Integrations & APIs

holobiomicslab Skill

Use when after identifying structural clusters (isotopologue groups, adduct groups, and cross-assay links) and assigning features to correlation clusters via hierarchical clustering.

holobiomicslab Skill

Use when you have untargeted metabolomics data (MS/MS spectra) and need to annotate metabolites at scale.

holobiomicslab Skill

Use when you have untargeted LC-MS metabolomics data preprocessed with XCMS and need to filter out low-quality peak integrations that could introduce false positives or noise into metabolite quantification.

holobiomicslab Skill

Use when you have extracted peak data (chemical shift values in ppm, multiplicities, integration) from a processed NMR spectrum (JCAMP, RAW, or mzML format) and need to match these peaks against known NMR signals to propose or confirm structural assignments.

holobiomicslab Skill

Use when after submitting a POST request to the /api/smart3/search endpoint with peak data as a JSON payload, you receive an HTTP response and need to extract classification predictions and confidence scores.

holobiomicslab Skill

Use when normalizing multi-batch metabolomics intensity matrices where QC samples are available alongside biological samples, and when you need to detect whether QC samples are representative of the biological population (i.e., whether they follow the same systematic drift).

holobiomicslab Skill

Use when you have paired spatial transcriptomics and spatial metabolomics datasets from the same sample(s) that are at different spatial resolutions or coordinate systems, and you need to integrate them for joint analysis of cross-modal spatial patterns.

holobiomicslab Skill

Use when when building a Streamlit web application that must coordinate stateful workflow execution across multiple reruns triggered by user interactions (e.

holobiomicslab Skill

Use when you need to support multiple external services (CIR, CTS, PubChem, IDSM, BridgeDb, RDKit) for chemical identifier conversions (.

holobiomicslab Skill

Use when when a GUI widget (e.g., isotopes display, compound list, or analysis parameter panel) must show or hide content according to user selections stored in application preferences, and the current implementation either shows all content regardless of preference or lacks a preference-reading.

holobiomicslab Skill

Use when when you have mwTab-formatted Mass Spectrometry or Nuclear Magnetic Resonance experimental data from the Metabolomics Workbench that must be converted to JSON for API integration, data sharing across systems, or validation against a defined JSON schema.

holobiomicslab Skill

Use when after loading centroided .mzML LC–MS runs and before executing full peak detection and integration.

holobiomicslab Skill

Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or file-level headers programmatically—e.

holobiomicslab Skill

Use when you have a Universal Spectrum Identifier (USI) string referencing a spectrum in a supported metabolomics repository (GNPS, MassBank, MetaboLights, Metabolomics Workbench, MassIVE, or MS2LDA) and need to create an embeddable, scannable reference for publication or data integration that.

holobiomicslab Skill

Use when when you have (1) a molecular network graph from GNPS with node identifiers and edges, (2) LC-MS/MS features quantified across fractions in a feature table, and (3) bioassay measurements (e.

holobiomicslab Skill

Use when when annotating .msp files with metadata from multiple external web services and you need to monitor which services are slow or unreliable.

holobiomicslab Skill

Use when when building a multi-backend visualization library where users specify both a plot type (spectrum, chromatogram, peakmap) and a backend (matplotlib for static output, Bokeh or Plotly for interactive), and you need to avoid code duplication across backends while keeping the user-facing API.

holobiomicslab Skill

Use when you have a list of metabolite identifiers sourced from one metabolome database (e.g., HMDB IDs, PubChem CIDs) and need to map them to equivalent identifiers in other databases for data integration, cross-referencing, or standardization in downstream metabolomics analysis.

holobiomicslab Skill

Use when when you have paired spatial metabolomics and spatial transcriptomics measurements from the same tissue samples and need to identify how metabolite distributions relate to gene expression patterns at aligned spatial coordinates.

holobiomicslab Skill

Use when after converting mass-spectrometry data from an existing format (mzML, mzXML, or vendor-specific formats) into mzPeak using command-line tools or API calls.

holobiomicslab Skill

Use when after preprocessing and normalizing joint ST/SM AnnData objects using joint_adata_sm_st and normalize_total_joint_adata_sm_st, when you need to align spatial transcriptomics and metabolomics data to a unified latent resolution for multi-omics integration and cross-modal spatial pattern.

holobiomicslab Skill

Use when you have raw or partially organized natural products data from multiple sources (GNPS molecular networking, AntiSMASH BGC predictions, BigScape clustering, MIBiG metadata) and need to prepare them for NPLinker integration.

holobiomicslab Skill

Use when when you have Thermo Fisher Scientific Orbitrap .raw files (e.g., from Q Exactive HF instruments) and need to extract spectral, chromatographic, or metadata directly into R for downstream statistical analysis, benchmarking, or integration with Bioconductor workflows.

holobiomicslab Skill

Use when your analysis requires MS/MS spectra from public proteomics datasets but you want to avoid manual download and format conversion.

holobiomicslab Skill

Use when you have LC-MS data from authentic standards run in positive and negative ESI modes, converted to .mzML format, and you need to build an in-house metabolite reference library for untargeted identification workflows.

holobiomicslab Skill

Use when when you have raw LC-MS all-ion fragmentation (AIF) chromatograms in centroid mode and need to prepare them for metabolite annotation using fragment ion matching.

holobiomicslab Skill

Use when after bias-correcting ATAC-seq cutsite signal (via ATACorrect) when you have a bias-corrected bigWig file and need to compute per-position footprint scores within defined accessible regions (peaks, called footprints, or regulatory regions) to detect and quantify transcription factor.

holobiomicslab Skill

Use when when running NPLinker in PODP mode (as opposed to local mode), you need to fetch and validate project metadata from PODP, orchestrate downloads of GNPS molecular networking data, AntiSMASH BGC predictions, BigScape clustering results, and MIBiG reference metadata, then organize them into.

holobiomicslab Skill

Use when when refactoring a mass-spectrometry formula-prediction codebase that has deprecated a monolithic scoring function (FDRNet) and requires a modular, symmetric Siamese design to independently embed spectrum and molecular-formula features before combining them.

holobiomicslab Skill

Use when when performing targeted quantification of known compounds in LC-MS data using TARDIS, especially when the instrument acquired data with multiple overlapping m/z scan windows.

holobiomicslab Skill

Use when when you have NMR peak assignments (1H and 13C chemical shift values) and need to submit them to the /api/smart3/search endpoint for automated structure classification. Use this skill before making API calls to ensure peak data conforms to the expected JSON schema.

holobiomicslab Skill

Use when when you have received POST requests containing peaks data as form parameters (chemical shift, multiplicity, integration values) and need to accept, validate, and normalize those values before formatting them into a query compatible with an external NMR prediction service such as.

holobiomicslab Skill

Use when when you have a user-provided or system-generated query string containing a chemical structure in unknown or mixed format, and you need to route it to a structure-specific API endpoint (such as ClassyFire) that requires knowing whether the input is SMILES, InChI, IUPAC nomenclature, or.

holobiomicslab Skill

Use when after completing sample alignment in JPA (Part 5) or when ingesting a peaklist or aligned feature matrix from prior peak-picking runs, parse feature metadata to enable EIC export or multi-sample feature annotation.

holobiomicslab Skill

Use when after Blueshift or Gravity processing has produced a feature abundance table with annotations, but before final reporting or integration with sample/injection metadata.

holobiomicslab Skill

Use when you have a GNPS mass spectral molecular network (classical or feature-based) and MS2LDA-derived Mass2Motif data, and you need to annotate network nodes with both chemical class information from GNPS library matches and substructural motifs from MS2LDA to enable joint interpretation of.