Coding & Dev Tools

holobiomicslab Skill

Use when you have multiple independent implementations of the same data format reader (e.g., Rust, Python, R versions) and need to verify they produce identical or equivalent output.

holobiomicslab Skill

Use when you have raw mass spectrometry data (mzML, mzXML, or CDF format) from at least 3 samples and need to automatically identify candidate peak regions in the TIC chromatogram before extracting ion-level parameters for XCMS or MZmine2 processing.

holobiomicslab Skill

Use when when you have loaded imzML MSI data into napari and need to focus analysis on a specific anatomical or morphological region rather than the entire image.

holobiomicslab Skill

Use when you have acquired Bruker Solarix FT-ICR-MS raw data (e.g., ESI_NEG_SRFA.d) and need to programmatically access the transient time-domain signal and metadata for zero-filling, apodization windowing (e.g., Hanning), or mass calibration.

holobiomicslab Skill

Use when you need to set up a LipoCLEAN analysis for MS-DIAL lipid identifications and do not yet have a configuration file, or you are switching between MS-DIAL versions 4 and 5 and need version-specific parameter defaults (e.g., column names and scaling factors that differ between versions).

holobiomicslab Skill

Use when when you have FT-ICR MS peak data with assigned molecular formulas (e.g., from CoreMS, Formularity, or similar formula assignment tools) and need to compute thermodynamic indices (DBE, GFE, AImod, NOSC) or classify peaks by elemental composition.

holobiomicslab Skill

Use when after installing a Python package or cloning its repository, to verify that the primary command-line interface is functional and discoverable before attempting analysis workflows.

holobiomicslab Skill

Use when when you have one or more peptide sequences (as strings) and need to predict their theoretical isotopic distribution for comparison against experimental MS peaks, validation of mass calibration, or simulation of expected peptide signals in a mass spectrometry assay.

holobiomicslab Skill

Use when you have 1D mass spectrometry signal data (e.

holobiomicslab Skill

Use when you have centroided LC-MS data (.mzML format) and a curated list of targeted metabolites or lipids (with m/z, retention time, and polarity) that you want to quantify and quality-assess across multiple analytical runs, and you need both per-run AUC values and averaged QC metrics for each.

holobiomicslab Skill

Use when you have raw LC-MS or GC-MS data files from a mass spectrometer (in mzML, NetCDF, or mzXML format) and need to detect chromatographic peaks, correct m/z bias via mass calibration (e.

holobiomicslab Skill

Use when when you have received or cloned a CCS reference library (such as the DTCCSN2 library for U13C labeled lipids) bundled with lipidomics software and need to verify its integrity, understand its lipid class composition, or extract metadata before using it for CCS bias calculation or.

holobiomicslab Skill

Use when after constructing feature tensors encoding atom adjacency matrices, bond types, and chemical properties from canonical SMILES—and before feeding graphs into a GNN training loop—to enable reproducible, portable, and memory-efficient storage of graph objects that will be loaded in batches.

holobiomicslab Skill

Use when you have mass spectrometry feature data stored in HDF5 format (.h5 files) and need to load specific dimensional columns (m/z, drift time, retention time, intensity) for multi-dimensional alignment, CCS calibration, or isotope detection.

holobiomicslab Skill

Use when when you have raw peak table data from mass spectrometry or other metabolomic instruments in either a standardized tabular format or one of 12 common software tool outputs (e.

holobiomicslab Skill

Use when you have Bruker Solarix raw transient data (.d folders containing ser or fid files) from an FT-ICR instrument and need to load it into a Python environment for noise thresholding, peak picking, mass calibration, or molecular formula assignment.

holobiomicslab Skill

Use when when designing a library that needs to support multiple plotting backends (e.g., matplotlib, bokeh, plotly) and you want to avoid reimplementing parameter validation, storage, and dispatch logic for each backend.

holobiomicslab Skill

Use when when you have an indexed gzip-compressed mzML file (mzML.gz with an internal index) and need to retrieve specific spectra or chromatogram data blocks by integer index without decompressing the entire archive.

holobiomicslab Skill

Use when when converting mzML files to imzML format and the source mzML contains multiple scan filters (e.g., different MS/MS isolation windows, ionization modes, or mass ranges acquired in a single imaging experiment).

holobiomicslab Skill

Use when you have FTICR-MS direct injection (mzML) data with identified chromatographic peaks and need to correct systematic m/z bias.

holobiomicslab Skill

Use when after mass tracks have been aligned across all samples (either via pairwise alignment for ≤10 samples or nearest-neighbor clustering for larger cohorts), and you need to generate a single representative m/z per aligned bin for downstream feature extraction and annotation.

holobiomicslab Skill

Use when you have a ProForma 2.0 peptidoform string (e.

holobiomicslab Skill

Use when you have a Thermo Orbitrap .raw file and need to (1) verify that a targeted acquisition method (e.g., PRM) maintains consistent scan spacing across all cycles; (2) extract only scans matching a specific precursor ion and fragmentation method;

holobiomicslab Skill

Use when when you have execution time data for visualization scripts across multiple backends (matplotlib, Bokeh, Plotly) and need to determine which backend offers the fastest median performance for specific mass spectrometry plot types (chromatogram, mobilogram, peakmap, peakmap-marginals.

holobiomicslab Skill

Use when you have acquired MS/MS spectra in .msp format (e.g., from MassBank or experimental acquisition) and need to transform them into a structured library format compatible with automated annotation tools.

holobiomicslab Skill

Use when after a mass spectrum has been matched against a reference m/z file (e.g., SRFA.ref) and a sufficient number of calibration points (≥5) have been identified within a given PPM tolerance window.

holobiomicslab Skill

Use when you have LC-MS/MS data preprocessed with MZmine2 into an MGF file (containing MS1 and MS2 spectra) and a feature table (peak areas per sample), and you want to relate MS1 features to each other based on predicted molecular substructures and chemical properties rather than arbitrary.

holobiomicslab Skill

Use when after peak clustering has been completed in pyINETA (i.

holobiomicslab Skill

Use when after obtaining structural clusters from the MAMSI framework using different parameter configurations (e.

holobiomicslab Skill

Use when you have MS/MS spectra with assigned precursor formulas and need to annotate the chemical composition of individual fragment peaks for metabolite structure elucidation or fragmentation pathway analysis. Apply this skill when you want to avoid external fragmentation tree computation (e.

holobiomicslab Skill

Use when after library-matching has produced ranked candidate spectra with MS2Deepscore embeddings.

holobiomicslab Skill

Use when when you have manually labeled LC-MS peaks as 'High quality' or 'Low quality' using NeatMS's annotation tool and need to create training/validation/test batches.

holobiomicslab Skill

Use when you have: (1) tandem MS/MS spectra in MGF, mzXML, mzML, or mzData format from LC-MS/MS analysis; (2) a set of predicted RiPP precursor peptides derived from genomic biosynthetic gene cluster mining (via antiSMASH, BOA, or raw FASTA);

holobiomicslab Skill

Use when you have high-resolution tandem MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or searched at scale (millions of spectra).

holobiomicslab Skill

Use when when you have two or more MsBackend objects (e.g., multiple MsBackendMemory, MsBackendDataFrame, or MsBackendMzR instances) containing distinct sets of MS spectra and you need to consolidate them into a single backend for downstream analysis, parallel processing, or export.

holobiomicslab Skill

Use when when you need to read proprietary or binary data formats (e.g., Thermo Fisher .raw files) from R but the native implementation is in .NET/C#, and direct language bindings are unavailable or impractical. Use this when the target assembly requires Windows/.