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HolobiomicsLab

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1. ▌
   Metabolomics Lcms Data Preprocessing · holobiomicslab

   Use when when you have raw LC-MS metabolomics data from multiple disease groups (e.g., .mzML or .npy format files) that must be converted into a uniform, normalized feature representation before training a deep learning classifier to distinguish disease states.
   0 installs
2. ▌
   Modification Notation Interpretation · holobiomicslab

   Use when you have a ProForma 2.0 peptidoform string (e.g., DLTDYLM[Oxidation]K) and need to extract the underlying peptide sequence and map modification positions to enable fragment ion annotation, mass calculation, or spectral matching.
   0 installs
3. ▌
   Molecular Formula Database Filtering · holobiomicslab

   Use when when you need to constrain a large metabolite database to a specific instrumental range (e.g., m/z 100–1000) before generating virtual chemical mixtures for LC-MS/MS simulation, or when you need to verify that a reported filtered database count can be reproduced from raw database files.
   0 installs
4. ▌
   Molecular Formula Quality Assessment · holobiomicslab

   Use when immediately after formula assignment from raw FT-ICR MS peak detection, when you have a peak intensity matrix with assigned molecular formulas and need to remove spurious or low-confidence assignments before calculating thermodynamic indices, determining compound classes, or performing.
   1 install
5. ▌
   Molecular Network Feature Annotation · holobiomicslab

   Use when when you have both (1) a molecular network graph from GNPS with MS/MS feature nodes and edges, and (2) a quantitative bioassay matrix (fractions × bioactivity measurements) from parallel LC-MS/MS fractionation of the same sample extract.
   2 installs
6. ▌
   Molecular Network Graph Construction · holobiomicslab

   Use when after completing dereplication and cosine similarity clustering in the MolNotator pipeline, when you have merged deduplicated molecular predictions and ion annotations and need to construct the final network representation for visualization and compound identification.
   0 installs
7. ▌
   Molecular Network Graph Manipulation · holobiomicslab

   Use when you have a GNPS-generated classical or feature-based molecular network (in graphml or JSON format) and corresponding MS2LDA or chemical class assignment data, and you need to embed substructural motif identifiers, confidence scores, or chemical class labels as node/edge attributes for.
   0 installs
8. ▌
   Molecular Structure Input Formatting · holobiomicslab

   Use when when you have a molecular structure in any representation (drawn structure, PDB file, common name) and need to input it into mass spectrum prediction tools like ICEBERG or SCARF, or when screening candidates from chemical databases like PubChem.
   0 installs
9. ▌
   Ms Adduct Annotation And Recognition · holobiomicslab

   Use when when processing LC-MS peak tables from isotope tracing experiments where multiple ionization adducts ([M+H]+, [M+Na]+, [M+NH4]+, etc.) and in-source fragments have generated redundant features at different m/z values that represent the same underlying metabolite.
   0 installs
10. ▌
    Ms1 Full Scan Acquisition Simulation · holobiomicslab

    Use when when you need to prototype, test, or benchmark MS1-only acquisition strategies on a defined set of metabolites (e.
    0 installs
11. ▌
    Ms2 Fingerprint Distance Calculation · holobiomicslab

    Use when after MS2 fingerprints have been generated by counting MS2 peaks and neutral losses in each sample, and you have aligned them into a MemoMatrix (sample-by-fingerprint matrix).
    0 installs
12. ▌
    Msconvert Integration And Invocation · holobiomicslab

    Use when when you have vendor-format LC-MS acquisition files (Thermo .raw, Bruker .d, Sciex .ms, Agilent, Waters formats) that need to be ingested into a quality control or data processing pipeline that requires open, standardized spectral formats.
    0 installs
13. ▌
    Multi Assay Cross Linking Validation · holobiomicslab

    Use when you have statistically significant features from multiple LC-MS assays with different ionization modes (e.g., positive and negative ESI) and need to collapse redundant feature representations into single structural entities.
    2 installs
14. ▌
    Multi Dataset Integration Mzrt Space · holobiomicslab

    Use when you have multiple CSV feature tables from independent metabolomic experiments, each with RT and m/z annotations, and you need to produce a single consolidated feature matrix for comparative analysis across all samples.
    0 installs
15. ▌
    Multi Task Loss Function Formulation · holobiomicslab

    Use when when training an object detection network that must predict both discrete labels (e.g., true peak vs. false peak) and continuous coordinates (e.
    2 installs
16. ▌
    Mzml File Parsing And Roi Extraction · holobiomicslab

    Use when when you have a real mzML file from an untargeted metabolomics LC-MS/MS experiment and need to extract the chemical features it contains—either to simulate a data-dependent acquisition (DDA) strategy on those same compounds, to benchmark different fragmentation controllers, or to reproduce.
    0 installs
17. ▌
    Neural Network Architecture Training · holobiomicslab

    Use when you have a pretrained TCN spectrum encoder from formula prediction and need to train a rescoring model that ranks formula candidates by confidence. The input is a set of spectra with ground-truth formula labels and multiple candidate formulas per spectrum.
    0 installs
18. ▌
    Overfitting Detection And Prevention · holobiomicslab

    Use when when training a fresh CNN model from scratch on labeled LCMS data (e.g., MS1 peak classification in NeatMS), particularly when aiming for a specific performance target (e.g., AUC ROC > 0.9) and you need to avoid wasting compute time on redundant epochs or degrading validation performance.
    0 installs
19. ▌
    Parent Fragment Relationship Mapping · holobiomicslab

    Use when after ISF features have been identified in Part 4 of the ISFrag workflow and you need to export or visualize the hierarchical structure of detected in-source fragments relative to their parent ions.
    0 installs
20. ▌
    Parent Product Relationship Tracking · holobiomicslab

    Use when when you have applied biotransformation rules to generate candidate product structures from a set of input molecules (represented as SMILES strings) and need to document which product structures were derived from which parent structures.
    2 installs
21. ▌
    Peak Detection Threshold Application · holobiomicslab

    Use when converting raw MS/MS spectra from library files (e.g., .msp format) into structured library entries, or when annotating experimental LC–MS features against fragment databases.
    0 installs
22. ▌
    Peak Intensity Distribution Analysis · holobiomicslab

    Use when after executing feature detection and quantification on raw LC-MS data (mzML or NetCDF format) using an automated pipeline such as MetaboAnalystR 4.0, and before proceeding to downstream normalization, scaling, or functional analysis.
    0 installs
23. ▌
    Peak Quality Classifier Optimization · holobiomicslab

    Use when after calculating 12 peak-quality metrics on a development set of extracted ion chromatograms (EICs) and labeled peaks, when you need to select both the classification algorithm and its optimal hyperparameters before training a final model on held-out test data.
    0 installs
24. ▌
    Peptide Sequence Composition Parsing · holobiomicslab

    Use when you have peptide or protein sequences (as FASTA strings or text identifiers) and need to compute their mass, isotopic envelope, charge state, isoelectric point, or chromatographic retention time for MS matching, peak annotation, or property prediction.
    0 installs
25. ▌
    Peptide Spectrum Matching Evaluation · holobiomicslab

    Use when when you have a tandem mass spectrum (MSMS) with known peptide sequence and wish to assess whether enabling neutral loss annotation (e.g., NH3: −17.026549, H2O: −18.010565) increases the proportion of observed m/z peaks that can be matched to predicted fragment ions.
    2 installs
26. ▌
    Physicochemical Property Computation · holobiomicslab

    Use when you have one or more peptide or protein sequences in string format and need to calculate their mass, isotopic envelope (m/z and intensity pairs), charge state behavior, isoelectric point, or predicted chromatographic retention.
    0 installs
27. ▌
    Ppm Error Validation In Metabolomics · holobiomicslab

    Use when when annotating m/z features from Cardinal MSImagingExperiment objects or LC-MS datasets against metabolite databases (HMDB, Lipidmaps) and you need to exclude matches where the mass difference exceeds your instrumental accuracy or analysis tolerance.
    1 install
28. ▌
    Prm Acquisition Event Identification · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file containing PRM data and need to verify that acquisition of a specific precursor ion (e.g., LGGNEQVTR++ at m/z 487.2567) is happening at regular intervals consistent with your instrument method design.
    0 installs
29. ▌
    Probability Product Kernel Denoising · holobiomicslab

    Use when you have raw MS2 spectra (m/z and intensity pairs) that you want to match against a large training dataset of annotated library spectra (e.g., GNPS), and you need to reduce noise and computational burden before applying kernel-based scoring methods such as IOKR.
    0 installs
30. ▌
    Prominence Controlled Peak Selection · holobiomicslab

    Use when after initial peak detection on composite mass tracks via local maxima and smoothing, when you have unfiltered peak lists (JSON or structured format) containing prominence values and need to reduce the number of detected features while maintaining signal quality.
    0 installs
31. ▌
    Qc Reference Chromatogram Extraction · holobiomicslab

    Use when when processing a batch of LC-MS samples in mzML or mzXML format where at least one file has been designated as a quality control (QC) file, extract its TIC or BPC before performing retention time correction.
    0 installs
32. ▌
    Quality Control Threshold Validation · holobiomicslab

    Use when after executing Formation formatting on processed feature tables (output from Blueshift or Gravity modules).
    0 installs
33. ▌
    Ranked Result Extraction And Display · holobiomicslab

    Use when after running annotateRC on LC–MS AIF data when you need to inspect whether a feature has multiple plausible annotations (e.g., isobaric lipids, isomers with the same fatty-acyl chain) or when the rank-1 annotation confidence is borderline and alternatives should be evaluated.
    2 installs
34. ▌
    Retention Time Correlation Filtering · holobiomicslab

    Use when you have detected multiple LC-MS features (m/z peaks) across a chromatogram and need to distinguish true chemical relationships (isotopes differing by 1.003 Da, adducts with characteristic mass shifts, neutral loss fragments) from noise or unrelated peaks.
    2 installs
35. ▌
    Retention Time Prediction Validation · holobiomicslab

    Use when after training a GNN-RT model on preprocessed molecular graph data (from Train.py) or after applying transfer learning to an in-house dataset (from Transferlearning.
    0 installs
36. ▌
    Rippp Candidate Structure Generation · holobiomicslab

    Use when after identifying precursor peptides from genome assemblies via BGC mining, when you need to enumerate the chemical space of PTM variants (lantibiotic, lassopeptide, cyanobactin, or other RiPP classes) before matching tandem mass spectra against a constructed database using Dereplicator or.
    2 installs
37. ▌
    Rsd Threshold Parameter Optimization · holobiomicslab

    Use when when preparing XCMS peak tables for quality classification and you observe that the default RSD threshold (0.3 or 30%) is either too permissive (retaining noisy EICs) or too stringent (discarding valid signals).
    0 installs
38. ▌
    Sample Centric Metabolite Annotation · holobiomicslab

    Use when after MZmine feature detection and molecular networking on a single LC-MS/MS DDA sample, when you have a feature table (with retention time, m/z, fragmentation spectra) and sample-level taxonomical metadata, and you want to assign both spectral identity and predicted chemical structure to.
    2 installs
39. ▌
    Sampledata Annotation And Assignment · holobiomicslab

    Use when after loading multiple LC-MS .mzML files into an MsExperiment object using MsBackendMzR backend, when you have a documented injection sequence (e.
    0 installs
40. ▌
    Search Results Filtering And Parsing · holobiomicslab

    Use when you have loaded DIA mass spectrometry search results containing feature identification data with associated Q-value scores, and you need to restrict the analytes available in selection drop-downs to those meeting a quality cutoff (typically 1% FDR equivalent) before visualization or manual.
    0 installs
41. ▌
    Siamese Network Embedding Generation · holobiomicslab

    Use when you have preprocessed MS/MS spectra binned into 10,000 equally-sized m/z bins (10–1000 m/z range) with square-root-transformed intensities, and you need to generate 200-dimensional spectral embeddings for structural similarity prediction, visualization via dimensionality reduction (e.
    0 installs
42. ▌
    Simulation Control Loop Architecture · holobiomicslab

    Use when you have a set of metabolites or chemical formulas to analyze and want to evaluate how different MS/MS fragmentation strategies (e.g., TopN, exclusion lists, dynamic window selection) would perform without access to real instrument time.
    1 install
43. ▌
    Sirius Spectral Request Construction · holobiomicslab

    Use when when you have processed LC-MS/MS data with precursor m/z, ionization mode, collision energy (if available), and fragment peak lists (m/z and intensity pairs), and need to query CSI:FingerID for molecular fingerprint predictions as part of an automated metabolite identification workflow.
    0 installs
44. ▌
    Spatial Correlation Filtering In Msi · holobiomicslab

    Use when after identifying candidate parent–adduct mass-difference pairs (via massdiff, histogram binning, and adductMatch), apply this skill to discriminate true molecular adducts from coincidental mass matches.
    0 installs
45. ▌
    Spec2vec Model Loading And Inference · holobiomicslab

    Use when you have discovered Mass2Motifs or other fragmentation pattern representations via LDA and need to generate vector embeddings to query a reference motif database (MotifDB) for structural annotation candidates.
    0 installs
46. ▌
    Spectra Data Representation Backends · holobiomicslab

    Use when you are creating a new backend to expose MS data (m/z, intensity, retention time, and other spectral properties) from a specific storage format or data source (e.g., mzML files, SQL databases, in-memory matrices, or spectral libraries) to Spectra objects.
    1 install
47. ▌
    Spectral Feature Chemical Assignment · holobiomicslab

    Use when you have spectral feature data annotated by both in silico structural tools (e.
    0 installs
48. ▌
    Spectral Library Annotation Matching · holobiomicslab

    Use when when you have downloaded a GNPS archive (GNPS1 or GNPS2 workflows) and need to map experimental spectra to known library compounds for annotation enrichment. Apply this skill after spectral data (spectra.
    0 installs
49. ▌
    Spectral Library Matching Annotation · holobiomicslab

    Use when you have MS2 spectral data (precursor m/z, retention time, and fragment ion patterns) from UPLC-HRMS analysis of environmental or biological samples and need to assign compound identities by comparing against known reference spectra.
    0 installs
50. ▌
    Spectral Library Matching Evaluation · holobiomicslab

    Use when you have a trained spectral embedding model (e.g., MSBERT, Spec2Vec) and need to benchmark its library matching accuracy against reference spectra on a test dataset.
    0 installs
51. ▌
    Spectral Library Similarity Matching · holobiomicslab

    Use when you have an unknown experimental mass spectrum (e.g., from liquid chromatography–mass spectrometry) and need to retrieve the most structurally similar candidate molecules from a database of millions of predicted or experimental spectra.
    0 installs
52. ▌
    Spectral Match Threshold Application · holobiomicslab

    Use when after running spectral matching (e.g., GNPS library search, SIRIUS in silico annotation) and obtaining an annotation table with confidence scores, apply threshold filtering to remove low-confidence or spurious matches before downstream analysis (e.
    2 installs
53. ▌
    Spectral Metadata Enrichment Via API · holobiomicslab

    Use when you have .msp spectrum files with minimal metadata (e.g., only compound name and mass) and need to augment them with chemical structure descriptors, identifiers, and properties from external databases.
    0 installs
54. ▌
    Spectral Peak Detection Local Maxima · holobiomicslab

    Use when you have a 1D intensity array (e.g., a single MS1 or MS2 spectrum extracted from an MZA HDF5 file) and need to identify prominent peaks with their m/z indices and heights.
    0 installs
55. ▌
    Spectral Similarity Network Building · holobiomicslab

    Use when when you have detected LC-MS/MS features (MS1 peaks with MS2 fragmentation spectra) from untargeted metabolomics experiments and seek to organize them into a chemical hierarchy for comparative metabolomic analysis.
    0 installs
56. ▌
    Spectrum Filtering And Normalization · holobiomicslab

    Use when you have raw or minimally processed tandem MS spectra (in mzML, mgf, or other standard formats) and need to prepare them for spectral matching, library searching, or quantitative analysis.
    2 installs
57. ▌
    Spectrum Vector Similarity Searching · holobiomicslab

    Use when when clustering large collections (thousands to millions) of tandem mass spectra and you need to compute a sparse pairwise distance matrix for density-based clustering.
    0 installs
58. ▌
    Sterol Lipid Isomer Characterization · holobiomicslab

    Use when you have LC-IM-MS/MS experimental data (raw mzML or vendor format) containing signals from N-Me derived unsaturated sterol lipids and need to assign double-bond positions and stereochemistry to individual sterol isomers rather than sum compositions.
    2 installs
59. ▌
    Tandem Mass Spectra Peptide Matching · holobiomicslab

    Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) and wish to identify peptidic natural products or ribosomally synthesized and post-translationally modified peptides (RiPPs) against a known structure database or custom RiPP structure database.
    0 installs
60. ▌
    Uncertainty Estimation Across Models · holobiomicslab

    Use when when you have multiple independently trained models (e.g., ROASMI_1 through ROASMI_5) making predictions on the same set of compounds or samples, and you need to assess confidence in individual predictions.
    0 installs
61. ▌
    Unit Test Design For Scoring Metrics · holobiomicslab

    Use when when implementing new scoring components (inchikey score, neighbourhood score, or similar structural/spectral similarity metrics) that are integrated into an MS/MS candidate re-ranking pipeline.
    0 installs
62. ▌
    Vendor Format To Standard Conversion · holobiomicslab

    Use when when ingesting raw LC-MS/MS output from a mass spectrometry instrument and you need to prepare it for metabolite identification, fragmentation tree computation, or molecular formula annotation.
    0 installs
63. ▌
    Web Application Documentation Mining · holobiomicslab

    Use when you have access to a project README or repository documentation (Zenodo deposit, GitHub, or local clone) describing multiple domain-specific web applications, and you need to produce a machine-readable inventory of those applications with verified live URLs and associated publications for.
    0 installs
64. ▌
    XML Structured Metadata Construction · holobiomicslab

    Use when when you have synthesized or assembled mass spectrometry spectral data (m/z values, intensities, retention times) and need to encode it as a portable, standard mzML file format rather than a proprietary binary or text representation.
    0 installs
65. ▌
    Chemical Graph Connectivity Validation · holobiomicslab

    Use when after a machine learning model has generated predicted molecular structures (connectivity graphs and molecular formulas) from 1D NMR spectra. Use it to quantify accuracy on a held-out test set, measure degradation when applying the model beyond its training scope (e.
    0 installs
66. ▌
    Conditional Allocation Design Patterns · 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;
    2 installs
67. ▌
    Dataset Storage Interface Architecture · 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.
    0 installs
68. ▌
    Fusion Pooling Strategy Implementation · 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.
    0 installs
69. ▌
    Metabolite Reference Library Filtering · holobiomicslab

    Use when you have defined one or more proton NMR spectral regions-of-interest (ROIs) with lower and upper chemical-shift bounds (in ppm) from an experimental NMR spectrum of a biological sample, and you need to identify which metabolites in a reference database (HMDB) have published 1H NMR shifts.
    0 installs
70. ▌
    Nmr Spectral Data Format Serialization · 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
71. ▌
    Nmr Spectral Preprocessing And Phasing · 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.
    0 installs
72. ▌
    Galaxy W4m Lcms Processing Workflow · holobiomicslab bundle

    Use when running the Workflow4Metabolomics LC-MS pipeline end to end on a Galaxy instance — MSnbase import, xcms peak detection, correspondence, alignment and gap filling, CAMERA annotation, three-table conformance, batch correction, statistics — in the stage order the wrappers' datatypes enforce.
    0 installs
73. ▌
    Chromatin Domain Boundary Detection · holobiomicslab

    Use when you have generated a .hic contact map from Hi-C raw sequencing data and need to identify topologically associating domains (TADs) or other chromatin structural boundaries.
    0 installs
74. ▌
    Compartment Strength Quantification · holobiomicslab

    Use when when you have a binned Hi-C cooler file, an associated eigenvector track (from prior eigs_cis calculation), and need to measure how strongly the genome is partitioned into active (A) and inactive (B) compartments.
    0 installs
75. ▌
    Computational Complexity Validation · holobiomicslab

    Use when when an algorithm claims linear or sublinear time/space complexity (e.g., matrix-free spectral embedding) and you need to verify that claim holds for datasets at the scale intended (10 million+ cells).
    0 installs
76. ▌
    Hpc Cluster Scheduler Configuration · holobiomicslab

    Use when when installing HiC-Pro on a shared HPC cluster or multi-node computing environment where job submission must be routed through a scheduler rather than running locally.
    0 installs
77. ▌
    Illumina Array Data Processing Epic · holobiomicslab

    Use when you have raw Illumina EPIC or 450k methylation array data (.idat files or beta-valued matrices) and need to perform comprehensive quality assessment, probe correction, batch effect adjustment, and identification of differentially methylated regions or blocks across sample groups.
    0 installs
78. ▌
    Narrow Peak Calling Score Threshold · holobiomicslab

    Use when after generating a q-value bedgraph track from ChIP-Seq pileup versus local lambda comparison, and you need to identify statistically significant narrow peaks with defined boundaries.
    0 installs
79. ▌
    Python Package API Interface Design · holobiomicslab

    Use when you are building or refactoring a scientific Python library and need to decide how to organize and expose utility functions (e.g., adaptive coarse-graining, filtering, analysis routines) so that end users can import and call them reliably.
    0 installs
80. ▌
    R Package Installation Verification · holobiomicslab

    Use when after installing R or modifying an R environment via conda, package managers, or container images; before running any pipeline step that depends on R packages for statistical analysis, visualization, or data normalization.
    2 installs
81. ▌
    Single Cell Chromatin Data Handling · holobiomicslab

    Use when after calling peaks and annotating cells in an ArchR project, when you need to perform trajectory analysis using STREAM or other external tools that require a peak-by-cell matrix in a specific tabular format (CSV or TSV) rather than native ArchR objects.
    0 installs
82. ▌
    Transcription Factor Motif Matching · holobiomicslab

    Use when you have corrected ATAC-seq footprint scores (from ATACorrect and ScoreBigwig) at open chromatin regions and a motif database (e.g., JASPAR PWMs), and you need to determine which TF motif matches are actually occupied across one or more experimental conditions.
    0 installs
83. ▌
    Batch Script Performance Profiling · holobiomicslab

    Use when you have a collection of N scripts (e.g., 19 gallery examples) that must run on multiple backends or configurations, and you need to produce a reproducible benchmark table showing per-script execution times and aggregate totals.
    0 installs
84. ▌
    Binary Classifier Ablation Testing · holobiomicslab

    Use when you have a trained binary molecular classifier (like BitterPredict) and want to understand which groups of chemical descriptors drive its predictions.
    0 installs
85. ▌
    Cardinal Imaging Object Conversion · holobiomicslab

    Use when you have mass spectrometry imaging data in Cardinal format (versions 2.
    0 installs
86. ▌
    Chemical Structure Standardization · holobiomicslab

    Use when when you have raw molecular structures in SMILES or SDF format that must be prepared as input to a descriptor-based classifier (e.g., BitterPredict).
    0 installs
87. ▌
    Chemical Transformation Annotation · holobiomicslab

    Use when you have computed a histogram of pairwise mass differences from MS peaks and want to determine which observed mass differences correspond to known chemical species such as matrix adducts (e.g. [M+Na]+, [M+K]+), salt ions, or neutral losses.
    0 installs
88. ▌
    Container Networking Configuration · holobiomicslab

    Use when when deploying a multi-component research application (e.g., MAGMa's four subproject services) as containerized microservices that need to communicate internally—specifically when you have identified service interdependencies (e.
    0 installs
89. ▌
    Converter Specification Validation · holobiomicslab

    Use when adding a new converter class to MSMetaEnhancer or when modifying an existing converter's __init__ method to add/remove conversions.
    2 installs
90. ▌
    Encoder Output Dimension Reduction · 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.
    2 installs
91. ▌
    File Format Detection By Extension · holobiomicslab

    Use when when building a file I/O abstraction layer that must support multiple serialization formats (e.g., uncompressed mzML, gzip-compressed mzML, indexed gzip mzML, or SQLite-backed mzML) and route each to its correct handler class without exposing format logic to downstream consumers.
    0 installs
92. ▌
    File Handler Interface Integration · holobiomicslab

    Use when you have mass spectrometry data stored in a non-standard format (SQLite database, custom indexed gzip files, or other database backends) and want to enable pymzML's Reader to access it with both random-access by spectrum ID and sequential iteration capabilities, avoiding the need to.
    0 installs
93. ▌
    Ft Icr Ms Analysis Tool Evaluation · holobiomicslab

    Use when you are evaluating or selecting FT-ICR MS software for a specific metabolomics workflow and need to assess which tools support your required analytical dimensions (e.g., Van Krevelen diagrams, PERMANOVA, thermodynamic indices, chemodiversity metrics, transformation networks).
    0 installs
94. ▌
    Github Release Metadata Comparison · 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.
    2 installs
95. ▌
    Gnn Model Inference And Prediction · holobiomicslab

    Use when you have a pre-trained GNN model checkpoint, a test dataset with molecular representations (SMILES, 3D coordinates, adducts) and ground-truth labels, and need to quantify how well the model generalizes to held-out data.
    0 installs
96. ▌
    Inference Performance Benchmarking · holobiomicslab

    Use when you have trained two or more graph neural network models on the same CCS dataset split (using identical hyperparameters, loss functions, and optimization settings) and need to rigorously compare their held-out test performance to determine which architecture balances prediction accuracy.
    1 install
97. ▌
    Intensity Drift Artifact Detection · holobiomicslab

    Use when processing raw MS intensity tables from long measurement sequences where you observe systematic, time-dependent changes in signal magnitude (e.g., progressive increase or decrease in peak intensity across a run).
    2 installs
98. ▌
    Mass Spectrometry Benchmark Design · holobiomicslab

    Use when when claiming that one mass spectrometry processing library achieves higher throughput than competitors, or when evaluating whether a new or optimized implementation delivers the expected computational efficiency gains.
    0 installs
99. ▌
    Mass Spectrometry Data Integration · holobiomicslab

    Use when you have multiple mzML or HDF5 feature tables from the same study acquired on the same or similar instruments and need to align feature coordinates across samples to correct for systematic shifts in mass-to-charge, drift time, or retention time caused by instrumental drift, column aging.
    0 installs
100. ▌
     Molecular Cheminformatics Pipeline · holobiomicslab

     Use when you have raw molecular structures in SMILES or SDF format and need to prepare molecular descriptors as input to a descriptor-based classifier (e.g., BitterPredict.m).
     2 installs