Coding & Dev Tools

holobiomicslab Skill

Use when you have multiple rows in a table that describe the same logical entity (e.g., multiple measurements from the same sample, or repeated attributes under a common identifier) and need to merge them into a single dictionary entry keyed by that shared field.

holobiomicslab Skill

Use when you have multiple MS/MS spectra (replicates) for a single metabolic feature (same m/z and RT window) and need to identify which fragments are reproducibly detected across replicates versus noise.

holobiomicslab Skill

Use when when working with raw or partially processed tandem mass spectrometry (MS/MS) spectra that contain low-intensity background noise peaks.

holobiomicslab Skill

Use when you have imported raw mass spectrometry data in formats such as MGF, MSP, mzML, or mzXML and need to clean the spectral data prior to similarity comparisons, metadata validation, or export.

holobiomicslab Skill

Use when you have a sparse pairwise distance matrix derived from nearest neighbor indexing of MS/MS spectra (or similar high-dimensional objects) and need to partition spectra into groups based on local density and neighborhood connectivity.

holobiomicslab Skill

Use when your project JSON document contains genome identifiers but lacks organism name or taxonomic annotations. The platform needs to auto-populate these fields to enable browsing and cross-linking with public genomic databases. Trigger this skill when you have genome IDs (e.

holobiomicslab Skill

Use when you have a tandem mass spectrum (MSMS) of a known or hypothesized peptide, along with its ProForma 2.

holobiomicslab Skill

Use when you have downloaded raw HMDB data (hmdb_metabolites.zip or pickle file) and need to generate a representative set of chemical objects for simulating LC-MS/MS acquisition strategies.

holobiomicslab Skill

Use when when converting MS/MS spectra from .msp format library files (e.g., MassBank) into a custom fragment library for metabolite annotation, and the source spectra are tagged with ionization mode information (positive or negative).

holobiomicslab Skill

Use when you have raw LC-MS/MS spectral data in .mgf format (or vendor-specific raw data that can be converted to .mgf via MZmine or similar tools) and need to prepare it for interactive exploration using the specXplore dashboard.

holobiomicslab Skill

Use when you need to verify that a QIIME 2 artifact (e.g., a Chemical Feature Tree from q2-qemistree, a FeatureTable[Frequency], or a Phylogeny[Rooted] object) has been correctly produced, before using it as input to downstream analyses.

holobiomicslab Skill

Use when a user uploads a JSON project file to the platform and you need to verify it matches the required format defined in app/public/schema.json before accepting it into the database.

holobiomicslab Skill

Use when when a new file format specification exists as a living document (e.

holobiomicslab Skill

Use when when you have integrated genomic data (GCFs from AntiSMASH via BigScape clustering) and metabolomic data (spectra and molecular families from GNPS molecular networking) and need to identify and rank which secondary metabolites detected in spectra are likely produced by which biosynthetic.

holobiomicslab Skill

Use when you have raw LC-MS peak intensity data with mass-to-charge ratios and need to match them to known metabolites. This skill must be applied before the matching stage if you are working with a KEGG database (KeggDB or sample.keggDB) and require a precomputed adduct/fragment lookup table.

holobiomicslab Skill

Use when you have a Thermo Fisher Scientific .raw file and need to (1) enumerate all scans and their metadata, (2) identify which scans are MS1 vs. MSn to enable level-specific filtering, (3) retrieve scan ranges or specific scan numbers for targeted spectral extraction, or (4) plan.

holobiomicslab Skill

Use when when analyzing tandem mass spectra with unknown precursor adduct identity, especially for positive-mode data containing non-protonated adducts ([M+Na]+, [M+K]+, [M+NH4]+).

holobiomicslab Skill

Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment. Use it to remove features that are poorly reproducible or show inconsistent signal across samples relative to instrument/technical variation.

holobiomicslab Skill

Use when you have raw LC/HRMS data files in mzXML, mzML, or netCDF format and need to identify individual and aggregated aligned peaks with their retention time and m/z values before applying spectral deconvolution or chemical annotation. This is the obligatory first step when using IDSL.

holobiomicslab Skill

Use when after GNPS_GC molecular networking job completion, when you have retrieved raw network output files and need to extract, validate, and structure the network topology for further metabolite assignment, comparative network analysis, or visualization.

holobiomicslab Skill

Use when you have raw MS2 spectral data (MGF, mzML, or msp format) and need to generate a sample-level fingerprint for comparison across metabolomics samples, especially when samples were acquired using different LC methods, mass spectrometer technologies, or exhibit poor feature overlap or large.

holobiomicslab Skill

Use when when you have a GNPS molecular network (classical or feature-based) and corresponding MS2LDA experiment results, and you want to annotate network nodes with discovered substructural motifs to support structural elucidation and chemical family interpretation.

holobiomicslab Skill

Use when after successfully constructing a nearest neighbor index from hashed spectrum feature vectors and before performing density-based clustering or similarity searches.

holobiomicslab Skill

Use when importing MS/MS spectral libraries (particularly from MoNA or GNPS) where SMILES or chemical structure identifiers are embedded in free-text or non-standard Comment fields rather than in dedicated SMILES/InChIKey fields, or when positive and negative ionization mode spectra are commingled.

holobiomicslab Skill

Use when after loading all MS1 scans from a raw or intermediate mass spectrum file (e.

holobiomicslab Skill

Use when you have .msp spectral library files with compound names but lack standardized chemical identifiers (SMILES, InChI, InChI Key, CAS number, IUPAC names, or molecular formulas).

holobiomicslab Skill

Use when when implementing or auditing a data replacement method (e.g., `mz<-`, `intensity<-`) in an MsBackend subclass that must enforce ordering or format constraints on peak data.

holobiomicslab Skill

Use when you have obtained a Rust source repository (e.g., mzpeak_prototyping) and need to compile it into a working command-line converter tool or library. Use this skill when the source includes a Cargo.

holobiomicslab Skill

Use when matching query mass spectra to a spectral library in the presence of unknown post-translational modifications (PTMs) or non-enzymatic modifications.

holobiomicslab Skill

Use when when you have a collection of normalized mass spectrometry spectra (peak intensities or binned m/z representations) and seek to enrich neural network training signals for metabolite identification by discovering latent spectral patterns.

holobiomicslab Skill

Use when when you have a scientific software tool (e.g., Met-ID) that is architected to support plugins or configuration-driven modules, and you need to register and apply a novel reagent, derivatizing matrix, or analytical method (e.

holobiomicslab Skill

Use when after molecular formula assignment and peak filtering are complete, when you have a filtered peak list (m/z values and molecular formulas) and want to discover biochemical transformations without prior knowledge of reaction networks.

holobiomicslab Skill

Use when you have a GNPS mass spectral molecular network (in graphml or cytoscape format) and want to enrich its nodes with chemical class information derived from GNPS public library spectral matches.

holobiomicslab Skill

Use when you have tandem MS/MS spectrum data in standard peak file formats (mzML, mzXML, or MGF) and need to cluster spectra based on precursor mass and fragment ion similarity.

holobiomicslab Skill

Use when you have a GNPS mass spectral molecular network and wish to annotate its nodes with both chemical class assignments (from GNPS public library matches) and MS2LDA-derived substructural motifs (from classical or feature-based LDA experiments) in a single integrated operation, typically for.

holobiomicslab Skill

Use when when you need to understand how a Java application routes input data to processing modules based on declared data types, conditionally branches on instrument or format types (e.