← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

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

1. ▌
   Local Maxima Identification · holobiomicslab

   Use when you have raw LC-HRMS profile-mode data and need to identify candidate chromatographic peaks before classification or feature extraction.
   0
   installs
2. ▌
   Maplet Function Composition · holobiomicslab

   Use when you have metabolomics data that requires sequential processing through multiple analytical steps (e.
   0
   installs
3. ▌
   Metabolic Model Gap Filling · holobiomicslab

   Use when you have consensus metabolic reconstructions in SBML or JSON format for community members and need to resolve incomplete reactions, missing cofactor availability, or blocked pathways that prevent feasibility of biomass production.
   0
   installs
4. ▌
   Metabolite Id Normalization · holobiomicslab

   Use when you have metabolite identifiers sourced from or annotated against heterogeneous metabolome databases (HMDB, ChEBI, PubChem, KEGG, LipidMaps) and need to resolve ambiguity in metabolite identity, create a unified metabolite reference table, or enable cross-database queries in a metabolomics.
   0
   installs
5. ▌
   Metadata Structure Checking · holobiomicslab

   Use when after loading a metadata file but before merging it with positive and negative mode m/z peaklists. Apply this skill when you have a candidate metadata table (e.
   0
   installs
6. ▌
   Model Layer Name Validation · holobiomicslab

   Use when when deploying a TensorFlow Serving instance for the NP Classifier or any model-agnostic service where client code hardcodes layer names; before running inference pipelines; after model updates or configuration changes to catch layer name drift early.
   0
   installs
7. ▌
   Molecular Format Conversion · holobiomicslab

   Use when when ingesting raw chemical structure data from multiple external sources (publications, databases, contributor submissions) that use different molecular file formats (SMILES strings, SDF files, or other representations), and you need to unify them into a single canonical format before.
   0
   installs
8. ▌
   Multi Format Data Ingestion · holobiomicslab

   Use when you have raw metabolomics data files in one or more of the supported formats (.raw from Thermo instruments, .d directories from Agilent, or mzXML open-format exports) and need to ingest them into SMART for preprocessing, visualization, or statistical analysis.
   0
   installs
9. ▌
   Multi Omic Data Integration · holobiomicslab

   Use when you have raw or processed TWIM-MS data with arrival time and m/z dimensions, and you need to assign biomolecular class labels and compute class-specific CCS values across multiple compound classes simultaneously, particularly when you lack pre-identified feature peaks or want to bypass.
   0
   installs
10. ▌
    Multiomics Data Integration · holobiomicslab

    Use when when you have matched multiomics measurements across the same samples or cell lines (transcriptomics, proteomics, metabolomics, epigenomics, etc.) and need to train predictive models that learn regulatory relationships across biomolecular classes.
    0
    installs
11. ▌
    Multiple Testing Correction · holobiomicslab

    Use when whenever you have performed Fisher's exact test or another statistical enrichment test on multiple pathways, lipid categories, or metabolite sets simultaneously (typically ≥2 tests, often 50–100+ tests in practice).
    0
    installs
12. ▌
    Mzml Mzxml Spectrum Reading · holobiomicslab

    Use when when you have raw mzML or mzXML files containing uncompressed m/z and intensity arrays and need to load spectra into a uniform data contract before compression, cross-format comparison, or algorithmic processing.
    0
    installs
13. ▌
    Mzpeak Format Io Operations · holobiomicslab

    Use when you have mass spectrometry run data (spectra, chromatograms, instrument metadata) that must be stored in or recovered from the mzPeak format, or when you need to validate that a mzPeak implementation correctly supports both read and write paths for round-trip fidelity.
    0
    installs
14. ▌
    Nested JSON Path Resolution · holobiomicslab

    Use when when applying str directives during JSON-to-JSON conversion and the source value is not a direct field but is nested within a table structure—specifically when you need to reference a specific record by record_id, or traverse a sequence of field names (table → fields → nested value) to.
    0
    installs
15. ▌
    Network Graph Serialization · holobiomicslab

    Use when you have applied graphical lasso (GLASSO) to estimate a sparse inverse covariance matrix from a feature matrix and need to convert the non-zero precision matrix entries into an explicit graph representation suitable for visualization, topology analysis, or overlay with PCA scores.
    0
    installs
16. ▌
    Nuget Dependency Resolution · holobiomicslab

    Use when you are preparing to build a .NET project (WPF, class library, or console application) and need to ensure all declared NuGet package dependencies are available in the build environment. This is particularly necessary when the project uses custom or private package sources (e.
    0
    installs
17. ▌
    Openms API Surface Exposure · holobiomicslab

    Use when when you need to make OpenMS C++ classes, functions, or data structures callable from Python code, or when verifying that a newly bound C++ component can be imported and instantiated without errors in a Python environment.
    0
    installs
18. ▌
    Pandas Accessor Integration · holobiomicslab

    Use when you have mass-spectrometry data in a Pandas DataFrame and need to expose plot kinds (spectrum, chromatogram, mobilogram, peakmap) as a `.plot(kind='...
    0
    installs
19. ▌
    Postgresql Record Insertion · holobiomicslab

    Use when after successful gensim LDA inference has produced a JSON result file (e.g., myexp.ldaresult.json) and you need to make those topic assignments and model parameters queryable and accessible to a Django web application.
    0
    installs
20. ▌
    Ppm Mass Accuracy Filtering · holobiomicslab

    Use when when processing imzML/ibd Imaging Mass Spectrometry datasets and you need to extract ion density maps for specific analytes or isotopes. Apply this skill after importing the .imzML metadata and .
    0
    installs
21. ▌
    Python Object Serialization · holobiomicslab

    Use when after constructing a peak properties dictionary via csv_to_peak_properties or other data transformation steps, and before passing the dictionary to subsequent SMITER simulation functions (fragmentor selection, noise injection, mzML generation).
    0
    installs
22. ▌
    Pytorch Graph Serialization · holobiomicslab

    Use when you have constructed molecular graphs with atom features (atomic number, degree, formal charge, hybridization) and bond features (bond type, aromaticity) from SMILES or MOL files using RDKit, and need to feed them into a PyTorch-based GNN training pipeline without memory overhead or I/O.
    0
    installs
23. ▌
    Pytorch Inference Execution · holobiomicslab

    Use when you have a pretrained PyTorch model with released weights (e.g., JESTR on NPLIB1), a prepared dataset with input features (spectra m/z–intensity arrays, molecular graphs), a GPU environment with CUDA 11.
    0
    installs
24. ▌
    Pytorch Tensor Manipulation · holobiomicslab

    Use when when you have parsed molecular graph representations (atom nodes, bond edges, feature vectors) from SMILES or molecular structure files and need to prepare them for forward passes through a pre-trained GNN encoder in PyTorch.
    0
    installs
25. ▌
    Qt Widget Rendering Control · holobiomicslab

    Use when you need to restrict a Qt widget's display to a subset of its managed items—such as filtering isotope species in a metabolomics visualization—where the active subset is defined by application preferences stored outside the widget itself.
    0
    installs
26. ▌
    R Data Frame Transformation · holobiomicslab

    Use when when you have autoQ output containing peak area measurements for isotopologues in data frame format and need to prepare data for metBarPlot visualization or cross-sample comparison. Specifically, use this skill when val.to.
    0
    installs
27. ▌
    R Data Object Serialization · holobiomicslab

    Use when you have mzPeak files (Parquet-based archives containing mass spectrometry spectra and chromatogram data) that you want to analyze in R, and you need to convert the Arrow columnar representation into native R objects that can be passed to downstream analysis functions (e.
    0
    installs
28. ▌
    R List Object Serialization · holobiomicslab

    Use when after extracting structured metadata (e.g., instrument parameters, scan counts, time ranges) from Thermo Fisher Scientific .
    0
    installs
29. ▌
    R Package Version Detection · holobiomicslab

    Use when before launching the DaDIA metabolomics pipeline or any analysis that requires specific R package versions. Apply this skill when you have access to an R environment and need to verify that R ≥4.0, XCMS ≥3.11.4, and metaMS ≥1.25.1 are installed and compatible.
    0
    installs
30. ▌
    Ranked Gene List Generation · holobiomicslab

    Use when you have identified significant differential metabolites (DAMs) from metabolomic profiling, mapped them to genes via enrichment (e.g., MSEA), and possess a gene/protein interaction network (e.g., STRING).
    0
    installs
31. ▌
    Repository File Enumeration · holobiomicslab

    Use when you need to inventory sequence files in a repository's designated directory and cross-reference them against public databases to identify sequences that are unique to the curated archive.
    0
    installs
32. ▌
    REST API Client Integration · holobiomicslab

    Use when you have a batch of chemical compounds (identifiers and structures in SMILES, InChI, or IUPAC format) that need to be submitted to a remote REST API for classification or analysis, and you require the server's response (query ID and status) to track or retrieve results asynchronously.
    0
    installs
33. ▌
    Runtime Comparison Analysis · holobiomicslab

    Use when when a new version or variant of a tool claims performance improvements over a prior version (e.g., MASST+ vs. MASST), and you need empirical evidence that the claimed speedup (e.g., ~100-fold reduction in search time) is real, reproducible, and quantifiable.
    0
    installs
34. ▌
    Schema Conformance Checking · holobiomicslab

    Use when you have a collection of records in a standardized format (e.g., MassBank plain-text or structured records) that must be validated before commit or publication.
    0
    installs
35. ▌
    Semantic Metabolite Ranking · holobiomicslab

    Use when you have an unknown metabolite with unknown mass spectrum and need to prioritize structural candidates from databases (PubChem, HMDB) by their likelihood of being the true compound.
    0
    installs
36. ▌
    Sequence To Feature Mapping · holobiomicslab

    Use when when you have a list of polypeptide sequences (plain text, CSV, or FASTA format) and need to compute their monoisotopic mass and average mass for downstream mass spectrometry interpretation, database matching, or physico-chemical property annotation.
    0
    installs
37. ▌
    Shifted Dot Product Scoring · holobiomicslab

    Use when matching query mass spectra to a spectral library in the presence of unknown post-translational modifications (PTMs) or non-enzymatic modifications.
    0
    installs
38. ▌
    Shiny Interface Development · holobiomicslab

    Use when you have a complete R package (e.g., pmartR) implementing a multi-step omics analysis pipeline (upload → transform → filter → normalize → test → visualize), and you want to make those steps accessible to scientists who lack R expertise.
    0
    installs
39. ▌
    Software Regression Testing · holobiomicslab

    Use when after implementing code changes to MS2Query (e.g., modifying the workflow branching logic for true library matches vs. analog search results), before committing or pushing to the repository.
    0
    installs
40. ▌
    Spectral Data Preprocessing · holobiomicslab

    Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct-injection MS (DI-MS), ASAP-MS, or other ambient ionization instruments (AI-MS, LDI-MS), and you need to identify peaks of interest, assign confidence scores, and prepare the data for database matching or species.
    0
    installs
41. ▌
    Spectral Peak Normalization · holobiomicslab

    Use when when preparing query spectra and library spectra for similarity-based matching via dot product scoring, particularly in open modification spectral library searches where you need to match modified query spectra to unmodified library counterparts without the results being biased by.
    0
    installs
42. ▌
    Spectral Topic Modeling Lda · holobiomicslab

    Use when when you have a collection of normalized mass spectrometry spectra (peak intensities or binned m/z representations) and seek to enrich neural network training signals for metabolite identification by discovering latent spectral patterns.
    0
    installs
43. ▌
    Spectrum Embedding Indexing · holobiomicslab

    Use when you have pre-computed Word2vec embeddings of mass spectra and need to retrieve the k most similar spectra from a library of hundreds of thousands to millions of candidates.
    0
    installs
44. ▌
    Tanimoto Similarity Scoring · holobiomicslab

    Use when when running iterative reaction network expansion (Pickaxe) and you need to reduce the combinatorial explosion of generated compounds by prioritizing those structurally similar to a reference set (e.g., known metabolites, drug targets, or desired scaffolds).
    0
    installs
45. ▌
    Tensorflow Model Conversion · holobiomicslab

    Use when you have downloaded pre-trained Keras models and need to prepare them for deployment in a TensorFlow Serving container. Use this skill when you must convert legacy or freshly downloaded Keras model files to HDF5 format for compatibility with TensorFlow 2.3.0 serving infrastructure.
    0
    installs
46. ▌
    Workflow Build System Usage · holobiomicslab

    Use when when you have a Nextflow workflow repository with a Makefile, and you need to execute the workflow for local testing or validation. Triggers include: (1) first-time setup of a downloaded workflow; (2) regression testing after code changes;
    0
    installs
47. ▌
    Compound Ground Truth Matching · holobiomicslab

    Use when when you have pre-computed embeddings for query and reference MS/MS spectra, computed their cosine similarity matrix, and need to measure retrieval success by verifying whether the correct compound (identified by SMILES string) appears in the top-1, top-5, or top-10 ranked candidates from.
    0
    installs
48. ▌
    Data Augmentation Metabolomics · holobiomicslab

    Use when you have preprocessed and normalized ROI feature data extracted from mzXML or mzML mass spectrometry files and seek to increase feature representation and robustness before statistical modeling or machine learning.
    0
    installs
49. ▌
    Spatial Coordinate Mapping Msi · holobiomicslab

    Use when after loading and preprocessing a Cardinal MSImagingExperiment object (with normalized peaks and optional spatial segmentation results), and before conducting spatial statistical tests or co-localization analyses.
    0
    installs
50. ▌
    Chromatogram Alignment Warping · holobiomicslab

    Use when you have baseline-corrected and smoothed 2D-TIC chromatogram objects from individual GCxGC-MS samples that exhibit retention-time variations relative to a reference chromatogram, and you need to align peak positions across both dimensions before joining multiple samples for multiway PCA or.
    0
    installs
51. ▌
    Chromatographic Noise Modeling · holobiomicslab

    Use when you need to generate blank or background-only .mzML files for method validation, when you want to create synthetic negative controls with realistic instrumental noise but no analyte peaks, or when you need to simulate serum matrix background (e.
    0
    installs
52. ▌
    Chromatography Data Decimation · holobiomicslab

    Use when working with large GCIMS matrices where computational speed or memory constraints are a concern, after filtering retention time (e.g., 0–1100 s) and drift time (e.g., 5–16 ms) ranges and applying Savitzky-Golay smoothing. Use it as a preprocessing step before alignment operations.
    0
    installs
53. ▌
    Cluster Statistics Integration · holobiomicslab

    Use when after peak clustering has been performed on aligned GCIMS samples and a peak table matrix has been constructed, but the matrix contains NA values because some samples did not yield detected peaks at certain cluster positions.
    0
    installs
54. ▌
    Control Flow Diagram Synthesis · holobiomicslab

    Use when when you need to understand how a multi-instrument mass spectrometry platform (such as mzmine) selectively routes data to different processing pipelines based on declared input type (LC, GC, IMS, or MS Imaging).
    0
    installs
55. ▌
    Drift Retention Time Alignment · holobiomicslab

    Use when you have GCIMS samples exhibiting misalignment across drift time (typically 5–16 ms range) and retention time (typically 0–1100 s range) caused by pressure/temperature fluctuations or chromatographic column degradation, and you need to normalize sample positions before downstream peak.
    0
    installs
56. ▌
    Gaussian Peak Shape Evaluation · holobiomicslab

    Use when after peak detection on a composite mass track has identified candidate peaks in a mass chromatogram, and before compiling the final feature table.
    0
    installs
57. ▌
    Gc Ims Matrix Table Generation · holobiomicslab

    Use when after integratePeaks has been executed with a chosen integration method (e.g., fixed_size with RIP saturation threshold of 0.1) on a clustered, baseline-corrected GC-IMS dataset.
    0
    installs
58. ▌
    Gcxgc Ms Multivariate Analysis · holobiomicslab

    Use when after preprocessing a set of aligned 2D-TIC (two-dimensional Total Intensity Chromatogram) matrices from GCxGC-MS experiments—when you have multiple samples across distinct biological groups (e.
    0
    installs
59. ▌
    Imputation Algorithm Selection · holobiomicslab

    Use when you have a metabolomics dataset with left-censored missing values (e.g., below limit of quantification in LC/MS or GC/MS) and need to evaluate multiple imputation approaches.
    0
    installs
60. ▌
    Mass Spectrometry Data Parsing · holobiomicslab

    Use when you have received raw or vendor-converted centroid mzML files from LC-MS, GC-MS, or DI-MS platforms and need to extract MS1 spectra before building mass tracks, performing peak detection, or constructing composite feature maps.
    0
    installs
61. ▌
    Mona Metadata Field Extraction · holobiomicslab

    Use when when you have loaded a MoNA mass spectral library (GC-MS or LC-MS/MS) in MSP format and observe that SMILES strings are present in the Comment field rather than in a dedicated SMILES metadata field.
    0
    installs
62. ▌
    Ranking Task Loss Optimization · holobiomicslab

    Use when you have multiple pre-trained neural network models (e.g., MLP and GNN) that produce overlapping predictions on the same set of candidates, and your evaluation metric is rank-based (average rank, Rank@K) rather than point-wise accuracy or RMSE.
    0
    installs
63. ▌
    Workflow Routing Configuration · holobiomicslab

    Use when when you have raw mass spectrometry data files from multiple acquisition modalities (LC-MS, GC-MS, ion mobility, or imaging) and need to automatically route each to the correct downstream analysis module without manual intervention.
    0
    installs
64. ▌
    Xcms Data Import Preprocessing · holobiomicslab

    Use when you have raw LC-MS or GC-MS data files from a mass spectrometer (in mzML, NetCDF, or mzXML format) and need to detect chromatographic peaks, correct m/z bias via mass calibration (e.
    0
    installs
65. ▌
    4d Lcimmsms Feature Extraction · holobiomicslab

    Use when you have raw LC-IM-MS/MS data files from sterol lipid analysis and need to identify unsaturated sterol isomers by matching experimental collision cross section values against a quantum chemistry calculation-assisted CCS prediction database.
    0
    installs
66. ▌
    Annotation Object Manipulation · holobiomicslab

    Use when after completing metabolite annotation of LC-MS AIF features using the annotateRC function, when you need to persist ranked candidate matches, inspect multiple candidate annotations per feature, visualize matched ions in ranked spectra, or export pseudo-MS/MS spectra for external analysis.
    0
    installs
67. ▌
    Attention Mechanism Validation · holobiomicslab

    Use when after instantiating a transformer encoder module for mass spectrometry data processing (e.g., in IDSL_MINT), before training on large MS/MS datasets or running inference on test spectra.
    0
    installs
68. ▌
    Automated Lipid Identification · holobiomicslab

    Use when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to systematically identify and annotate lipid A molecular structures.
    0
    installs
69. ▌
    Blank Sample Feature Filtering · holobiomicslab

    Use when you have a feature quantification table exported from MZmine3 processing of non-targeted LC-MS/MS data and your experimental design includes blank (negative control) samples.
    0
    installs
70. ▌
    Chemical Coverage Optimization · holobiomicslab

    Use when your LC-MS feature table is incomplete or has low chemical coverage because traditional peak extraction algorithms (e.g., standard XCMS workflows) systematically miss features at m/z and retention time positions corresponding to known suspect compounds in your database.
    0
    installs
71. ▌
    Chemical Similarity Clustering · holobiomicslab

    Use when you have untargeted LC-MS/MS metabolomic data (MS1 features with MS2 fragmentation spectra) preprocessed by MZmine2 into a feature table (BIOM format) and MGF file, and you want to construct a chemically-informed hierarchy of features for alpha/beta-diversity analysis or to group features.
    0
    installs
72. ▌
    Clustering Metrics Computation · holobiomicslab

    Use when when you have executed multiple clustering tools on the same tandem-MS dataset and need to quantitatively compare their performance using normalized, comparable metrics rather than raw cluster assignments alone.
    0
    installs
73. ▌
    Cnn Inference On Spectral Data · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) in memory or on disk, a trained CNN model checkpoint available, and you need to generate molecular embedding vectors for matching against a reference database of known metabolites.
    0
    installs
74. ▌
    Cross Sample Feature Alignment · holobiomicslab

    Use when you have run mass detection and chromatogram building independently on each LC-MS/MS sample and produced per-sample feature lists with m/z, retention time, and intensity values.
    0
    installs
75. ▌
    Cross Spectrum Negative Mining · holobiomicslab

    Use when when training a Siamese architecture rescore model for MS/MS-based molecular formula prediction and you have an imbalanced training set with far fewer negative than positive spectrum pairs.
    0
    installs
76. ▌
    Cross Split Metric Aggregation · holobiomicslab

    Use when when you have a pre-trained model and need to report stable, generalizable performance on a fixed training set with multiple held-out test splits. Specifically: when you have 10 (or n) random query/reference splits on the same dataset (e.
    0
    installs
77. ▌
    Data Format Conversion CSV Tsv · holobiomicslab

    Use when after completing data merging, cleanup, and batch correction steps in the FBMN-STATS pipeline, when you have a processed feature quantification table combined with sample metadata in memory (R data frame or Python pandas DataFrame) and need to preserve it for multivariate statistical.
    0
    installs
78. ▌
    Deep Learning Model Evaluation · holobiomicslab

    Use when after training a Siamese neural network on MS/MS spectrum pairs, use this skill to quantify prediction performance on a disjoint test set (e.g., 3600+ spectra from 500 unseen compounds).
    0
    installs
79. ▌
    Diagnostic Fragment Annotation · holobiomicslab

    Use when when you have centroided, data-dependent acquisition (ddMS2) spectra in mzML format with extracted precursor m/z values and associated fragment ion lists, and you need to discriminate PFAS features from background signals using characteristic fragmentation patterns.
    0
    installs
80. ▌
    Dimensionality Reduction T Sne · holobiomicslab

    Use when you have computed high-dimensional embeddings (e.
    0
    installs
81. ▌
    Feature Group Adduct Detection · holobiomicslab

    Use when you have a feature table from LC-MS analysis (containing m/z, retention time, and intensity values) and need to identify which detected features represent the same molecular species ionized under different adduction states.
    0
    installs
82. ▌
    Feature Group Spectral Mapping · holobiomicslab

    Use when after sample alignment and isotopologue/adduct grouping are complete, when you need to associate MS2 spectral data (DDA-acquired) with the consolidated feature groups to enable MS/MS-based compound annotation or to bundle MS1 quantification with MS2 evidence.
    0
    installs
83. ▌
    Feature List Format Validation · holobiomicslab

    Use when a user supplies a custom feature list from external feature-finding software (vendor tools, alternative open-source pipelines) instead of using pyOpenMS automatic detection, or wishes to augment/replace pyOpenMS results with pre-processed features.
    0
    installs
84. ▌
    Feature Statistical Annotation · holobiomicslab

    Use when after LC-MS feature detection, alignment, and quantification are complete and you have a feature table with m/z and retention time attributes. Use this skill when you have access to a reference list of molecules of interest (e.
    0
    installs
85. ▌
    File Format Robustness Testing · holobiomicslab

    Use when when processing MS spectral data from multiple open mass spectra libraries (OMSLs) in mixed formats (MSP, MGF, JSON, CSV), especially when source data exhibits missing fields, malformed entries, inconsistent adduct representations, or non-standard format variants that may cause silent.
    0
    installs
86. ▌
    Fragment Intensity Aggregation · holobiomicslab

    Use when after extracting raw MS/MS spectra from mzML files but before consensus spectrum generation, when you observe high-resolution fragment lists where nearby peaks (within a specified mass tolerance, typically 0.
    0
    installs
87. ▌
    Fragment Ion Database Matching · holobiomicslab

    Use when you have centroid-mode LC-MS AIF chromatograms processed through xcms and RAMClustR, a feature table with target m/z and retention time values, and access to fragment libraries (e.g., LipidPos for lipids).
    0
    installs
88. ▌
    Fragment Ion Spectral Matching · holobiomicslab

    Use when after pointwise correlation analysis and exact mass difference refinement have identified candidate ion-species pairs that may share a common analyte origin.
    0
    installs
89. ▌
    Full Scan Acquisition Strategy · holobiomicslab

    Use when you need to assess MS1-level ionization efficiency, peak detection sensitivity, and chromatographic separation without the overhead of MS/MS fragmentation. Use it to benchmark full-scan detection across chemically diverse samples (e.
    0
    installs
90. ▌
    Ggplot2 Geom Treemap Rendering · holobiomicslab

    Use when after running qc_summary() on a filtered mpactr object and aggregating ion counts by filter status category (passed/failed).
    0
    installs
91. ▌
    Graph Based Feature Annotation · holobiomicslab

    Use when you have a GNPS molecular network (in GML or GraphML format) and corresponding MS2LDA substructural feature assignments or chemical class predictions, and you want to systematically propagate these annotations to individual network nodes to enable feature-aware visualization and.
    0
    installs
92. ▌
    Hierarchical Database Indexing · holobiomicslab

    Use when when you have a large combinatorial chemical space (e.g., all regioisomeric positions of lipid double bonds across carbon counts and saturation levels) and need to query it repeatedly against experimental mass spectrometry spectra.
    0
    installs
93. ▌
    High Dimensional Data Indexing · holobiomicslab

    Use when when you have millions of high-dimensional objects (e.g., MS/MS spectra converted to feature-hashed vectors) and need to compute pairwise similarities or retrieve nearest neighbors efficiently.
    0
    installs
94. ▌
    Instrument Type Filtering Gnps · holobiomicslab

    Use when you have a large, mixed-instrument GNPS spectral dataset and need to create an instrument-specific training set for FIDDLE or similar deep learning models. Use this skill when your configuration file specifies an instrument allowlist (e.
    0
    installs
95. ▌
    Intensity Threshold Evaluation · holobiomicslab

    Use when you have processed LC-MS data (mzML or vendor format) and need to validate that internal standards and target analytes produce peak intensities within expected operational ranges.
    0
    installs
96. ▌
    Inter Scan Interval Validation · holobiomicslab

    Use when after acquiring a PRM experiment on a Thermo Fisher Orbitrap instrument when you need to verify that the mass spectrometer's data acquisition controller executed the scheduled method with correct temporal spacing.
    0
    installs
97. ▌
    Interpretable Machine Learning · holobiomicslab

    Use when when you have tandem mass spectra data and need to predict a binary molecular property (e.g., presence of a functional group like a sulfo group) while maintaining full interpretability of the model's decision logic.
    0
    installs
98. ▌
    Iokr Fingerprint Space Ranking · holobiomicslab

    Use when when you have paired MS2 spectra and BGCs with structural candidates (e.g., from MIBiG homology), and you want to rank which BGC likely produces which spectrum using a compound-class-agnostic method.
    0
    installs
99. ▌
    Iokr Kernel Regression Scoring · holobiomicslab

    Use when when you have paired genomics (antiSMASH-detected BGCs with MIBiG homology assignments) and metabolomics data (MS2 spectra from GNPS), and you need to score BGC-spectrum links using molecular structure similarity rather than strain co-occurrence patterns.
    0
    installs
100. ▌
     Ionization Mode Classification · holobiomicslab

     Use when when converting raw MS/MS spectral records (e.g. from .msp format) into metabolite fragment database entries for MetaboAnnotatoR, and the output filenames or library index must distinguish between positive and negative ionization modes to ensure correct library selection during annotation.
     0
     installs