structure, or the effect of batch correction. Scaling is essential because metabolites often have widely different absolute concentrations;

holobiomicslab Skill

Use when you have raw GC-MS data in netCDF or vendor-specific binary format and need to separate co-eluting compounds and extract clean mass spectra for each individual chemical component prior to molecular networking, spectral matching, or metabolite identification workflows.

holobiomicslab Skill

Use when you have paired scATAC-seq peak matrices and scRNA-seq gene expression matrices from the same cells (multiome data) and need to perform joint clustering, visualization, or correlation analysis across both chromatin accessibility and gene expression in a single coordinate system.

holobiomicslab Skill

Use when you have selected a subset of ReDU public tandem MS files with GNPS chemical annotations (level 2 or 3 spectral library matches) and wish to explore sample relationships via principal component analysis.

holobiomicslab Skill

Use when when implementing or modifying a numerical compression/decompression component (e.g., Numpress for mass-spectrometry m/z and intensity arrays) and you need to verify that round-trip encoding and decoding preserves numerical fidelity.

tomevault-io Bundle

Generate complete FastAPI backend scaffolds from OpenAPI 3.x specifications. Automatically creates SQLAlchemy models, Pydantic schemas, FastAPI routers, CRUD operations, database migrations, pytest tests, and Next.js TypeScript clients. Use when user provides an OpenAPI/OpenSpec file (.yaml/.json) or pastes spec content, and wants to generate API code. Triggers on phrases like "generate API from spec", "build backend from OpenAPI", "create FastAPI from this spec", "implement these endpoints", or when user shares OpenAPI specification files. Supports Python 3.12+, FastAPI, SQLite, SQLAlchemy, Alembic, pytest, and Next.js App Router. Use when this capability is needed.

holobiomicslab Skill

Use when you have a GNPS-format TSV metadata table with mandatory columns (ATTRIBUTE_Species, ATTRIBUTE_Organe, and optional genus/family columns) and need to prepare cleaned, standardized taxonomy strings for integration into the Literature Component or cross-referencing with external reference.

holobiomicslab Skill

Use when you have a set of differentially accessible peaks (output from differential accessibility testing, e.g., tl.

holobiomicslab Skill

Use when you have a sparse chromatin accessibility matrix (ATAC-seq or DNAse-seq counts per peak per sample), matched peak-annotation assignments (e.

holobiomicslab Skill

Use when you have acquired a versioned QC workflow definition file (YAML or JSON) from a metabolomics QC system release (e.g., v1.0.

holobiomicslab Skill

Use when when you need to understand the modular composition of a multi-component research software project, particularly before onboarding, refactoring, or deploying it.

holobiomicslab Skill

Use when you have a dashboard_data.json file (JSON export from the msFeaST pipeline) and need to interactively explore quantification tables, metadata, and spectral data on a desktop machine (macOS, Linux, or Windows).

holobiomicslab Skill

Use when your metabolomic dataset contains missing values (common in untargeted or targeted mass spectrometry data) and you need to perform PCA for outlier detection at multiple standard deviation thresholds (e.g., 3 SD, 4 SD, 5 SD) on principal component scores.

holobiomicslab Skill

Use when after implementing a neural network component that will feed into a downstream architecture (e.g., a transformer).