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HolobiomicsLab

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1. ▌
   Siamese Network Inference 2 · holobiomicslab

   Use when you have a collection of cleaned MS/MS spectra (in formats like mzML, mgf, msp, mzxml, or json) and need to predict molecular structural similarities between spectrum pairs without pre-computing RDKit fingerprints.
   0 installs
2. ▌
   Smiles Parsing Validation 2 · holobiomicslab

   Use when when you have a dataset of molecular structures encoded as SMILES strings that will be processed downstream (e.
   0 installs
3. ▌
   Spectral Library Matching 2 · holobiomicslab

   Use when you have one or more MS/MS spectra in .mgf format (or USI identifiers) and need to: (1) identify unknowns by searching against domain-curated reference data; (2) assign Level 2 metabolomics annotations via GNPS library matches; (3) aggregate matches across organism lineages (e.
   0 installs
4. ▌
   Tree To Query Translation 2 · holobiomicslab

   Use when you have a shallow decision tree trained on ChemEcho feature vectors (peak or neutral loss formulas) and need to deploy it as an executable query against tandem mass spectrometry data.
   0 installs
5. ▌
   Batch Record Processing 2 · holobiomicslab

   Use when when you have a repository containing hundreds or thousands of structured records (e.g., MassBank records in standardized format) that must be validated for correctness before release or merge.
   1 install
6. ▌
   Docker Image Deployment 2 · holobiomicslab

   Use when when you have a containerized scientific tool available on Docker Hub (e.
   2 installs
7. ▌
   Mz Binning And Indexing 2 · holobiomicslab

   Use when immediately after parsing mzML files into (m/z, scan_number, intensity) tuples when you need to build mass tracks from raw MS1 spectra. Use it when working with high-resolution instruments (e.
   0 installs
8. ▌
   Cdf File Format Parsing 2 · holobiomicslab

   Use when when you have multiple CDF files from mass spectrometry imaging experiments (e.g., root tissue MALDI-MS data) that need to be ingested into Matlab for linear imaging analysis. Trigger: presence of .
   0 installs
9. ▌
   Lipid Database Querying 2 · holobiomicslab

   Use when you have acquired full-scan mass spectrometry imaging data (e.g., from a mouse bladder or tissue section) with detected m/z features and want to assign chemical identities to those features by querying a structured lipid database.
   0 installs
10. ▌
    Ms2 Spectrum Consolidation 2 · holobiomicslab

    Use when after peak picking, sample alignment, and isotopologue/adduct grouping are complete, and you have DDA-MS2 scans associated with grouped feature ions.
    0 installs
11. ▌
    Binary File Format Parsing 2 · holobiomicslab

    Use when you encounter a proprietary or undocumented binary file (e.
    0 installs
12. ▌
    Breath Biomarker Discovery 2 · holobiomicslab

    Use when you have GC–MS data from human breath samples and need to identify marker metabolites for disease diagnosis, phenotyping, or biomarker discovery without a predefined target list. Your data is noisy or conventional peak picking has produced high false-positive rates.
    0 installs
13. ▌
    Candidate Ranking By Score 2 · holobiomicslab

    Use when you have a query mass spectrum and a set of candidate molecular structures, and you need to prioritize candidates by their likelihood of matching the query. Typical triggers include: (1) you have computed or extracted spectral features (e.
    0 installs
14. ▌
    Ccs Library Format Parsing 2 · holobiomicslab

    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.
    0 installs
15. ▌
    Compound Identifier Lookup 2 · holobiomicslab

    Use when you have an experimental MS/MS spectrum (m/z and intensity pairs in mzML/mzXML format from DDA or targeted acquisition on Thermo, Waters, or Bruker instruments) and need to identify the unknown compound by comparing it against a reference database.
    0 installs
16. ▌
    Docker Container Execution 2 · holobiomicslab

    Use when you have GNPS-style MGF spectral files as input and need to run Mass2SMILES MS/MS-to-structure inference without installing TensorFlow, CUDA, or Python dependencies locally.
    0 installs
17. ▌
    Dual Branch Feature Fusion 2 · holobiomicslab

    Use when when you have molecular input data available in two or more distinct formats (e.g., RDKit-extracted fingerprints AND torch_geometric Graph objects representing molecular topology) and your prediction target (e.
    0 installs
18. ▌
    Feature Annotation Mapping 2 · holobiomicslab

    Use when you have a trained decision tree model on ChemEcho sparse feature vectors and need to convert a specific decision path (root to leaf) into a deployable query.
    2 installs
19. ▌
    Gradient Flow Verification 2 · holobiomicslab

    Use when after implementing a composite loss function that combines multiple loss terms (e.g., InfoNCE contrastive loss and MSE reconstruction loss) in a PyTorch module, and before running full-scale training on MS/MS spectra data.
    0 installs
20. ▌
    Jupyter Notebook Execution 2 · holobiomicslab

    Use when when you have three coordinated mass spectrometry data tables (quantification, metadata, spectral) ready for integrated preprocessing and statistical analysis, and you need to generate a standardized JSON artifact for downstream interactive exploration rather than static tabular outputs.
    2 installs
21. ▌
    Large Scale Data Retrieval 2 · holobiomicslab

    Use when you have a query mass spectrum (or a metabolite reference spectrum from public data) and need to search it against a large-scale spectral repository (≥billions of spectra, e.g., GNPS library) where execution time and resource efficiency are critical.
    0 installs
22. ▌
    Lipid Nomenclature Mapping 2 · holobiomicslab

    Use when you need to generate a comprehensive, non-redundant inventory of lipid species that span a defined lipid class (e.g., phosphatidylcholine, triacylglycerol) and a range of fatty acid compositions (e.g., C14:0 to C22:6).
    0 installs
23. ▌
    Lipid Spectral Data Export 2 · holobiomicslab

    Use when after generating a complete lipid spectral library with adduct-specific fragmentation patterns and retention time metadata, when you need to deploy the library for targeted or data-dependent acquisition on specific mass spectrometry instruments—either Excalibur-controlled orbitrap.
    0 installs
24. ▌
    Metabolite To Gene Mapping 2 · holobiomicslab

    Use when you have metabolomic data (e.g., from LC-MS or GC-MS comparing patient to controls) showing differential abundant metabolites (DAMs), candidate genes from exome sequencing or variant calling, and access to a protein–protein or gene–gene interaction network (e.g., STRING).
    2 installs
25. ▌
    Model Artifact Persistence 2 · holobiomicslab

    Use when after a deep neural network model has completed training on LC-MS spectral peak classification data and you need to preserve the learned weights and architecture for downstream inference, validation on held-out test sets, or sharing with collaborators.
    0 installs
26. ▌
    Nmr Spin System Simulation 2 · holobiomicslab

    Use when when you have known metabolite concentrations and their spin-system coupling constants (J-values) and need to generate synthetic ¹H NMR spectra for method validation, metabolite library construction, or as a training dataset.
    0 installs
27. ▌
    Pytorch Module Composition 2 · holobiomicslab

    Use when when you need to extract both local spatial patterns and global long-range dependencies from sequential or spectral data (e.g., 1H NMR spectra), and neither CNNs nor Transformers alone are sufficient.
    1 install
28. ▌
    Pytorch Module Development 2 · holobiomicslab

    Use when when constructing a composite loss function for contrastive learning on structured data (e.
    0 installs
29. ▌
    REST API Endpoint Querying 2 · holobiomicslab

    Use when when you need to verify that a deployed model service (such as TensorFlow Serving) is running and exposing the correct input and output layer names before sending classification requests.
    0 installs
30. ▌
    Sample Metadata Extraction 2 · holobiomicslab

    Use when when you have an Excel file uploaded by a user following the InjectionDesign template schema and need to convert it into a modifiable, structured sample list that preserves up to three classification dimensions and QC type assignments for LC/GC-MS multi-omics experiments.
    0 installs
31. ▌
    Spectral Alignment Scoring 2 · holobiomicslab

    Use when you have paired MS/MS spectra (known compound and its structural analog) with assigned precursor m/z, charge, and SMILES; you want to quantify which parts of the molecular structure could have undergone modification by scoring peak alignment quality.
    0 installs
32. ▌
    Spectral Query Formulation 2 · holobiomicslab

    Use when you have a query mass spectrum (or representative metabolite spectrum from public data) and need to identify it by searching against large spectral reference databases (millions to billions of spectra).
    0 installs
33. ▌
    Spectrum Alignment Scoring 2 · holobiomicslab

    Use when after generating probability predictions for potential modification sites (via ModiFinder.
    0 installs
34. ▌
    Lipid Library Curation 2 · holobiomicslab

    Use when you have obtained MobiLipid or a similar IM-MS lipidomics package that bundles a CCS reference library for labeled lipids, and you need to verify library integrity, validate that all expected lipid species are present with plausible numeric CCS values, and prepare a canonical curated.
    2 installs
35. ▌
    Mass Accuracy Validation 2 · holobiomicslab

    Use when after implementing or modifying an mzML parser module that converts mzML files into MS-DIAL's internal data model, and before integrating the parser into the production analysis pipeline.
    2 installs
36. ▌
    Smiles String Validation 2 · holobiomicslab

    Use when you have MSBERT-preprocessed spectral datasets (GNPS, MoNA, or MTBLS1572 format) with SMILES annotations before training a spectral embedding or compound identification model.
    0 installs
37. ▌
    Poisson Noise Generation 2 · holobiomicslab

    Use when when preparing augmented variants of ion images (single-channel 2D arrays or multi-channel spectral images) for contrastive learning in mass spectrometry imaging tasks.
    0 installs
38. ▌
    Spectral Image Filtering 2 · holobiomicslab

    Use when when generating augmented variants of single-channel or multi-channel ion images for contrastive learning in mass spectrometry imaging analysis.
    0 installs
39. ▌
    Cross Method Rt Calibration 2 · holobiomicslab

    Use when when you have predicted retention times from a DNN model trained on one chromatographic method (CM) and need to rank or filter metabolite candidates on a different chromatographic method, but have only a small set of calibration molecules (≥10) with known RTs on both source and target.
    0 installs
40. ▌
    Git Repository Tag Checkout 2 · holobiomicslab

    Use when when you need to reproduce or validate a specific historical release artifact (e.g., a Semantic Release v1.0.
    2 installs
41. ▌
    Im Ms Drift Time Correction 2 · holobiomicslab

    Use when when you have IM-MS lipidomics data acquired on samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and need to quantify systematic CCS bias and apply lipid class-specific bias correction to all measured CCS values, particularly when multiple lipids per lipid.
    0 installs
42. ▌
    Lipid Feature Normalization 2 · holobiomicslab

    Use when after raw lipidomic and metabolomic data files have been generated by the Multi-ABLE method and loaded into the R environment, but before performing multivariate statistical analysis to identify differential lipids and metabolites.
    0 installs
43. ▌
    Mass Accuracy Ppm Filtering 2 · holobiomicslab

    Use when when you have a set of candidate molecular formulae for a measured m/z value and need to rank them by how closely their theoretical m/z matches the observed value.
    0 installs
44. ▌
    Metabolite Feature Flagging 2 · holobiomicslab

    Use when after drift correction and before imputation, when you have a MetaboSet object with LC-MS peak abundances and need to remove features with insufficient detection consistency across QC samples.
    0 installs
45. ▌
    Metadata Field Verification 2 · holobiomicslab

    Use when you have located a workflow definition file (YAML or JSON) from a versioned release and need to confirm that all mandatory workflow metadata fields (name, version, inputs, outputs, steps) are declared, properly formatted, and cross-references are resolved before validation or execution.
    2 installs
46. ▌
    Model Comparison Evaluation 2 · holobiomicslab

    Use when when you have multiple candidate spectrum prediction models (e.g., FFN vs. GNN encoders, NEIMS vs. MassFormer vs. ICEBERG) and need to determine which performs better on a shared task like tandem mass spectrum prediction.
    2 installs
47. ▌
    Ms Ms Spectrum Purification 2 · holobiomicslab

    Use when processing LC-MS/MS data acquired in DDA mode that contains chimeric (co-fragmented) MS/MS spectra—i.e., when a single MS/MS scan contains fragments from multiple precursor ions due to co-isolation.
    2 installs
48. ▌
    Nextflow Workflow Execution 2 · holobiomicslab

    Use when you have .mzML or .abf LC-HRMS metabolomics raw data files and need to perform peak detection, feature identification, and chromatogram alignment reproducibly across different compute environments (local workstations, HPC clusters).
    2 installs
49. ▌
    Reference Library Alignment 2 · holobiomicslab

    Use when when you have IM-MS lipidomics data with measured CCS values from samples spiked with U13C labeled internal standards, and you need to assess systematic CCS bias or enable CCS correction by comparing measured lipids against known library entries with validated CCS values.
    0 installs
50. ▌
    Release Artifact Generation 2 · holobiomicslab

    Use when when a software project has reached a stable milestone (v-tagged commit) and you need to produce official distribution artifacts with verified version metadata, checksums, and release documentation that can be validated against a published GitHub release record.
    0 installs
51. ▌
    Retention Time Scan Mapping 2 · holobiomicslab

    Use when when you have loaded an LC-MS spectrum file (mzML, mzXML, or equivalent) into the GNPS LCMS Visualization Dashboard and need to annotate extracted ion chromatograms with the precise retention time or scan ID positions where MS2 events occurred.
    0 installs
52. ▌
    Sample Metadata Integration 2 · holobiomicslab

    Use when when you have LC-MS peak table data in Excel format (e.g., from MS-DIAL peak picking) with separate compartments for sample information, feature properties, and intensity values, and you need to construct a structured R object that enforces consistency between sample metadata (e.
    0 installs
53. ▌
    Snr Based Signal Validation 2 · holobiomicslab

    Use when after composite map peak detection has generated a full unfiltered peak list with SNR values computed for each candidate peak.
    2 installs
54. ▌
    Spectral Feature Extraction 2 · holobiomicslab

    Use when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) and need to feed it into a CNN-based metabolite annotation pipeline.
    0 installs
55. ▌
    Spectral Similarity Scoring 2 · holobiomicslab

    Use when when you have extracted low-resolution mass spectra from individual chromatographic peaks in GC-MS data and need to match them against a spectral library (e.g., PNNLMetV20191015.MSL) to identify the unknown compound.
    2 installs
56. ▌
    Spectrum Metadata Filtering 2 · holobiomicslab

    Use when importing mass spectra from multiple open mass spectra libraries (OMSLs) or databases with heterogeneous metadata quality. Use when you observe spectra annotated with negative adducts (e.
    1 install
57. ▌
    Spectrum Similarity Scoring 2 · holobiomicslab

    Use when you have an unknown MS/MS spectrum (query spectrum with m/z and intensity pairs) and a reference spectral library (local or public: GNPS, MASSBANK, DrugBANK), and you need to identify the -matching compounds by ranking library entries by spectral similarity.
    0 installs
58. ▌
    Tree Based Model Validation 2 · holobiomicslab

    Use when after training a decision tree classifier on ChemEcho sparse feature vectors (representing tandem mass spectra fragmentation patterns), especially when the goal is to deploy predictions as executable queries or to validate that learned splits correspond to chemically meaningful.
    2 installs
59. ▌
    Hpc Job Parallelization 2 · holobiomicslab

    Use when you have a filtered set of conformers (100s–1000s) from ASE-ANI that each require independent quantum calculations via QUICK, and you have access to HPC resources with multiple cores or nodes. Parallelization is necessary when serial execution would exceed practical time budgets (e.
    2 installs
60. ▌
    Eic Signal Peak Detection 2 · holobiomicslab

    Use when after EIC candidate generation from LC/HRMS data (mzXML, mzML, or netCDF formats), when you need to localize discrete peaks within chromatographic profiles and assign retention time boundaries, apex intensities, and quality scores prior to peak annotation or cross-sample alignment.
    0 installs
61. ▌
    Metadata Field Validation 2 · holobiomicslab

    Use when you have received new or updated MassBank records (in plain-text or structured format) that must be integrated into the MassBank-data repository and you need to ensure they conform to the MassBank format specification before acceptance.
    0 installs
62. ▌
    Dimple Pipeline Execution 2 · holobiomicslab

    Use when when you have deposited mass spectrometry imaging data in NetCDF (CDF) format paired with MATLAB workspace files (.
    2 installs
63. ▌
    Image Intensity Jittering 2 · holobiomicslab

    Use when when preparing ion images (single-channel 2D arrays or multi-channel spectral images) from mass spectrometry imaging for contrastive learning in DeepION's COL or ISO modes.
    0 installs
64. ▌
    Spatial Feature Embedding 2 · holobiomicslab

    Use when when analyzing imaging mass spectrometry datasets where you need to reduce high-dimensional peak intensity features while preserving spatial structure, and when automatic peak picking and marker ion identification are required.
    0 installs
65. ▌
    Lipid Identification Scoring 2 · holobiomicslab

    Use when after peak picking has generated a peaklist of experimental fragment m/z values (from Q-Exactive orbitrap, Agilent/Bruker/SCIEX Q-TOF UHPLC-HRMS/MS, or direct infusion/imaging experiments) and you need to compare those fragments against the LipidMatch in-silico fragmentation library.
    0 installs
66. ▌
    M Z Alignment Across Samples 2 · holobiomicslab

    Use when after mass track construction for individual samples, when you need to establish consensus m/z values across a cohort of LC-MS samples to build a unified feature table.
    0 installs
67. ▌
    Ms Ms Spectrum Preprocessing 2 · holobiomicslab

    Use when you have raw MS/MS spectra (in MGF or mzML format) with unscaled peak intensities and noise artifacts, and you plan to rank chemical formulas, predict adducts, or score precursor–spectrum agreement using a machine learning model such as MIST-CF.
    0 installs
68. ▌
    Candidate Metabolite Ranking 2 · holobiomicslab

    Use when when you have generated a set of predicted metabolite structures from BioTransformer's metabolism prediction engine and need to assign identity to observed compounds from LC-MS/MS, spectral, or chromatographic experiments.
    1 install
69. ▌
    Cohort Performance Reporting 2 · holobiomicslab

    Use when you have NMR metabolite measurements from peripheral blood samples (plasma/serum) paired with processing delay metadata (pre-centrifugation and post-centrifugation times) and need to benchmark metabolic parameter stability across delay windows.
    0 installs
70. ▌
    Command Line Tool Invocation 2 · holobiomicslab

    Use when you need to bootstrap a tool workflow by generating a version- or instrument-specific default configuration file (e.g., for MS-DIAL 4 vs. 5), execute an analysis on formatted input files (e.g., MS-DIAL export .txt files), or capture tool output for downstream validation.
    2 installs
71. ▌
    Dataset Integrity Assessment 2 · 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
72. ▌
    Exact Mass Database Matching 2 · holobiomicslab

    Use when after feature detection and alignment on raw MS data, when you have a list of unknown feature m/z values and need to assign them to known xenobiotic metabolites or their predicted biotransformation products.
    2 installs
73. ▌
    Gnps Library Format Assembly 2 · holobiomicslab

    Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, molecular weight, annotation fields) that must be combined into a single structured library entry suitable for spectral library.
    0 installs
74. ▌
    Hybrid Model Fusion Strategy 2 · holobiomicslab

    Use when you have 1H NMR spectral data from complex mixtures and need to identify component compounds, but a single architecture (CNN or Transformer alone) fails to capture both fine local patterns in peak structures and long-range dependencies across the full spectral range.
    0 installs
75. ▌
    Linux Command Line Execution 2 · holobiomicslab

    Use when you have vendor-specific raw mass spectrometry data (ThermoFisher .raw, Agilent .
    0 installs
76. ▌
    Lipid A Structure Annotation 2 · holobiomicslab

    Use when when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to identify and annotate lipid A structures at scale.
    2 installs
77. ▌
    M Z Alignment Across Samples 3 · holobiomicslab

    Use when you have extracted mass tracks (EICs) from multiple LC-MS samples at 0.001 amu resolution and need to construct a sample-agnostic m/z reference frame.
    0 installs
78. ▌
    Mass Feature To Node Mapping 2 · holobiomicslab

    Use when you have an untargeted metabolomics feature table with m/z values, retention times, and intensity measurements, a metabolic network representation with compound nodes and chemical formulas, and you want to infer functional pathway activity directly from features without performing.
    0 installs
79. ▌
    Metabolite Spectral Matching 2 · holobiomicslab

    Use when you have an experimental mass spectrum (or a set of spectra from LC-MS/MS data) and need to identify the underlying metabolite(s) by comparing against known reference spectra in GNPS or a local indexed repository.
    0 installs
80. ▌
    Ms Ms Spectrum Preprocessing 3 · holobiomicslab

    Use when you have raw or semi-processed MS/MS spectral data from bottom-up tandem mass spectrometry experiments (data-dependent acquisition) that you intend to input to de novo peptide sequencing tools like Casanovo.
    2 installs
81. ▌
    Network Node Label Spreading 2 · holobiomicslab

    Use when you have an untargeted metabolomics dataset with a two-layer network topology already constructed (one layer representing biochemical knowledge/pathways, the other representing data-driven MS2 similarity), seed metabolites with reliable annotations from database matching or curation, and.
    0 installs
82. ▌
    Pathway Database Integration 2 · 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
83. ▌
    Precursor Product Mz Parsing 2 · holobiomicslab

    Use when you have raw MRM sample files from a LC-MS/MS instrument and need to systematically recover all precursor m/z and product m/z pairs for each transition. Use this as an initial parsing step before quantitation, method optimization, or transition verification workflows.
    0 installs
84. ▌
    Qc Sample Quality Assessment 2 · holobiomicslab

    Use when after drift correction and before imputation when you have LC-MS data with designated QC samples and you need to remove features with poor reproducibility across QC replicates.
    1 install
85. ▌
    R Package Function Execution 2 · holobiomicslab

    Use when you have raw Bruker NMR spectral data files (1D 1H format) stored in a directory structure and need to prepare them for automated metabolite identification and quantification in ASICS.
    2 installs
86. ▌
    Retention Time Peak Matching 2 · holobiomicslab

    Use when after drift correction and quality flagging, when you have a feature abundance matrix with associated metadata (Feature_ID, m/z, retention time) and need to identify which features likely represent the same underlying metabolite or adduct series before statistical analysis or metabolite.
    0 installs
87. ▌
    Simulation Output Validation 2 · holobiomicslab

    Use when after executing a multi-stage simulation workflow in R and/or MATLAB, when you have generated intermediate and final outputs (tables, figures, model objects) and need to confirm that all artifacts conform to the documented format, structure, and expected content before downstream analysis.
    0 installs
88. ▌
    Spectral Mz Window Filtering 2 · holobiomicslab

    Use when when you have resolved mzML or mzXML spectrum files and need to isolate signals for a target m/z value (e.g., 870.954) across all retention times or a specific scan.
    0 installs
89. ▌
    Sterol Isomer Classification 2 · holobiomicslab

    Use when you have LC-IM-MS/MS raw data from sterol-containing tissue samples and need to assign detected peaks to specific structural isomers (e.g., distinct double bond positions or saturation patterns in C27–C29 sterols).
    0 installs
90. ▌
    Stocsy Metabolite Assignment 2 · holobiomicslab

    Use when use STOCSY when you have preprocessed 1H NMR spectral data with an unidentified peak of interest (driver signal at a specific δ ppm value) and need to determine its metabolite identity by finding correlated signals across the spectrum.
    2 installs
91. ▌
    Two Layer Topology Traversal 2 · holobiomicslab

    Use when you have an untargeted metabolomics dataset with partial metabolite annotations (from database matching or prior curation) and need to extend annotation coverage to unannotated metabolites.
    0 installs
92. ▌
    YAML JSON Structural Parsing 2 · 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.
    0 installs
93. ▌
    Expert Review Preparation 2 · holobiomicslab

    Use when when a paper describes a computational or statistical method and you need to verify that claims are supported by available code, data, or documentation before human expert evaluation.
    0 installs
94. ▌
    Cross Domain Token Mapping 2 · holobiomicslab

    Use when when building a unified sequence model (e.
    0 installs
95. ▌
    Spectral Metadata Grouping 2 · holobiomicslab

    Use when processing a mass spectrometry dataset (in FragHub JSON format or similar) where duplicate spectral records are suspected or known to exist. The input dataset should already be in a standardized format with computed or retrievable SPLASH keys.
    0 installs
96. ▌
    Validator Tool Integration 2 · holobiomicslab

    Use when you have a repository of structured records (e.g., mass spectrometry data, metadata, or domain-specific formats) and need to enforce validation rules systematically across all records.
    0 installs
97. ▌
    Python Environment Pinning 2 · holobiomicslab

    Use when when you have access to a research repository or README documenting a machine learning implementation (e.g., Keras/TensorFlow-based deep learning model) and need to reproduce the computational environment exactly. Triggers include: (1) README explicitly lists pinned versions (e.
    0 installs
98. ▌
    Nps Classification Prediction 2 · holobiomicslab

    Use when you have acquired a mass spectrum from an unknown suspected illicit drug analyte and need to compare it against a synthetic NPS database to rank candidate identities by similarity.
    0 installs
99. ▌
    Adduct Mass Offset Assignment 2 · holobiomicslab

    Use when when you have an LC-MS feature table with m/z and retention time columns and need to identify which observed ions correspond to the same neutral compound under different ionization conditions and isotopic enrichment.
    0 installs
100. ▌
     Adduct Regex Pattern Matching 2 · holobiomicslab

     Use when ingesting mass spectrometry spectra from heterogeneous databases or libraries where adduct annotations may be incomplete, incorrectly formatted, or inconsistent with the ionization mode. Use it before downstream analysis (e.
     0 installs