← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 7.4k skills
• 0 followers
• 1 day ago last updated

1. ▌
   Compound Class Annotation Parsing · holobiomicslab

   Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.
   0 installs
2. ▌
   Compound Structure Representation · holobiomicslab

   Use when when you have experimental MS/MS data (peak lists, precursor m/z, charge state, adduct type) paired with a chemical structure (SMILES or structural identifier), and need to create a unified Compound object for spectral alignment, modification-site prediction, or comparative fragmentation.
   0 installs
3. ▌
   Computational Variation Detection · holobiomicslab

   Use when after peak detection and feature alignment in a metabolomic LC–MS/MS or GC–MS workflow, when you have a feature table (rows=metabolic features, columns=samples) split into separate .csv files for peak height and peak area.
   2 installs
4. ▌
   Cross Tool Performance Comparison · holobiomicslab

   Use when when you have raw tandem MS metabolomics data in vendor formats (.
   0 installs
5. ▌
   Cross Workflow Format Translation · holobiomicslab

   Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) or GNPS2 (https://gnps2.org) and need to parse spectra (spectra.mgf), molecular family networks (molecular_families.tsv), spectral library annotations (annotations.
   0 installs
6. ▌
   Data Summarization And Tabulation · holobiomicslab

   Use when after obtaining structural clusters from the MAMSI framework using different parameter configurations (e.
   0 installs
7. ▌
   De Novo Precursor Mass Annotation · holobiomicslab

   Use when when you have unknown MS/MS spectra with observed precursor m/z values and want to infer the molecular formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo setting without access to spectral libraries.
   0 installs
8. ▌
   Dependency Requirement Validation · holobiomicslab

   Use when before launching the DaDIA pipeline or any multi-package R workflow that has strict version constraints. Use this skill when you have access to an R environment and need to confirm that R ≥4.0, XCMS ≥3.11.4, and metaMS ≥1.25.
   0 installs
9. ▌
   Differential Metabolite Detection · holobiomicslab

   Use when you have normalized and aligned lipidomic and metabolomic spectral features from the Multi-ABLE method across multiple biological samples grouped by phenotype (e.
   0 installs
10. ▌
    Disease Classification Prediction · holobiomicslab

    Use when you have raw LC-MS metabolomics data from multiple disease groups (in .npy or .
    0 installs
11. ▌
    Environment Dependency Management · holobiomicslab

    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.
    0 installs
12. ▌
    Feature Grouping By Molecular Ion · holobiomicslab

    Use when after peak picking and sample alignment have produced an aligned feature table with m/z and retention time coordinates.
    0 installs
13. ▌
    Feature Table Parsing And Loading · holobiomicslab

    Use when you have extracted volatile organic compound (VOC) features from individual breath samples (mzML or mzXML files) and wish to consolidate multiple per-sample feature tables into a single aligned feature table, or you need to programmatically access feature metadata (m/z, intensity, scan.
    0 installs
14. ▌
    File Format Export And Validation · holobiomicslab

    Use when after executing MassQL queries on mass spectrometry data that produce tabulated results (e.g., MS1 or MS2 scan metadata, peak intensities, retention times), and you need to persist those results for archival, sharing, or downstream statistical analysis.
    0 installs
15. ▌
    Fragment Peak Chemical Annotation · holobiomicslab

    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.
    0 installs
16. ▌
    Fragmentation Spectrum Extraction · holobiomicslab

    Use when you have raw or peak-detected mass spectrometry data (mzXML, mzML, or netCDF format) from untargeted metabolomics or exposomics studies and need to separate composite fragmentation spectra into individual constituent spectra for annotation.
    0 installs
17. ▌
    Fuzzy Analog Search Fragmentation · holobiomicslab

    Use when when you have experimental MS/MS spectra and want to discover structurally similar compounds beyond exact spectral library matches—particularly useful for identifying chemical analogs, homologs, or isomers that share fragmentation logic but differ in molecular structure.
    0 installs
18. ▌
    In Source Fragment Identification · holobiomicslab

    Use when you have an LCMS feature table (from XCMS, MS-DIAL, MZmine2, or other feature extraction software) with m/z, retention time, and intensity columns, plus MS2 spectral annotations from DDA data, and you need to identify which features are in-source fragments rather than distinct metabolites.
    0 installs
19. ▌
    Intensity Distribution Simulation · holobiomicslab

    Use when when you need to create synthetic noisy MS/MS spectra from clean baseline spectra to validate denoising algorithms, compare denoising performance across noise levels, or generate ground-truth test datasets where the true signal and noise composition are known and controllable.
    0 installs
20. ▌
    Ion Image Quantification Workflow · holobiomicslab

    Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal standards.
    0 installs
21. ▌
    Ion Species Annotation Assignment · holobiomicslab

    Use when after temporal correlation has identified feature pairs with matching intensity profiles across time-resolved MS scans, but before final candidate validation. Apply this skill when you need to distinguish between competing ion-species hypotheses (e.
    0 installs
22. ▌
    Isotope Pattern Spectral Matching · holobiomicslab

    Use when when you have LC/MS feature data with observed m/z and intensity values across multiple peaks (monoisotopic and isotopologues) and need to narrow candidate annotations from a metabolite database.
    0 installs
23. ▌
    Isotopologue Abundance Correction · holobiomicslab

    Use when you have LC-MS data from isotope labeling experiments where FAM measurements must be transformed to MDV values. Specifically, apply this when: (1) you have measured fractional abundances of isotopologues (FAM) in XLSX format from a high-resolution instrument (e.g., Orbitrap);
    0 installs
24. ▌
    Keras Regularizer API Integration · holobiomicslab

    Use when when extending an existing neural network class (e.g., SiameseModel) that lacks user-configurable regularization, and you need to prevent overfitting on moderate-sized training datasets (e.
    0 installs
25. ▌
    Peak Classification Validation · holobiomicslab

    Use when after training or loading a NeatMS neural network model, before applying it to filter false positive MS1 peaks in a new dataset.
    0 installs
26. ▌
    Percentile Threshold Filtering · holobiomicslab

    Use when you have computed multiple independent scoring functions (e.g., standardised strain correlation and IOKR) for a large set of potential genomic–metabolomic links and wish to identify subsets enriched for validated links.
    0 installs
27. ▌
    Pipeline Prerequisite Checking · holobiomicslab

    Use when before launching the DaDIA metabolomics pipeline or any multi-package workflow, when you have an R environment with potentially mixed or unknown package versions and need to confirm that R ≥4.0, XCMS ≥3.11.4, metaMS ≥1.25.
    0 installs
28. ▌
    Plot Customization And Styling · holobiomicslab

    Use when after generating a numerical visualization (e.g., confusion matrix, heatmap, or similarity array) using matplotlib, when you need to add axis labels, class names, colormaps, normalization annotations, colorbars, titles, and export the figure in a publication-ready format (PNG or PDF).
    0 installs
29. ▌
    Precursor Fragment Ion Pairing · holobiomicslab

    Use when you have raw LC-MS/MS data files (mzML/mzXML format from Thermo, Waters, or Bruker instruments) and a list of target compounds defined by precursor m/z values (and optionally retention time windows).
    0 installs
30. ▌
    Precursor Product Mass Pairing · holobiomicslab

    Use when you have centroided MS2 spectra from data-dependent acquisition (ddMS2) in mzML format and seek to prioritize potential PFAS features by detecting diagnostic fragment masses.
    0 installs
31. ▌
    Publication Figure Preparation · holobiomicslab

    Use when you have a mass spectrometry spectrum from a supported repository (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, MS2LDA, or MassIVE) and need to include it in a publication or supplementary material.
    0 installs
32. ▌
    Python Function Implementation · holobiomicslab

    Use when when you have classification predictions and ground-truth labels and need to generate a confusion matrix visualization with flexible normalization (by row, column, or all elements) and styling options for publication or diagnostic review.
    0 installs
33. ▌
    R Data Structure Serialization · holobiomicslab

    Use when after completing Part 4 (Identification of ISF Features) in the ISFrag workflow, when you have a feature table with identified ISF features and their hierarchical fragmentation relationships, and you need to export this relationship structure for interpretation, integration with external.
    0 installs
34. ▌
    Ranking Performance Evaluation · holobiomicslab

    Use when after running retention-order prediction experiments on a test or held-out evaluation dataset.
    0 installs
35. ▌
    Reaction Pathway Interpolation · holobiomicslab

    Use when after CREST (version >= 3.0.2) has identified an ensemble of low-energy conformers and stationary points (minima and transition states), and before submitting interpolated geometries to ORCA (version >= 6.0.
    0 installs
36. ▌
    Rescore Column Standardization · holobiomicslab

    Use when after running FIDDLE v2.0.0 inference on MS/MS spectra and obtaining ranked formula candidates with confidence scores, apply this skill when the rescore model outputs columns named Rescore (0), Rescore (1), ...
    0 installs
37. ▌
    Retention Time Drift Detection · holobiomicslab

    Use when you have LC-MS data processed through XCMS grouping that shows signs of RT drift (e.g., data acquired over extended periods or across many samples) and you suspect misalignment of feature groups.
    0 installs
38. ▌
    Signal Intensity Normalization · holobiomicslab

    Use when after loading raw LC-MS data from multiple disease groups when you need to compute correlations between metabolite signals and disease classes, or before training a deep learning model on metabolomics profiles.
    0 installs
39. ▌
    Signal Smoothing Preprocessing · holobiomicslab

    Use when when working with raw LC-HRMS profile-mode data containing noisy chromatographic signals, apply this skill before peak detection. Smoothing is particularly needed when the signal-to-noise ratio is low or when gradient-based peak detection would be compromised by high-frequency noise.
    0 installs
40. ▌
    Similarity Scoring For Spectra · holobiomicslab

    Use when you have LC-MS/MS query spectra in mgf format that you need to match against a custom database (e.g., prepared with CFM-id) to identify compounds. Apply this skill when you want to rank candidate compounds by spectral similarity and return scored match results for downstream interpretation.
    0 installs
41. ▌
    Sparse Feature Vector Handling · holobiomicslab

    Use when when you have tandem mass spectra (mz/intensity pairs with precursor m/z) and need to train an interpretable model (e.
    0 installs
42. ▌
    Spectral Corpus Representation · holobiomicslab

    Use when you have a collection of tandem mass spectrometry spectra in mzML or similar format and need to prepare them for LDA-based motif discovery.
    0 installs
43. ▌
    Spectral Feature Consolidation · holobiomicslab

    Use when when you have generated separate MemoMatrix objects from independent sample sets (e.g., sample set A and sample set B) and need to align and combine their MS2 fingerprint data into a single matrix for comparative analysis.
    0 installs
44. ▌
    Spectral Feature Normalization · holobiomicslab

    Use when when you have raw LC-MS metabolomics data in .mzML or .npy format from multiple disease groups with varying ionization efficiencies or detector sensitivities, and you need to train a deep learning model for disease classification.
    0 installs
45. ▌
    Spectral Library Data Modeling · holobiomicslab

    Use when when migrating an existing file-based spectral library (stored as JSON, CSV, or binary formats) into a production system that requires frequent subset queries by metadata filters, similarity scoring across large spectral collections, or integration into downstream tools like MS2Query that.
    0 installs
46. ▌
    Spectral Library Matching Ripp · holobiomicslab

    Use when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzXML, mzML, or mzData format) and genomic data from a target organism, and you want to identify RiPPs by matching experimental spectra against a database of predicted post-translationally modified RiPP structures derived from.
    0 installs
47. ▌
    Substructural Motif Annotation · holobiomicslab

    Use when you have created a GNPS molecular network (classical or feature-based workflow) and separately run an MS2LDA experiment on the corresponding MGF file, and you want to associate each network node with its constituent substructural motifs and visualize which motifs are shared between.
    0 installs
48. ▌
    Target List Coordinate Mapping · holobiomicslab

    Use when you have a CSV-formatted target list with m/z, retention time, or ion mobility identifiers and need to locate and extract peak abundances from raw MS data files (Agilent .d, Thermo .raw, Bruker .d, mzML) acquired across LC-MS, LC-IMS-MS, DDA, DIA, or direct infusion modes.
    0 installs
49. ▌
    Targeted Metabolite Extraction · holobiomicslab

    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.
    0 installs
50. ▌
    Theoretical Mz Grid Generation · holobiomicslab

    Use when you have a feature table from untargeted LC-MS (m/z, retention time, intensity) and need to annotate which observed m/z values correspond to isotopologues and adducts of the same neutral compound.
    0 installs
51. ▌
    Thermo Raw File Format Parsing · holobiomicslab

    Use when you have acquired multidimensional mass spectrometry data (MS1, MS/MS, or data-independent acquisition) from a Thermo instrument saved in the proprietary '.
    0 installs
52. ▌
    Annotation Confidence Assessment · holobiomicslab

    Use when after MS-FINDER in silico annotation has been executed on exported LC-MS features and multiple database matches (with HRR scores) have been returned.
    0 installs
53. ▌
    Clustered Peak Output Formatting · holobiomicslab

    Use when after peak clustering has been completed in pyINETA (i.
    0 installs
54. ▌
    Docker Environment Configuration · holobiomicslab

    Use when you need to deploy CloMet for the first time on a new system, or when you want to ensure reproducible execution of metabolomics data harmonization tasks without manual dependency management.
    0 installs
55. ▌
    File API Endpoint Implementation · holobiomicslab

    Use when when you need to construct a POST endpoint that ingests raw spectral data files from multiple vendor formats (jcamp, RAW, mzML) and must standardize them for downstream processing.
    0 installs
56. ▌
    Metabolite Dataset Preprocessing · holobiomicslab

    Use when you have raw NMR metabolomics measurements paired with pre-analytical metadata (e.g., processing delay times, sample type designations [plasma vs. serum], cohort identifiers) and need to investigate how delays affect measured metabolic parameters.
    0 installs
57. ▌
    Metabolite Identifier Annotation · holobiomicslab

    Use when you have observed compounds (from LC-MS/MS, GC-MS, NMR, or other analytical techniques) with unknown identity and you want to assign candidate metabolite structures by comparing them to computationally predicted metabolism pathways.
    0 installs
58. ▌
    Metabolomics Data Representation · holobiomicslab

    Use when you have a raw MGF file containing fragmented LC-MS-MS metabolomics spectra and want to apply Latent Dirichlet Allocation (LDA) to discover hidden topics (molecular families, biochemical patterns) across your sample set.
    0 installs
59. ▌
    Metabolomics File Format Parsing · holobiomicslab

    Use when you have mwTab-formatted files from the Metabolomics Workbench containing MS or NMR experimental metadata and tabular data sections (e.g., METABOLITES, DATA blocks), and need to load them into memory for downstream conversion, validation, or analysis rather than manual text parsing.
    0 installs
60. ▌
    Model Metadata Schema Inspection · holobiomicslab

    Use when when preparing to send peak data (1H and 13C NMR measurements) to a machine learning classification endpoint and you need to verify the current model's input/output names and schema, especially before implementing or updating code that constructs JSON payloads for the /api/smart3/search.
    0 installs
61. ▌
    Molecular Connectivity Inference · holobiomicslab

    Use when you have 1D ¹H and/or ¹³C NMR spectra (as preprocessed numerical arrays or peak lists) from an unknown organic molecule with ≤19 heavy atoms, and you need to recover its molecular formula and connectivity graph.
    0 installs
62. ▌
    Nmr Spectrum Object Construction · holobiomicslab

    Use when you have Bruker NMR spectral files (raw instrumental output) and need to prepare them for automated metabolite identification and quantification.
    0 installs
63. ▌
    Replicate Consistency Assessment · holobiomicslab

    Use when after NMR or MS data acquisition and preprocessing (phasing, baseline correction) when you have a SummarizedExperiment object containing assay intensity matrix with QC sample columns designated.
    0 installs
64. ▌
    Signal To Noise Ratio Assessment · holobiomicslab

    Use when when preparing a 1D 1H NMR spectral peak list for input to the NMRformer metabolite identification model, and you have access to peak intensity measurements and noise level estimates.
    0 installs
65. ▌
    Spatial Overlap Analysis Imaging · holobiomicslab

    Use when when annotating matrix-related peaks in MSI datasets where candidate peaks have identical or near-identical m/z values (isobaric ions), or when multiple peaks exhibit overlapping spatial distributions across the tissue image that could confound downstream annotation filtering.
    0 installs
66. ▌
    Spearman Correlation Computation · holobiomicslab

    Use when : (1) you have metabolomic data (NMR or MS-derived) and a continuous phenotype variable; (2) you need to quantify associations while controlling for known confounders (age, gender, disease status);
    0 installs
67. ▌
    Spectra To Structure Elucidation · holobiomicslab

    Use when you have one or more spectroscopic datasets (IR, Raman, UV-Vis, mass spectra, NMR) from an unknown compound and need to generate candidate molecular structures ranked by likelihood. Use this when retrieval-based approaches are infeasible (e.
    0 installs
68. ▌
    Spectral Roi Boundary Definition · holobiomicslab

    Use when when you have identified a spectral window of interest in a 1H NMR spectrum from a complex biological sample (serum, urine, CSF, tissue, saliva, or sweat) and need to systematically retrieve all metabolites from HMDB whose reference proton NMR chemical shifts fall within that window.
    0 installs
69. ▌
    Spectroscopic Data Preprocessing · holobiomicslab

    Use when when you have raw spectroscopic measurements in heterogeneous formats (IR, Raman, UV-Vis, mass spectra, or NMR) and need to feed them into a spectrum-conditioned diffusion model for de novo molecular structure elucidation.
    0 installs
70. ▌
    Summarized Experiment Subsetting · holobiomicslab

    Use when when you have a SummarizedExperiment containing metabolomic abundances and a corresponding vector of quality metrics (e.g., coefficient of variation computed across QC samples), and you need to filter to retain only features meeting a reproducibility threshold (e.g., CV ≤ 0.
    0 installs
71. ▌
    Tool Initialization Verification · holobiomicslab

    Use when after completing Docker installation and container build steps for CloMet, before attempting substantive data analysis or pipeline execution.
    0 installs
72. ▌
    Wasserstein Distance Computation · holobiomicslab

    Use when when you have both an observed NMR mixture spectrum and a candidate reconstructed spectrum (each represented as intensity distributions across chemical shift bins), and you need a scalar similarity metric to evaluate how closely the reconstruction matches the observed data.
    0 installs
73. ▌
    Atac Seq Signal Normalization · holobiomicslab

    Use when you have aligned ATAC-seq BAM files and need to detect transcription factor binding sites via footprint analysis. The skill is essential because raw Tn5 insertion signal contains systematic bias toward certain DNA sequences;
    0 installs
74. ▌
    Encode Hic Pipeline Execution · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited accession) and need to reproduce or validate Hi-C map generation following the ENCODE uniform processing standard, or you need to verify that your pipeline output conforms to reference format and.
    0 installs
75. ▌
    Genomic Coordinate Conversion · holobiomicslab

    Use when you need to map computed per-bin metrics (insulation scores, boundary calls, contact frequencies) back to genomic coordinates for export to BED/GFF format, cross-reference with external annotations, or validate that computed features fall within expected genomic ranges.
    0 installs
76. ▌
    Hi C Fastq Read Preprocessing · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a Hi-C wet-lab protocol and need to convert them into processed Hi-C contact maps (.hic files) for loop detection, TAD identification, or 3D structure inference. Use when starting from deposited public Hi-C datasets (e.
    0 installs
77. ▌
    Kmer Motif Synergy Assessment · holobiomicslab

    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.
    0 installs
78. ▌
    Monocle3 Trajectory Embedding · holobiomicslab

    Use when you have an ArchR project object with dimensionality reduction results (LSI or combined dimensions from scATAC-seq ± scRNA-seq) and want to infer pseudotime trajectories and cell-state transitions.
    0 installs
79. ▌
    Python Environment Management · holobiomicslab

    Use when you are preparing to run Hi-C data normalization or read alignment filtering steps that depend on Python modules (iced, pysam, numpy, scipy) and you need to ensure consistent module versions across multiple runs or compute nodes.
    0 installs
80. ▌
    Scatac Seq Peak Matrix Export · holobiomicslab

    Use when after completing peak calling and cell annotation in an ArchR project, when you intend to perform trajectory analysis using STREAM rather than ArchR's native monocle3 or Slingshot integrations, or when you need to share peak-by-cell matrices with collaborators using STREAM pipelines.
    0 installs
81. ▌
    Sparse Matrix Subset Indexing · holobiomicslab

    Use when when you have a chromVARDeviations object with multiple annotation sets (e.
    0 installs
82. ▌
    Tn5 Insertion Bias Correction · holobiomicslab

    Use when you have aligned ATAC-seq BAM files from Tn5-based chromatin accessibility assays and need to perform footprinting analysis.
    0 installs
83. ▌
    API Specification Extraction · holobiomicslab

    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.
    0 installs
84. ▌
    Backend Routing And Dispatch · holobiomicslab

    Use when you need to support multiple plotting backends for the same data visualization task, and you want to centralize backend selection logic so that users can specify their preferred rendering engine (matplotlib, bokeh, or plotly) at call time without modifying the core plotting logic.
    0 installs
85. ▌
    Command Line Tool Invocation · holobiomicslab

    Use when you have an existing mass spectrometry data file in a vendor or standard format (mzML, NetCDF, etc.) and need to convert it to mzPeak format for downstream analysis, visualization, or archival.
    0 installs
86. ▌
    Configuration Object Pattern · holobiomicslab

    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.
    0 installs
87. ▌
    Conversion Directive Parsing · holobiomicslab

    Use when you have validated intermediate JSON data (conforming to the Experiment Description Specification) and need to configure how it should be converted to a supported output format (e.g., mwTab for Metabolomics Workbench submission).
    0 installs
88. ▌
    Dataset Integrity Assessment · holobiomicslab

    Use when when you have downloaded a released version of a structured dataset (e.g., LOTUS from Zenodo) and need to confirm it matches the documented headline statistics before downstream analysis, or when auditing data integrity after ingestion into a processing pipeline.
    0 installs
89. ▌
    Enrichment Ratio Calculation · holobiomicslab

    Use when after generating combined or alternative scores for a set of BGC-metabolite (GCF-MF) link candidates, you need to evaluate whether a scoring function preferentially ranks true validated links higher than spurious ones.
    0 installs
90. ▌
    Export Tag Syntax Validation · holobiomicslab

    Use when you have a tabular file (CSV or Excel) that has been manually or semi-automatically tagged with export tags, and you need to verify tag correctness before running the extract command to convert the tagged table into intermediate JSON.
    0 installs
91. ▌
    Github Repository Operations · holobiomicslab

    Use when when you need to verify that a software package (such as MassQL) passes its periodic integration test suite as indicated by CI workflow badges in the project documentation, or when you must reproduce pass/fail results for package-testing workflows distinct from unit tests to establish.
    0 installs
92. ▌
    HTTP API Integration Testing · holobiomicslab

    Use when you have deployed a microservice (e.g., TensorFlow Serving, REST API) and need to verify that specific endpoints (e.g., /model/metadata, /classify) return responses with correct schema, field names, and data types before consuming them in production workflows or downstream applications.
    0 installs
93. ▌
    HTTP Endpoint Identification · holobiomicslab

    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.
    0 installs
94. ▌
    Mandatory Field Verification · holobiomicslab

    Use when after generating mzPeak files from prototype implementations (Rust, Python, R, or .NET) or after format conversion, and before integrating files into a mass spectrometry data repository or sharing them with collaborators. Use it when specification compliance is a hard requirement (e.
    0 installs
95. ▌
    Metabolomics Ora Methodology · holobiomicslab

    Use when you have a metabolomics dataset and want to perform pathway enrichment analysis using ORA, but need to first understand its behavior, limitations, and correct application through reproducible simulation.
    0 installs
96. ▌
    Model Deployment Preparation · holobiomicslab

    Use when you have a pre-trained Keras model and need to deploy it via a Docker-based TensorFlow Serving API (e.g., for molecular classification via SMILES), but the model's layer naming or format does not yet match the target runtime's expectations (e.
    0 installs
97. ▌
    Msp File Parsing And Writing · holobiomicslab

    Use when you have one or more .msp spectral library files (NIST format) that need to be ingested for metadata curation, enrichment via web services, or export after transformation. Use this skill as the entry and exit point for any .msp-based annotation or analysis pipeline.
    0 installs
98. ▌
    Mzml Data Access Abstraction · holobiomicslab

    Use when when building or extending a mass spectrometry data parser that must support multiple mzML storage formats (plain .mzML, indexed .mzML.gz, standard-compressed .mzML.
    0 installs
99. ▌
    Pathway Database Integration · holobiomicslab

    Use when you have intensity measurements (peak features, protein intensities, or gene expression values) with compound or gene annotations (KEGG IDs, ChEBI IDs, UniProt IDs, or ENSEMBL IDs), and you need to aggregate them into biologically meaningful pathway groups for differential analysis.
    0 installs
100. ▌
     Peak Abundance Normalization · holobiomicslab

     Use when after peak detection and before any comparative analysis (e.g., diversity indices, ordination, or statistical testing) when working with direct injection FT-ICR MS data where raw peak intensities vary across samples due to instrumental factors. The task_id=task_005 example applies it to S.
     0 installs