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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Peak Table Schema Validation · holobiomicslab

   Use when after converting peak-picker output (from MZmine, XCMS, MS-DIAL, or Compound Discoverer) into LipidMatch-compatible format. Use this skill when you need to verify that the converted file will be successfully read by LipidMatch before proceeding to lipid identification;
   0 installs
2. ▌
   Pull Request Change Tracking · holobiomicslab

   Use when investigating how a specific pull request (e.g., PR #72 introducing MS2Query's two-branch workflow split) modified the codebase architecture, control flow, or data routing.
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3. ▌
   Qcpool Sample Identification · holobiomicslab

   Use when you have Sciex Multiquant (≥v3.0.3) TXT export files containing metabolomics or lipidomics analytical sequences that include pooled QC samples, and you need to verify that QCpool samples were injected at the designed regular intervals and extract their positional metadata for quality.
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4. ▌
   Repository Source Code Setup · holobiomicslab

   Use when you need to validate that a published software tool (e.g., MassQL) executes correctly in your environment, reproduce published results, or contribute to development.
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5. ▌
   Repository Structure Parsing · holobiomicslab

   Use when when you encounter a multi-module scientific software project (e.
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6. ▌
   Simulation Output Validation · holobiomicslab

   Use when after executing a reproducible simulation pipeline (particularly for Over-representation Analysis in metabolomics), compare the newly generated outputs against reference results to confirm that the simulation was correctly implemented and that the computational environment did not.
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7. ▌
   Spectral Metadata Enrichment · holobiomicslab

   Use when you have a .msp spectral library file with sparse or incomplete metadata (e.
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8. ▌
   Structured Result Validation · holobiomicslab

   Use when after retrieving a JSON or tabular response from a web service endpoint (such as CANOPUS), validate the result before parsing or integrating it into your analysis pipeline.
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9. ▌
   Validation Report Generation · holobiomicslab

   Use when when you have loaded a project JSON document from the Pairing Omics Data Platform and need to identify and document constraint violations (such as whitespace in URL fields) defined in the JSON schema.
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10. ▌
    YAML JSON Structural Parsing · holobiomicslab

    Use when you have a versioned workflow definition file (YAML or JSON) from a specific release commit and need to verify it conforms to the project's schema specification, validate the presence of all required metadata fields (name, version, inputs, outputs, steps), and detect syntax errors or.
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11. ▌
    API Documentation Automation · holobiomicslab

    Use when when you have a Python package with docstrings in the source code and need to generate comprehensive, browsable HTML API documentation.
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12. ▌
    Arrow Columnar Data Decoding · holobiomicslab

    Use when when reading mzPeak files or other Parquet-backed mass spectrometry archives where spectral m/z and intensity arrays are stored in columnar layouts (point or chunked format) and you need to reconstruct them into Python NumPy arrays, pandas DataFrames, or equivalent in-memory structures for.
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13. ▌
    Artifact Removal In Ims Data · holobiomicslab

    Use when processing raw IM-MS data (UIMF or Agilent MassHunter .d format) that exhibits jagged peaks in low-abundance ions, isolated high-intensity noise spikes, or saturated detector signals that distort elution and mobility profiles.
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14. ▌
    Bgc Sequence Domain Scanning · holobiomicslab

    Use when you have BGC sequences (in FASTA or GenBank format) from antiSMASH or other sources and need to extract biosynthetic domain composition as the primary signal for GCF (Gene Cluster Family) clustering or similarity queries.
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15. ▌
    Big Slice Workflow Execution · holobiomicslab

    Use when you have a collection of antiSMASH-processed GenBank files (or custom BGC GenBank files prepared via the provided converter script) organized in a structured input folder, and you want to cluster them into Gene Cluster Families (GCFs) to chart biosynthetic diversity or identify.
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16. ▌
    Biobase Object Serialization · holobiomicslab

    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.
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17. ▌
    Bruker Transient Data Import · holobiomicslab

    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.
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18. ▌
    Calibration Curve Validation · holobiomicslab

    Use when when you have loaded standard compound MS intensity measurements with known concentrations and need to select between linear or quadratic regression models before applying the calibration to unknown samples.
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19. ▌
    Conditional Expression Logic · holobiomicslab

    Use when you need to create a derived image array where the output value at each pixel depends conditionally on the values of one or more element channels at that pixel. Common triggers include: (1) you want to mask or zero out pixels where an element concentration falls below a detection limit;
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20. ▌
    Consensus Mass Determination · holobiomicslab

    Use when after constructing individual mass tracks from mzTree data bins and before alignment across samples.
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21. ▌
    Cox Regression Model Fitting · holobiomicslab

    Use when you have expression or metabolomic feature matrices, paired with event indicators (e.g., disease recurrence, mortality) and follow-up times for a cohort of samples, and you need to derive risk scores or prognosis indices for survival prediction or patient stratification.
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22. ▌
    Cross Omics Feature Matching · holobiomicslab

    Use when when you have two feature matrices from different omics modalities (e.
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23. ▌
    Cross Origin Policy Override · holobiomicslab

    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.
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24. ▌
    Deep Learning Model Assembly · holobiomicslab

    Use when you have transformer encoder components and a prediction head specification, and need to wire them into a single trainable model that maps molecular structure inputs (SMILES, molecular graphs, or feature vectors) to scalar or vector molecular property predictions.
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25. ▌
    Deep Learning Model Training · holobiomicslab

    Use when you have raw or preprocessed mass spectrometry feature matrices (e.g., from low mass resolution or sparse acquisition) and want to enhance signal quality and spatial resolution across tissue or single-cell samples.
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26. ▌
    Docker Compose Orchestration · holobiomicslab

    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.
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27. ▌
    Dotnet Framework Development · holobiomicslab

    Use when you need to compile and test a .NET-based metabolomics or bioinformatics desktop application (e.g., MS-DIAL version 5 series) from source code, or you are implementing new parsing or data-processing modules that must integrate with WPF UI frameworks and ReactiveExtensions patterns.
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28. ▌
    Enrichment Score Computation · holobiomicslab

    Use when after you have normalized metabolite abundances across samples and mapped metabolites to pathway or ontology identifiers. Use it when your goal is to identify statistically significant metabolite pathways or classes rather than analyze individual metabolite abundance changes.
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29. ▌
    Enrichment Table Compilation · holobiomicslab

    Use when you have completed Fisher's exact test enrichment analysis on a set of metabolites or lipids against a pathway/ontology reference (e.
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30. ▌
    Feature Encoding Atoms Bonds · holobiomicslab

    Use when you have parsed SMILES or SDF molecular structures from a chemical dataset (e.g., SMRT dataset) and need to convert them into graph representations for input to a graph neural network or RT-Transformer model.
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31. ▌
    Feature Matrix Normalization · holobiomicslab

    Use when after aggregating Pfam domain hits from HMM scanning into a domain-feature matrix (rows = BGCs, columns = Pfam domains, cells = bit-scores or binary presence), and before computing pairwise distances or clustering BGCs into gene cluster families (GCFs).
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32. ▌
    Feature Matrix Preprocessing · holobiomicslab

    Use when you have raw metabolomics data in CSV format (samples as rows, features as columns, batch identifier in the first column) that contains missing values (zeros or NAs) and requires standardization before batch effect correction.
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33. ▌
    Feature Pair Mass Refinement · holobiomicslab

    Use when after temporal correlation has identified feature pairs with matching intensity profiles across direct-injection MS experiments.
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34. ▌
    Fragment Ion Peak Annotation · holobiomicslab

    Use when you have experimental MS/MS spectra matched against a reference library (via cosine similarity or dot-product scoring) and need to map individual fragment peaks in the experimental spectrum to their corresponding m/z and intensity values in the matched library entry.
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35. ▌
    Genbank Accession Validation · holobiomicslab

    Use when you have a collection of sequence files (e.g., in a `genbanks` directory) and need to determine which are publicly available via NCBI and which are maintained locally only. This is critical for repositories like MIBiG that curate sequence data with mixed provenance.
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36. ▌
    Glasso Regularization Tuning · holobiomicslab

    Use when when estimating a sparse network graph from a feature matrix using GLASSO and you need to determine the regularization strength.
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37. ▌
    Group Annotation Integration · holobiomicslab

    Use when you have an expression matrix (e.g., heatmap_test.csv with genes as rows and samples as columns) and a corresponding group annotation file (e.g., group_info.csv with sample IDs and their group assignments).
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38. ▌
    Gzip Index Structure Parsing · holobiomicslab

    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.
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39. ▌
    Integration Test Development · holobiomicslab

    Use when when you have implemented or modified a data ingestion module (e.g., mzML parser) and need to verify that file deserialization produces correct internal representations.
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40. ▌
    JSON Spectral Format Parsing · holobiomicslab

    Use when when you have raw mass spectrometry spectral data in JSON format from open mass spectra libraries (OMSLs) or other sources and need to validate structural completeness, check for required metadata fields (SMILES, InChI, InChIKey, precursor m/z, adduct), and separate spectra by acquisition.
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41. ▌
    Linear Axis Spatial Analysis · holobiomicslab

    Use when you have deposited mass spectrometry imaging datasets in NetCDF (CDF) format with accompanying MATLAB workspace files (.
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42. ▌
    Lipid Mass Spectral Matching · holobiomicslab

    Use when you have peak-picked LC-HRMS/MS or direct infusion MS/MS data (m/z, retention time, intensity) from Q-Exactive, Agilent, Bruker, or SCIEX instruments and need to annotate experimental fragment patterns to known lipid structures.
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43. ▌
    Mass Shift Tolerance Scoring · holobiomicslab

    Use when when searching for peptide spectra with unknown or open modifications (i.e., any mass shift within a broad tolerance range rather than a fixed set of known modifications).
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44. ▌
    Mass Spectrum Peak Detection · holobiomicslab

    Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct infusion MS (DI-MS), ASAP-MS, or other high-throughput ambient ionization methods, and need to identify which m/z signals represent true peaks of interest rather than noise or baseline drift.
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45. ▌
    Mass Spectrum Plot Rendering · holobiomicslab

    Use when after importing and preprocessing mass spectrometry data (in .raw, .
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46. ▌
    Matlab Data Structure Design · holobiomicslab

    Use when you have multiple CDF files containing mass spectrometry imaging data (spectra, m/z arrays, and spatial coordinates) that need to be ingested into MATLAB for the DIMPLE pipeline or similar linear-axis mass spectrometry imaging analysis.
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47. ▌
    Maven Pom Version Extraction · holobiomicslab

    Use when preparing a software release and you need to verify that all Maven modules declare identical version numbers before creating a release branch.
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48. ▌
    Mean Centering Normalization · holobiomicslab

    Use when apply mean-centering when you have a feature intensity table (samples × compounds) from metabolomics analysis and you need to standardize feature intensities by removing the average signal before multivariate analysis (e.g., PCA) or downstream statistical modeling.
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49. ▌
    Metabolic Ion Peak Filtering · holobiomicslab

    Use when you have a raw or extracted peak feature table (CSV or tabular format) containing mass-to-charge ratios, retention times, and intensity values across multiple samples from different experimental groups, and you need to identify which peaks show statistically significant differential.
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50. ▌
    Metabolomics Data Processing · holobiomicslab

    Use when when you have raw or partially processed metabolomics data (feature tables with sample metadata) and need to apply quality-control metrics, normalization, statistical inference, or advanced classification/variable selection without relying on a Galaxy instance.
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51. ▌
    Metabolomics Data Validation · holobiomicslab

    Use when you have raw or semi-processed m/z peak lists (positive and negative ion mode) and a sample metadata table, and you need to confirm they meet MetaboShiny's structural and semantic requirements before loading them into the normalization pipeline.
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52. ▌
    Mnar Data Quality Assessment · holobiomicslab

    Use when when you have applied multiple left-censored missing value imputation methods to metabolomics data and need to compare their performance quantitatively.
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53. ▌
    Module Loader Implementation · holobiomicslab

    Use when you have mass spectrometry imaging data in multiple vendor or open-source formats and need to programmatically route each file to its correct processing handler based on file extension, avoiding hardcoded conditional chains and enabling extensible format support.
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54. ▌
    Molecular Structure Decoding · holobiomicslab

    Use when after running spectrum-conditioned diffusion generation that produces latent molecular representations, when you need to convert continuous or abstract model outputs into discrete chemical formats suitable for structure matching, library comparison, or chemical database lookup.
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55. ▌
    Molecular Structure Encoding · holobiomicslab

    Use when you have molecular structures (SMILES strings or molecular graphs) that need to be input to a transformer model for property prediction (e.g., Collision Cross Section), and the model requires tokenized or embedded representations rather than raw chemical notation.
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56. ▌
    Msbackend API Implementation · holobiomicslab

    Use when you need to create a new backend to integrate MS data from a novel file format, database, or in-memory storage system into the Spectra ecosystem. Use this skill when existing backends (MsBackendMemory, MsBackendMzR, MsBackendSql, etc.) do not support your data source or storage paradigm.
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57. ▌
    Network Stability Assessment · holobiomicslab

    Use when you have constructed a network object (from correlation data, adjacency matrices, or edge lists) and need to evaluate which nodes are most critical to network integrity, how the network responds to the removal of highly connected nodes, or whether the network exhibits robust or fragile.
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58. ▌
    Node Pair Edge Deduplication · holobiomicslab

    Use when your input network contains multiple edge types (Biochemical, Structural, Mass Spectral, Correlation) linking the same node pairs, and you want to export or visualize a single-edge-per-pair network to avoid visual clutter and ambiguous interpretations.
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59. ▌
    Numeric List Slot Management · holobiomicslab

    Use when when extending the MsBackend virtual class to create a custom backend for mass spectrometry data, and you need to store peak m/z and intensity values as variable-length numeric vectors indexed by spectrum.
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60. ▌
    Oldens Method Implementation · holobiomicslab

    Use when you have trained multi-layer perceptron neural networks on paired microbiome-metabolome data and need to extract interpretable feature attribution scores from the learned weights to identify microbe-metabolite interaction relationships.
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61. ▌
    Package Metadata Compilation · holobiomicslab

    Use when when a package README or publication claims to install a large, fixed number of tools (e.g., 'approximately 89 tools') but does not enumerate them explicitly.
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62. ▌
    Peak Labeling And Annotation · holobiomicslab

    Use when immediately after automatic peak detection on a raw or processed MS spectrum when you have a list of candidate peaks with m/z and intensity values but lack systematic identifiers, confidence estimates, or ranked ordering.
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63. ▌
    Perl Entry Point Development · holobiomicslab

    Use when you are building a standalone Perl application for Windows that uses Prima for GUI rendering and depends on external binaries (e.g., Gnuplot 5.4.2) that must be verified before the user can interact with the main interface.
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64. ▌
    Protocol Metadata Extraction · holobiomicslab

    Use when you have experimental protocol information scattered across multiple rows in a spreadsheet or table (e.
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65. ▌
    Protonation State Assignment · holobiomicslab

    Use when you have SMILES-encoded molecular structures and need to model their behavior under electrospray ionization (ESI) or other ionization methods in mass spectrometry.
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66. ▌
    Pytest Output Interpretation · holobiomicslab

    Use when after running `pytest tests/` on a Python package (especially one with dev extras installed), you need to determine if the full test suite passed, identify which tests failed, and extract error messages or stack traces for debugging.
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67. ▌
    Python Code Style Validation · holobiomicslab

    Use when preparing Python code for contribution to a project that documents style requirements (black and/or flake8), during pre-commit validation in a CI/CD pipeline, or when reviewing pull requests to enforce uniform code standards across the repository.
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68. ▌
    Python Dependency Management · holobiomicslab

    Use when when initializing a new Python project environment, reproducing a published analysis, or building documentation that requires external dependencies. Specifically apply this skill when you have a requirements.txt file listing pinned versions and need to ensure all downstream tools (e.
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69. ▌
    Random Missing Value Masking · holobiomicslab

    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).
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70. ▌
    Raw File Routing And Queuing · holobiomicslab

    Use when you have collected raw MS files via an uploader tool and need to automatically forward them to a data processor for proteomics analysis, ensuring format compatibility and maintaining linkage to the original upload session and user project.
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71. ▌
    Reference Database Screening · holobiomicslab

    Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, use this skill to match those predictions against a curated reference database of known molecular embeddings.
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72. ▌
    Reference Quality Validation · holobiomicslab

    Use when when you have curated structure-organism pairs with associated reference metadata and need to verify that each pair's literature citations are present, non-conflicting, and complete before publishing them as a high-confidence validated dataset.
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73. ▌
    Repository Environment Setup · holobiomicslab

    Use when when you have received a GitHub repository URL for a computational workflow (e.g., ENPKG full workflow) and need to prepare your local machine to execute the workflow.
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74. ▌
    Search Engine Output Parsing · holobiomicslab

    Use when you have PSM output files from one or more search engines (e.g., MaxQuant msms.txt, MSGFPlus .mzid, Sage .sage.
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75. ▌
    Simulation Result Validation · holobiomicslab

    Use when you have obtained a repository containing simulation scripts (e.g., Type I error or power analysis scripts) and need to verify that executing those scripts produces the same summary statistics and findings reported in the associated publication or documentation.
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76. ▌
    Smiles Structure Preparation · holobiomicslab

    Use when you have a SMILES input file of small organic molecules and need to predict their collision cross sections or other molecular properties via quantum mechanics.
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77. ▌
    Spatial Filtering Ion Images · holobiomicslab

    Use when preparing raw ion image data from mass spectrometry imaging for deep learning-based representation learning.
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78. ▌
    Spectral Baseline Correction · holobiomicslab

    Use when you have loaded raw MSI spectral data (imzML format) in profile or centroid mode and need to remove background noise and baseline artifacts before intensity normalization or ROI analysis.
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79. ▌
    Spectral Metadata Validation · holobiomicslab

    Use when processing heterogeneous mass spectral datasets from multiple open libraries (e.g., MassBank, UNPD, GMD) where structural identifiers, precursor m/z, and adduct information are frequently incomplete or inconsistent across records.
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80. ▌
    Spectral Noise Reduction Msi · holobiomicslab

    Use when you have imported raw MSI spectral data in imzML format and observe high background noise or low signal-to-noise ratio that would obscure biochemical annotations or ROI analysis.
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81. ▌
    Spectrum Metadata Validation · holobiomicslab

    Use when after importing raw mass spectrometry data from mzML, mzXML, msp, MGF, or JSON formats using matchms, when you need to ensure that metadata fields (e.
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82. ▌
    Tabular Data Standardization · holobiomicslab

    Use when when you have received raw MRM lipidomics export files in vendor-specific formats (TSV, CSV) with inconsistent column naming, unparsed lipid identifiers (e.g., 'PC(36:1)' as a single string), and unknown data quality issues.
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83. ▌
    Taxonomy Metadata Extraction · holobiomicslab

    Use when you have executed a spectrum search against one or more domain-specific MASSTs (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, or foodMASST) and need to systematically extract taxonomic lineages (kingdom, phylum, class, order, family, genus, species, strain) and sample metadata.
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84. ▌
    Test Coverage For Edge Cases · holobiomicslab

    Use when integrating a new metadata validation step into a conversion pipeline that fetches structured chemical identifiers (SMILES, InChI, CAS numbers, IUPAC names) from external services.
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85. ▌
    Tic Peak Boundary Estimation · holobiomicslab

    Use when after sliding-window analysis has identified candidate TIC peaks but before parameter extraction from Extracted Ion Chromatograms (EICs).
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86. ▌
    Tool Parameter Configuration · holobiomicslab

    Use when you have selected a specific SECIMTools module (e.
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87. ▌
    Tool XML Wrapper Integration · holobiomicslab

    Use when you have standalone metabolomics analysis tools (Python scripts, R packages, MATLAB compiled applications) that you want to expose through Galaxy's UI and make composable into reproducible workflows.
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88. ▌
    Vendor Export Schema Mapping · holobiomicslab

    Use when raw MRM lipidomics data arrives in vendor-specific export formats (e.g., Sciex, Waters, Thermo TSV/CSV) with inconsistent or proprietary column naming, numeric encoding, and lipid nomenclature.
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89. ▌
    Virtual Environment Creation · holobiomicslab

    Use when before installing ENPKG dependencies for the first time, or when setting up the workflow on a new machine or user account. Trigger when you have cloned enpkg_full or enpkg_workflow and need to install runtime and optional development dependencies in isolation.
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90. ▌
    Compound Class Annotation Workflow · holobiomicslab bundle

    Use when you want chemical-class-level annotations for untargeted LC-MS/MS features rather than exact structures — determine molecular formulas with SIRIUS, compute CSI:FingerID fingerprints, and predict compound classes with CANOPUS and NPClassifier (superclass / class / pathway), producing a class-annotated feature table for chemical-inventory and enrichment analysis.
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91. ▌
    Ce Ms Eof Marker Identification · holobiomicslab

    Use when when processing CE-MS test files and you need to identify and extract the migration time of the EOF marker (e.g., Paracetamol) to normalize compound migration times across runs.
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92. ▌
    Metadata Annotation Integration · holobiomicslab

    Use when you have chemical annotations (GNPS spectral library matches) assigned to MS/MS samples and a validated ReDU sample-information template (TSV) with categorical metadata (e.g., sample type, extraction method, ionization source).
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93. ▌
    Ms2 Data Preprocessing Pipeline · holobiomicslab

    Use when you have raw MS2 spectra files (mzML, mgf, msp, mzxml) that may contain multiple MS2 spectra per feature and require reduction or standardization before library matching.
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94. ▌
    Roi Detection Mass Spectrometry · holobiomicslab

    Use when you have raw or converted mass spectrometry data (CE-MS or LC-MS in mzXML or mzML format) and need to identify candidate metabolite regions before feature extraction.
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95. ▌
    Spectral Retrieval Ranking Task · holobiomicslab

    Use when when you have pre-computed dense embeddings for query spectra (unknown compounds) and reference spectra (spectral library), and you need to rank library entries by similarity to each query for compound identification or structural similarity retrieval.
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96. ▌
    Axis Label Format Customization · holobiomicslab

    Use when when designing injection plate layouts in InjectionDesign and needing to display sample positions with clear, domain-appropriate labels on the y-axis (e.g., row identifiers, well coordinates, or sample indices).
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97. ▌
    Centroided Ms Feature Detection · holobiomicslab

    Use when you have vendor-independent centroided mzML files from data-dependent acquisition (ddMS2) HRMS experiments and need to extract a reproducible feature list with mass, chromatographic, and intensity dimensions as input to PFAS prioritization, suspect screening, or other MS-based analyses.
    0 installs
98. ▌
    Chemical Identifier Unification · holobiomicslab

    Use when when you have raw GC-MS output (CSV with columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
    0 installs
99. ▌
    Chromatogram Netcdf File Import · holobiomicslab

    Use when you have raw GCxGC-MS chromatogram data in NetCDF (CDF) format from an instrument and need to load it into R for preprocessing (smoothing, baseline correction, peak alignment) and multivariate analysis.
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100. ▌
     Chromatographic Peak Resolution · holobiomicslab

     Use when when you have loaded raw GC-MS data in netCDF or mzML format and visual or statistical inspection reveals overlapping chromatographic peaks (i.e., multiple m/z ions co-eluting at the same retention time window).
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