← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 11k skills
• 0 followers
• last month last updated

1. ▌
   Mass Spectrometry Query Semantics 2 · holobiomicslab

   Use when when you need to express complex mass spectrometry search patterns (e.g., isotope envelope detection, neutral loss patterns, intensity relationships across m/z ranges) in a human-readable format that can be executed against spectral data files (mzML, mzXML) or spectral repositories.
   0 installs
2. ▌
   Mass To Charge Tolerance Matching 3 · holobiomicslab

   Use when you have statistically significant LC-MS features and need to group them into structural clusters. Specifically, use it after selecting features by p-value threshold (e.g., p < 0.
   2 installs
3. ▌
   Mass Track Extraction And Binning 2 · holobiomicslab

   Use when when you have centroid mzML files from LC-MS metabolomics acquisition and need to construct sample-level mass tracks before cross-sample alignment. Specifically: you are starting fresh with vendor-converted or pre-processed mzML input;
   2 installs
4. ▌
   Metabolic Parameter Visualization 2 · holobiomicslab

   Use when when you have paired NMR metabolite measurements and corresponding processing metadata (pre-centrifugation delay, post-centrifugation delay, sample type, cohort) for a blood sample cohort and need to determine which metabolites remain stable across the expected or observed delay range, or.
   0 installs
5. ▌
   Metabolomic Heatmap Visualization 2 · holobiomicslab

   Use when after completing feature annotation and reaction assignment in an untargeted metabolomics workflow, specifically when you have a feature-by-sample intensity matrix aligned with metabolite identities and want to communicate cluster structure, reaction pathway groupings, and feature.
   0 installs
6. ▌
   Ms Ms Spectral Data Preprocessing 2 · holobiomicslab

   Use when when you have MS/MS spectral data (raw or intermediate format) that must be fed into the Mass2SMILES Docker container or similar deep learning models for MS/MS-to-structure inference.
   0 installs
7. ▌
   Msconvert Parameter Configuration 2 · holobiomicslab

   Use when you have acquired raw mass spectrometry data from ThermoFisher, Agilent, or compatible vendors in their native formats (.raw, .d, or equivalent) and need to prepare it for nontargeted analysis using MSThunder on a Linux system.
   0 installs
8. ▌
   Msi Feature Metadata Preservation 2 · holobiomicslab

   Use when you are converting a processed Cardinal MSImagingExperiment object (containing normalized peaks, optional spatial shrunken centroids segmentation, and feature m/z annotations) into a Seurat object for downstream pathway analysis, differential metabolite expression, or integrative.
   0 installs
9. ▌
   Pathway Rank Stability Assessment 2 · holobiomicslab

   Use when when you have completed a PALS pathway analysis on a clean metabolomics peak intensity matrix and pathway annotation set, and you need to verify that the ranked pathway discoveries are not artifacts of favorable data quality.
   2 installs
10. ▌
    Peak Picking Algorithm Comparison 2 · holobiomicslab

    Use when you have claims in a paper or tool documentation that one peak picking method outperforms others (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms'), but the specific comparison metrics, numerical results, and source tables are not provided in the abstract or introduction.
    2 installs
11. ▌
    Peak Table Filtering Metabolomics 2 · holobiomicslab

    Use when after generating a peak table from XCMS peakTable() output in an untargeted LC-MS metabolomics workflow, if your experimental design includes quality control (QC) samples (SampleType='LQC') and you want to exclude noisy or unstable EICs before building a peak quality classifier.
    1 install
12. ▌
    Ppm Tolerance Scoring And Ranking 2 · holobiomicslab

    Use when you have extracted a list of candidate molecular formulae for a given m/z value and need to rank them by plausibility.
    0 installs
13. ▌
    Precursor List Formatting For Dda 2 · holobiomicslab

    Use when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an Orbitrap instrument using Excalibur software.
    0 installs
14. ▌
    Public Database Query Integration 2 · holobiomicslab

    Use when you have an experimental MS/MS spectrum (m/z and intensity pairs with known precursor m/z) and need to identify the compound by searching against public repositories or a local reference library.
    2 installs
15. ▌
    Quality Control Metric Evaluation 2 · holobiomicslab

    Use when you have measured IM-MS lipidomics data spiked with U13C labeled internal standards and need to assess whether CCS bias remains within acceptable limits for each lipid class-adduct combination.
    0 installs
16. ▌
    R Script Validation And Execution 2 · holobiomicslab

    Use when when you have obtained an R-based bioinformatic program (such as DNMS2Purifier.
    0 installs
17. ▌
    R Statistical Model Serialization 2 · holobiomicslab

    Use when after training a customized R statistical or machine learning model on annotated training data, you need to persist the trained model object for reuse in downstream analysis workflows without retraining.
    0 installs
18. ▌
    Retention Time Prediction Scoring 2 · holobiomicslab

    Use when you have a list of candidate metabolites for an unknown compound (from mass-to-structure search or library matching), experimental retention time(s) from one or more chromatographic methods, and access to a trained DNN RT predictor and meta-learned RT projection model.
    0 installs
19. ▌
    Signal To Noise Ratio Computation 2 · holobiomicslab

    Use when after peak detection in nontargeted LC-MS workflows when you have a feature table with detected peaks and need to assign quality scores or filter low-confidence features.
    0 installs
20. ▌
    Small Molecule Structure Matching 2 · holobiomicslab

    Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the observed compounds by matching their experimental features (mass-to-charge ratio, retention time, spectral signature) to.
    0 installs
21. ▌
    Spectral Database Query Execution 2 · holobiomicslab

    Use when when you have an unknown mass spectrum (query spectrum) and need to search it against a reference database of billions of spectra to find matching or structurally related compounds.
    0 installs
22. ▌
    U13c Labeled Lipid Identification 2 · holobiomicslab

    Use when you have measured CCS values from (LC-)IM-MS samples spiked with U¹³C labeled internal standards (e.
    0 installs
23. ▌
    Web Service Deployment Validation 2 · holobiomicslab

    Use when when you need to confirm that a publicly hosted academic web service (such as molDiscovery) is live and responding at a documented endpoint URL, or when troubleshooting access issues reported by end users.
    0 installs
24. ▌
    Ccs Reference Data Extraction 2 · holobiomicslab

    Use when you have obtained or need to prepare a DTCCS_N2 reference library for U13C-labeled lipids (typically provided as part of a lipidomics tool distribution) and need to extract, validate, and normalize its contents into a machine-readable table format before using it for CCS bias calculation.
    0 installs
25. ▌
    Conformer Ensemble Processing 2 · holobiomicslab

    Use when you have a set of conformers that have already been filtered by ASE-ANI neural network potentials and need to extract quantum-mechanical electronic properties (polarizability tensor, dipole moment) required for collision cross section calculation.
    2 installs
26. ▌
    Per Lipid Class Normalization 2 · holobiomicslab

    Use when you have IM-MS lipidomic data from samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract), measured CCS values stratified by lipid class and adduct type, and access to the DTCCS_N2 reference library for U13C lipids.
    0 installs
27. ▌
    Saturated Peak Reconstruction 2 · holobiomicslab

    Use when processing IM-MS data files (Agilent .d or UIMF format) that contain high-abundance ions suspected of signal saturation, particularly in untargeted or discovery proteomics/metabolomics workflows where dynamic range compression would obscure quantitative relationships.
    0 installs
28. ▌
    Smiles Canonicalization Rdkit 3 · holobiomicslab

    Use when when processing raw SMILES strings from external databases or user input that may contain non-canonical tautomeric forms, variable stereochemical notation, or redundant representations of the same chemical structure.
    0 installs
29. ▌
    Chromatographic Peak Processing 2 · holobiomicslab

    Use when after peak detection when you have a table of detected peaks with m/z values and retention times from LC/HRMS data, and you observe systematic m/z drift across a batch or population-scale study (n > 500 samples).
    0 installs
30. ▌
    Lc Hrms 2d Area Standardization 2 · holobiomicslab

    Use when after detecting local-maxima in LC-HRMS profile mode datasets and before training or inference with a CNN model for peak classification.
    0 installs
31. ▌
    Mass Spectrometry Preprocessing 2 · holobiomicslab

    Use when when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) that must be fed into a CNN model for metabolite annotation via compound fingerprint prediction.
    0 installs
32. ▌
    Search Performance Benchmarking 2 · holobiomicslab

    Use when when you have two or more implementations of a spectral search tool (e.g., MASST vs. MASST+) and need to quantify whether claimed performance improvements (e.g., '100-fold speedup') are reproducible.
    3 installs
33. ▌
    Unified Vocabulary Construction 2 · holobiomicslab

    Use when when you have parallel mass spectra and molecular structure data (e.g., CANOPUS or MassSpecGym datasets) and aim to train a single encoder-decoder model (e.g., BART) that must handle both modalities as input and output tokens.
    0 installs
34. ▌
    Binary Spectral Data Extraction 2 · holobiomicslab

    Use when you have parsed imzML XML metadata and loaded the corresponding .ibd binary intensity file, and need to extract specific ion images at one or more target m/z values.
    0 installs
35. ▌
    Bioinformatic Object Conversion 2 · holobiomicslab

    Use when when you have processed Cardinal MSI data (normalized peak intensities, optional SSC segmentation results) and need to transition to Seurat-based workflows for differential expression, pathway analysis, or integration with spatial transcriptomics data.
    0 installs
36. ▌
    Matlab Workspace Initialization 2 · holobiomicslab

    Use when when you have mass spectrometry imaging root datasets paired with accompanying .mat workspace files (as in the B73 and Oaxacan Green genotypes from Sama et al.
    0 installs
37. ▌
    Microbe Compound Identification 2 · holobiomicslab

    Use when you have collected MS/MS spectra from a microbial sample (pure culture, environmental isolate, or mixed community) and need to assign chemical identities to observed m/z features while simultaneously resolving which microbial taxa are likely producers of each metabolite.
    2 installs
38. ▌
    Mass Spectrometry Library Matching 2 · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (with ≥10 peaks, precursor m/z, and at least 5 fragment ions) and need to identify it by comparing against a curated spectral library with annotated InChIKeys or chemical structures.
    0 installs
39. ▌
    Attention Mechanism Implementation 2 · holobiomicslab

    Use when you have imaging mass spectrometry (IMS) datasets with peak intensity features organized as spatial graphs (nodes = pixels/voxels, edges = spatial adjacency), and you need to discover latent peak patterns for automatic peak picking or marker ion identification without manual feature.
    0 installs
40. ▌
    Chemical Transformation Annotation 2 · holobiomicslab

    Use when after computing all pairwise mass differences from MS imaging peaks and binning them into a histogram, use this skill when you need to prioritize which mass differences are most likely to represent real chemical adducts (rather than noise or measurement artifacts) by ranking them by.
    0 installs
41. ▌
    Compound Identification Validation 2 · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (in .
    0 installs
42. ▌
    Conditional Dispatch Routing Logic 2 · holobiomicslab

    Use when a mass spectrometry analysis pipeline must accept data from multiple sources with different identifier schemes (GNPS Task ID, Universal Spectrum Identifiers, or Feature-Based Molecular Networking task IDs), and you need to transparently route each to the correct loader without requiring.
    2 installs
43. ▌
    Controlled Vocabulary Term Mapping 2 · holobiomicslab

    Use when you have collected or inherited sample-information metadata from multiple sources (e.
    0 installs
44. ▌
    Dataset Size Threshold Enforcement 2 · holobiomicslab

    Use when when you have partitioned public MS/MS files from MassIVE using the ReDU File Selector into one or more filtered groups (G1–G6) and need to verify that each group's file count complies with computational constraints before submitting to GNPS molecular networking (3000 file limit) or.
    0 installs
45. ▌
    Deep Learning Model Initialization 2 · holobiomicslab

    Use when you have downloaded the LC-MS spectral peak dataset (DOI 10.25345/C5FD2F) and need to train a DNN model from scratch rather than using a pre-trained checkpoint.
    0 installs
46. ▌
    Encoder Output Dimension Reduction 2 · holobiomicslab

    Use when you have 512-dimensional representation vectors output from paired ResNet18 encoders processing augmented ion images, and you need to: (1) introduce an intermediate projection space to enable contrastive loss optimization without trivial/collapsed solutions, (2) further compress learned.
    1 install
47. ▌
    Feature Quality Assessment Metrics 2 · holobiomicslab

    Use when after nontargeted peak detection and segmentation has generated a feature table from raw LC-MS data (mzML or vendor format), apply quality assessment when you need to rank or filter features by confidence before annotation, adduct grouping, or MS/MS matching.
    0 installs
48. ▌
    Feature Table Row Count Validation 2 · holobiomicslab

    Use when after peak quality filtering has been applied to a composite map peak detection output using SNR (>2), goodness-of-fit (peakshape > 0.5), minimum peak height (default 1e5), and prominence (≥20% of peak_height) thresholds.
    0 installs
49. ▌
    File Grouping By Sample Attributes 2 · holobiomicslab

    Use when you have a validated ReDU sample-information metadata table (gnps_metadata.tsv) loaded from a MassIVE accession, and you need to partition public MS/MS files into multiple analysis cohorts by one or more sample attributes.
    0 installs
50. ▌
    Formula Network Extraction From Mz 2 · holobiomicslab

    Use when you have an observed m/z value from spatially-resolved mass spectrometry imaging and need to assign one or more plausible molecular formulae with confidence metrics.
    2 installs
51. ▌
    Github Release Metadata Comparison 2 · holobiomicslab

    Use when you have reproduced a release artifact locally (e.g., via Semantic Release or a build tool) and need to verify it matches the official GitHub release record.
    0 installs
52. ▌
    Gnps Molecular Network Integration 2 · holobiomicslab

    Use when you have computed frequent fragmentation patterns from a collection of MS/MS spectra using mineMS2, and you want to focus pattern interpretation on subsets of spectra that form meaningful network components (connected groups, cliques, or high-similarity pairs) in a GNPS molecular network.
    0 installs
53. ▌
    Gradient Space Optimization Search 2 · holobiomicslab

    Use when after fitting a Gaussian Process regression model to prior LC-MS gradient runs (retention times, separation efficiency scores, or compound identification counts).
    0 installs
54. ▌
    Hyperparameter Sweep Configuration 2 · holobiomicslab

    Use when when implementing multiple competing model architectures (e.
    0 installs
55. ▌
    Knowledge Graph Integration Design 2 · holobiomicslab

    Use when designing a metabolite annotation workflow that must simultaneously leverage established biochemical knowledge (pathway databases, reaction networks) and experimental evidence (mass spectrometry feature similarity, co-occurrence patterns).
    0 installs
56. ▌
    Lc Hrms Data Processing Evaluation 2 · holobiomicslab

    Use when you have processed the same set of untargeted LC/HRMS files (mzXML, mzML, or netCDF format) with two or more peak-picking tools and need to validate which tool produces higher-quality peaklists for organic small molecules.
    2 installs
57. ▌
    Mass Grid Construction And Mapping 2 · holobiomicslab

    Use when after mass track extraction from individual LC-MS samples, when you need to align mass tracks across a cohort to produce a unified feature matrix. Specifically: when study size is ≤10 samples, use pairwise anchor-prioritized alignment;
    0 installs
58. ▌
    Metabolite Feature Quality Control 2 · holobiomicslab

    Use when you have a metabolomic SummarizedExperiment object with replicate QC (quality control) samples and need to remove non-reproducible metabolic features before phenotype association modeling. Use it specifically when your workflow requires FDA-compliant reproducibility thresholds (CV < 0.
    0 installs
59. ▌
    Metabolite Set Decomposition Plage 2 · holobiomicslab

    Use when you have peak intensity data from metabolomics experiments with annotated metabolites assigned to known groupings (KEGG pathways, Reactome, GNPS Molecular Families, or MS2LDA Mass2Motifs) and need to identify which metabolite sets change significantly across experimental comparisons while.
    0 installs
60. ▌
    Compound Retrieval Hit At K Evaluation 2 · holobiomicslab

    Use when when you have generated spectral embeddings for a query set and a reference spectral library, computed pairwise cosine similarity scores between them, and need to quantify retrieval performance across ranked candidates (top-1, top-5, top-10).
    2 installs
61. ▌
    Conditional Allocation Design Patterns 2 · holobiomicslab

    Use when when designing a dataset storage layer that must handle variable dataset sizes, block layouts, and platform-specific constraints (e.g., Windows vs. non-Windows). Specifically: (1) you have parsed dataset metadata including cache-file flags, total point counts, and block configuration;
    1 install
62. ▌
    Cosine Annealing Schedule Optimization 2 · holobiomicslab

    Use when when training a regularized deep neural network for molecular property regression (e.g., retention time prediction on the METLIN SMRT dataset with 80,038+ samples), use cosine annealing warm restarts to escape plateaus and improve convergence.
    0 installs
63. ▌
    Dataset Storage Interface Architecture 2 · holobiomicslab

    Use when you have NMR dataset metadata (cache-file flag, total point count, block layout configuration) and need to select an appropriate storage backend that balances memory efficiency, access patterns, and platform-specific constraints.
    2 installs
64. ▌
    Deep Learning Model Checkpoint Loading 2 · holobiomicslab

    Use when when you have MS/MS spectra from GNPS or other libraries and need to apply a pre-trained FIDDLE model (TCN formula predictor or Siamese rescore architecture) without training from scratch. Use this skill before running inference on new samples or benchmarks.
    0 installs
65. ▌
    Feature Condition Comparative Analysis 2 · holobiomicslab

    Use when when you have molecular structures, a regression target (e.g. retention time), and want to establish whether one class of molecular features (e.g., fingerprints) outperforms another (e.g., descriptors) or whether combining them yields marginal gains.
    2 installs
66. ▌
    Feature Correlation Graph Construction 2 · holobiomicslab

    Use when after imputing missing values and before assigning Cluster_IDs in the notame preprocessing pipeline.
    0 installs
67. ▌
    Feature Flagging Threshold Calibration 2 · holobiomicslab

    Use when after drift correction in non-targeted LC-MS metabolomics workflows, when you need to decide which molecular features are sufficiently reproducible (low instrument/QC variance) and biologically informative (high QC-versus-biological signal ratio) to retain for downstream statistical.
    0 installs
68. ▌
    Fingerprint Vector Loading And Parsing 2 · holobiomicslab

    Use when when you have deposited or archived biosynfoni fingerprint vectors (such as from Zenodo 10.5281/zenodo.14822624) and need to ingest them into a Python workflow to compute distributional statistics, bit-frequency profiles, sparsity metrics, or pairwise similarity coefficients.
    0 installs
69. ▌
    Fragmentation Pattern Annotation Magma 2 · holobiomicslab

    Use when you have a tandem MS/MS spectrum of a structurally modified compound and a known reference structure (SMILES), and you need to annotate which fragment ions correspond to specific bonds or atoms in the molecule.
    0 installs
70. ▌
    Fragmentation Pattern Query Validation 2 · holobiomicslab

    Use when after converting a decision tree path into a MassQL query string, before deployment to production mass spectrometry workflows.
    0 installs
71. ▌
    Fusion Pooling Strategy Implementation 2 · holobiomicslab

    Use when you have extracted parallel feature streams from a CNN backbone (local spectral patterns) and a Transformer backbone (global dependencies) in 1H NMR spectra, and you need to fuse them into a single embedding for bi-encoder or cross-encoder processing before compound identification scoring.
    2 installs
72. ▌
    Image Based Feature Extraction Ms Maps 2 · holobiomicslab

    Use when you have a two-dimensional MS map (m/z vs retention time) from GC–MS or LC–MS data and need to discriminate analytes and identify marker features without false positives from peak picking; particularly useful for untargeted metabolomics at ppb sensitivity (e.
    2 installs
73. ▌
    Internal Standardization Lipid Mapping 2 · holobiomicslab

    Use when you have (LC-)IM-MS lipidomics data from samples spiked with U13C-labeled yeast extract, measured CCS values for both labeled and unlabeled lipids, and need to quantify systematic CCS bias between your instrument and a reference library before applying bias correction.
    0 installs
74. ▌
    Isotope And Adduct Pattern Recognition 2 · holobiomicslab

    Use when when processing MS1 mass tracks from a single sample and you have already constructed per-bin mass tracks with consensus m/z and intensity vectors.
    0 installs
75. ▌
    Lc Ms Dataset Acquisition And Curation 2 · holobiomicslab

    Use when when beginning an untargeted LC-MS metabolomics study and need to assemble a cohort of mzML files for processing; particularly when establishing performance baselines across sample counts (10, 50, 100+ samples), validating reproducibility, or preparing data for publication.
    0 installs
76. ▌
    Mass Spectrometry Data Format Handling 2 · holobiomicslab

    Use when you have raw MRM sample files from an LC-MS/MS instrument and need to programmatically identify and tabulate all precursor m/z and product m/z pairs for each MRM transition.
    0 installs
77. ▌
    Mass Spectrometry Imaging Data Loading 2 · holobiomicslab

    Use when you have raw or preprocessed MS imaging data archived as an RDS file or from a Zenodo deposit that includes the full m/z feature set (e.g., 10,200 m/z values spanning 150–1000 m/z range) and spectrum count (e.
    0 installs
78. ▌
    Metabolite Feature Table Normalization 2 · holobiomicslab

    Use when you have selected a subset of ReDU public tandem MS files with GNPS chemical annotations (level 2 or 3 spectral library matches) and wish to explore sample relationships via principal component analysis.
    0 installs
79. ▌
    Multi Domain Search Result Aggregation 2 · holobiomicslab

    Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST tools and need to synthesize results across domains (e.
    0 installs
80. ▌
    Multidimensional Signal Smoothing Imms 2 · holobiomicslab

    Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains jagged, low-abundance ion peaks or when saturation repair has been applied and the resulting reconstructed signals need artifact removal and enhancement.
    0 installs
81. ▌
    Multivariate Ordination Interpretation 2 · holobiomicslab

    Use when you have a collection of tandem MS/MS samples (stored in MassIVE) with GNPS spectral library annotations (m/z, retention time, compound identity), and you want to explore whether samples cluster by shared chemical features without predefined class labels.
    0 installs
82. ▌
    Nmr Spectral Data Format Serialization 2 · holobiomicslab

    Use when you have generated 1D FID time-domain data and Fourier-transformed frequency-domain 1H NMR spectra, or computed 2D COSY/HSQC correlation matrices, and need to write them to disk in a format that standard NMR software (e.
    0 installs
83. ▌
    Nmr Spectral Preprocessing And Phasing 2 · holobiomicslab

    Use when when working with raw 1H NMR FID data acquired on instruments like Bruker Avance spectrometers that require baseline correction, phase adjustment, and signal alignment before metabolite identification or statistical association testing can proceed reliably.
    2 installs
84. ▌
    Pathway Activity Propagation Inference 2 · holobiomicslab

    Use when when you have an untargeted metabolomics feature table (m/z values, retention times, intensity measurements, and p-values from statistical testing) and want to predict which metabolic pathways are active, but metabolite identification is incomplete, unreliable, or computationally expensive.
    2 installs
85. ▌
    Retention Time Alignment Index Mapping 2 · holobiomicslab

    Use when when processing multiple LC-MS samples with varying scan numbers or retention-time drift, before constructing composite mass tracks for peak detection.
    0 installs
86. ▌
    Retention Time Prediction Optimization 2 · holobiomicslab

    Use when when you have a retention-time dataset (e.g., SMRT or Eawag_XBridgeC18_364) in .xlsx format and need to train or adapt a graph neural network model to predict chromatographic retention times for new compounds.
    2 installs
87. ▌
    Robustness Analysis Under Perturbation 2 · holobiomicslab

    Use when you have completed pathway analysis using multiple competing methods (e.g., PALS, ORA, GSEA) on a metabolomics peak intensity dataset and need to verify that ranking results remain stable when input data is intentionally corrupted.
    2 installs
88. ▌
    Spectral Database Output Normalization 2 · holobiomicslab

    Use when you have executed batch spectral searches against two or more domain-specific MASST tools and received heterogeneous output formats (domain-specific HTML trees, JSON objects, TSV match tables) that need to be reconciled into a single normalized schema for downstream aggregation.
    0 installs
89. ▌
    Spectral Library Export And Formatting 2 · holobiomicslab

    Use when after theoretical spectra have been generated for lipid–adduct combinations with enumerated fragment masses and intensities, and you need to deploy them for downstream MS/MS analysis on Orbitrap (DDA via Excalibur) or SkyLine (targeted/PRM) workflows.
    0 installs
90. ▌
    Spectral Molecular Embedding Alignment 2 · holobiomicslab

    Use when you have MS/MS spectra in MGF or similar format and a reference library of molecular structures (SMILES or SDF), and your goal is to retrieve the most likely structures for an unknown compound spectrum by learning a joint embedding space rather than using traditional spectral similarity or.
    0 installs
91. ▌
    Structure Prediction From Mass Spectra 2 · holobiomicslab

    Use when you have GNPS-style MGF spectral files from MS/MS experiments and need to predict the molecular structure (as SMILES) of unknown compounds.
    0 installs
92. ▌
    Tandem Ms Spectral Data Interpretation 2 · holobiomicslab

    Use when you have untargeted MS2 spectral data in MS2MP-compatible format and need to assign KEGG pathway annotations to spectra without spectral library matching or manual compound identification.
    2 installs
93. ▌
    Unit Test Fixture Design And Execution 2 · holobiomicslab

    Use when when implementing or modifying a numerical compression/decompression component (e.g., Numpress for mass-spectrometry m/z and intensity arrays) and you need to verify that round-trip encoding and decoding preserves numerical fidelity.
    0 installs
94. ▌
    Graph Neural Network Model Loading 2 · holobiomicslab

    Use when when you need to evaluate GNN performance on collision cross section prediction using the enveda/ccs-prediction repository, either by loading an existing pre-trained model checkpoint or by retraining from scratch using deposited datasets and published hyperparameters.
    2 installs
95. ▌
    Container Port Mapping Configuration 2 · holobiomicslab

    Use when you need to deploy a containerized web application (such as MetFrag webapp on Tomcat) and make it accessible at a specific HTTP endpoint on the host machine. Use this skill when you have a Docker image with an internal service listening on a known port (e.
    0 installs
96. ▌
    In Silico Spectrum Metadata Curation 2 · holobiomicslab

    Use when when processing collections of in-silico mass spectra from OMSLs (Open Mass Spectra Libraries) where the adduct field is absent, null, or not explicitly specified in the source file;
    0 installs
97. ▌
    Retention Time Mz Feature Extraction 2 · holobiomicslab

    Use when you have LC-HRMS profile-mode data (e.g., netCDF or mzML format) and need to convert detected or reference chromatographic peaks into fixed-size 2D arrays (rt × mz regions) to train or apply a convolutional neural network for peak classification and bounding-box prediction.
    2 installs
98. ▌
    Cardinal To Seurat Object Conversion 2 · holobiomicslab

    Use when after completing Cardinal-based preprocessing (feature summarization, TIC normalization, peak processing, spatial segmentation, and SSC annotation), use this conversion when you need to leverage Seurat's downstream statistical methods—such as differential metabolite expression testing.
    0 installs
99. ▌
    Cross Database Entity Reconciliation 2 · holobiomicslab

    Use when you have chemical entity records scattered across two or more public repositories (e.g., HMDB, ChEMBL, PubChem, KEGG) and need a single authoritative, deduplicated knowledge base indexed by a queryable identifier (e.g., m/z value or chemical formula).
    0 installs
100. ▌
     Hdf5 File Format Reading And Writing 2 · holobiomicslab

     Use when you have isotope-corrected or raw ion-image intensity matrices from LipidQMap or similar MSI software and need to: (1) export them as persistent HDF5 containers for archival or sharing, (2) programmatically read an existing Cardinal::HDF5 export to extract intensity matrices and feature.
     0 installs