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HolobiomicsLab

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1. ▌
   Embedding Space Representation · holobiomicslab

   Use when you have pairs or triplets of MS/MS spectra with associated metadata (compound structural information, Tanimoto similarity scores) and want to learn embeddings that simultaneously preserve spectral similarity relationships and reconstruct peak intensities.
   0 installs
2. ▌
   Execution Time Metric Analysis · holobiomicslab

   Use when you have computation-time metrics from a gallery or benchmark suite comparing multiple plotting backends on the same data types (e.
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3. ▌
   Feature Alignment Metabolomics · holobiomicslab

   Use when you have detected multiple ion peaks from replicate injections of the same sample in untargeted metabolomics and need to consolidate them into a single feature table.
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4. ▌
   Feature Intensity Thresholding · holobiomicslab

   Use when after feature extraction from mzML/mzXML files when you have identified candidate peaks in breath spectrometry data but need to separate true VOC signals from instrument noise.
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5. ▌
   File Compression And Archiving · holobiomicslab

   Use when when a spectral processing operation produces multiple output artifacts in different formats (e.
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6. ▌
   File Format Handling CSV Excel · holobiomicslab

   Use when you have molecular descriptor data in CSV or EXCEL format and need to pass it to BitterPredict.m or another descriptor-based classifier.
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7. ▌
   Fixed Modification Propagation · holobiomicslab

   Use when your search engine output (PSM file) omits fixed modifications that were configured during the search (e.
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8. ▌
   Format Agnostic Data Ingestion · holobiomicslab

   Use when when you have mass spectrometry data in multiple formats (mzML, mzXML) that must be fed into a compression, analysis, or transformation pipeline that operates on a single canonical spectral data model.
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9. ▌
   Formula Parsing And Evaluation · holobiomicslab

   Use when you have multiple open elemental images (e.g., P31, Zn66) from LA-ICP-MS and need to create a new derived image by evaluating a per-pixel mathematical expression. Typical triggers include: combining isotope ratios (e.
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10. ▌
    Ftms Mass Calibration Workflow · holobiomicslab

    Use when when you have a processed Bruker Solarix FT-ICR mass spectrum object (from ReadBrukerSolarix) and a reference peak list file (SRFA.
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11. ▌
    Generic Hdf5 Library API Usage · holobiomicslab

    Use when when you have converted multidimensional MS data to MZA HDF5 format and need to programmatically read spectra, metadata, and ion mobility or mass-to-charge arrays in Python or R without vendor-specific dependencies.
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12. ▌
    Git Branch Workflow Validation · holobiomicslab

    Use when when preparing to create a release branch in a Maven-based multi-module project (e.g., NMRFx), use this skill to verify that all pom.xml files in the repository tree declare identical version strings. This is a prerequisite for safe release-branch naming (e.g., release/X.Y.
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13. ▌
    Hash Function Parameterization · holobiomicslab

    Use when when you have normalized or vectorized mass spectrometry spectral data (m/z and intensity pairs converted to feature vectors) and need to construct an LSH index for fast nearest-neighbor retrieval of similar spectra.
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14. ▌
    HTTP Post Request Construction · holobiomicslab

    Use when you need to submit structured chemical compound data (identifiers and structural representations) to a remote REST API that accepts POST requests and returns JSON responses, particularly when the API requires tab-separated compound inputs separated by newlines and a query label as the.
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15. ▌
    Image Visualization Formatting · holobiomicslab

    Use when you have loaded a normalized or raw pixel array (NumPy format) with associated metadata from MSI line-scan data, and need to generate publication-quality ion images with controlled intensity scaling, smoothing, and optional ratio or fractional abundance comparisons across multiple m/z.
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16. ▌
    Intensity Color Representation · holobiomicslab

    Use when when visualizing 2D peak maps (x=m/z, y=retention time or ion mobility, z=intensity) using pyOpenMS-viz with any plotting backend (matplotlib, bokeh, plotly).
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17. ▌
    Java Diagnostic Tool Operation · holobiomicslab

    Use when when you have deployed a JVM application in a Docker container with JAVA_OPTS heap size parameters and need to verify that the maximum and initial heap sizes are correctly configured before running memory-intensive workflows like metabolite fragmentation analysis.
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18. ▌
    Java Maven Build Orchestration · holobiomicslab

    Use when when you have access to a Java project with a Maven pom.xml defining multiple interdependent modules (e.
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19. ▌
    Lexer Tokenizer Implementation · holobiomicslab

    Use when when you need to parse a domain-specific query language (like MassQL) into an abstract syntax tree (AST), and the query strings must be decomposed into discrete lexical units before syntactic analysis.
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20. ▌
    Lipid Class Feature Annotation · holobiomicslab

    Use when when loading lipidomics data (from Skyline CSV, numerical matrix, or Metabolomics Workbench) and encountering parsing warnings or molecules with names that do not follow standard lipid nomenclature patterns (e.
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21. ▌
    Lipid Identifier Normalization · holobiomicslab

    Use when when you have a list of lipids identified by different database identifiers (e.
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22. ▌
    Log Transformation Application · holobiomicslab

    Use when apply log-transformation immediately after loading a raw metabolomics featuredata matrix (metabolite peak intensities as rows=samples, columns=metabolites) and before normalization.
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23. ▌
    Lotus Metadata Standardization · holobiomicslab

    Use when you have raw compound or natural-product metadata in spreadsheet or tabular form with inconsistent column names, missing structure information, or when you need to query against the LOTUS natural-product database and suspect the local copy is stale or absent.
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24. ▌
    Low Energy Structure Selection · holobiomicslab

    Use when after generating an ensemble of 3D conformers via RDKit conformation sampling, when you need to reduce the conformer set size before expensive quantum-chemical calculations (e.g., QUICK).
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25. ▌
    M Z Value Ordering Enforcement · holobiomicslab

    Use when when implementing or modifying data replacement methods (e.g., `mz<-`, `peaksData<-`) in a writable MsBackend subclass, or when accepting user-supplied m/z vectors destined for storage in a Spectra backend.
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26. ▌
    Mass Error Tolerance Filtering · holobiomicslab

    Use when when annotating full-scan MS or MS imaging data against a metabolite database (e.g., LipidMaps, HMDB) and you need to control the stringency of m/z matching. Use this filter to balance annotation sensitivity against specificity: tighter ppm tolerances (e.
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27. ▌
    Mass Spectrum Peak Aggregation · holobiomicslab

    Use when you have a processed mass spectrum object with assigned molecular formulas for individual peaks and need to summarize peaks by their heteroatom composition—e.
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28. ▌
    Mass Spectrum Query Processing · holobiomicslab

    Use when you have an unknown mass spectrum (as m/z and intensity arrays) and need to identify candidate compounds by matching against a mass spectral library.
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29. ▌
    Matrix Data Structure Handling · holobiomicslab

    Use when after feature filtering has removed low-abundance or highly sparse metabolites (e.g., >80% missingness), and before applying missing value imputation or normalization.
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30. ▌
    Matrix Directive Field Mapping · holobiomicslab

    Use when you have extracted tabular data in intermediate JSON form and need to convert a table of records into a list of dictionaries (array of objects) where each row becomes a dictionary entry, optionally removing sensitive or irrelevant fields and normalizing all values to strings for downstream.
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31. ▌
    Matrix Multiplication Pipeline · holobiomicslab

    Use when after completing 10-fold cross-validated training of MiMeNet neural networks on paired microbiome-metabolome datasets and identifying well-predicted metabolites (those with Spearman correlation coefficient above the 95th percentile of background distribution).
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32. ▌
    Metabolomic Feature Imputation · holobiomicslab

    Use when when a preprocessed metabolomic feature table (e.g., MS-Dial output) retains features and samples that passed filtering for missingness thresholds and m/z validity, but still contain scattered missing values (NA). This skill is appropriate after sample-level filtering (e.
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33. ▌
    Metaboprep Object Manipulation · holobiomicslab

    Use when you have imported raw (un)targeted metabolite data (from Metabolon, Nightingale, Olink, or SomaLogic platforms, or custom tab-delimited tables) and need to apply a uniform, reproducible QC and normalization pipeline.
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34. ▌
    Model Checkpoint Serialization · holobiomicslab

    Use when after successfully training a spectrum prediction model (FFN encoder, GNN encoder, intensity predictor, or fragment generator) to completion or at intermediate milestones, and before using that model for inference on test sets, structural elucidation queries, or transfer learning.
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35. ▌
    Module Assignment Biclustering · holobiomicslab

    Use when you have a trained neural network model of microbiome-metabolome associations and have derived a feature attribution score matrix (microbes × metabolites) quantifying the strength of each microbe-metabolite interaction.
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36. ▌
    Molecular Embedding Generation · holobiomicslab

    Use when when you have molecular structures (SMILES or explicit graph representations) and need fixed-size vector representations to feed into a prediction head or transfer learning task.
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37. ▌
    Molecular Structure Validation · holobiomicslab

    Use when ingesting SMILES strings from CSV or other bulk molecular input files before passing them to structure-based prediction tools.
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38. ▌
    Multiple Comparison Correction · holobiomicslab

    Use when after running ANOVA or G-test statistical analysis across multiple biomolecules in an omics dataset (e.
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39. ▌
    Mzml File Format Understanding · holobiomicslab

    Use when you have mass spectrometry raw data in mzML format (including compressed variants like mzML.
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40. ▌
    Network Node Attribute Mapping · holobiomicslab

    Use when you have a GLASSO-generated network graph and corresponding PCA scores from a prior dimensionality-reduction step, and you need to identify which nodes or sub-networks are associated with high or significant PCA scores.
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41. ▌
    Neural Network Model Inference · holobiomicslab

    Use when you have pre-trained MSGO model weights (PFAS or lipid variant) and a set of experimental mass spectra (either from reference evaluation sets or real wastewater/environmental samples) in CSV format with m/z and intensity pairs, and you need to obtain candidate molecular structures ranked.
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42. ▌
    Peak Validation Synthetic Data · holobiomicslab

    Use when after running a 1D peak detection function (e.g., mzapy.peaks.find_peaks_1d_localmax or mzapy.peaks.find_peaks_1d_gauss) on synthetic mass spectra with known peak locations and heights.
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43. ▌
    Pip Requirements File Creation · holobiomicslab

    Use when you have identified all pinned software dependencies for a Python project (typically from README, setup.py, or environment documentation) and need to create a machine-readable artifact that can reliably reconstruct that exact environment.
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44. ▌
    Pubchem Cross Reference Lookup · holobiomicslab

    Use when you have metabolite or compound identifiers in mixed formats (chemical name, InChI, InChIKey, SMILES) across multiple studies or datasets and need to: (1) unify them to a single canonical identifier (PubChem ID) for deduplication, (2) detect and resolve duplicate entries that differ only.
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45. ▌
    Quantile Normalization Rna Seq · holobiomicslab

    Use when apply quantile normalization after filtering a Salmon-derived count matrix for low-abundance features using edgeR, and before batch-effect correction or differential expression analysis.
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46. ▌
    Quantum Input File Preparation · holobiomicslab

    Use when you have a set of RDKit-generated conformers ranked by ASE-ANI single-point energies, and you need to submit the lowest-energy subset to quantum software (e.g. QUICK) for CCS-relevant electronic structure calculations.
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47. ▌
    Reference Database Maintenance · holobiomicslab

    Use when when preparing to run compound metadata enrichment or structure queries, check whether your reference databases (LOTUS, DrugBank, DrugCentral) are stale or missing.
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48. ▌
    Regression Accuracy Assessment · holobiomicslab

    Use when after fitting linear regression models to relate peak area intensities to known concentrations in targeted metabolomics curves (standard samples and quality control replicates).
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49. ▌
    Relative Abundance Calculation · holobiomicslab

    Use when after generating a frequency count table (e.g., from count_fold_changes output showing numbers of increased vs. decreased metabolites by class) and before creating proportional visualizations (pie charts, stacked bar plots).
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50. ▌
    Repeated Measures Anova Design · holobiomicslab

    Use when you have an imputed, long-format metabolomics dataset with repeated measurements (multiple time points) per subject, a categorical grouping variable (e.
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51. ▌
    REST API Endpoint Construction · holobiomicslab

    Use when you have pre-trained neural network models (e.g., Keras/TensorFlow) for chemical classification and need to expose them as a queryable HTTP service.
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52. ▌
    Retention Time Range Filtering · holobiomicslab

    Use when you have raw IM-MS data (Agilent MassHunter .d or UIMF format) and need to exclude early or late chromatographic regions—e.g., to skip dead volume, exclude blank runs, focus on a known analyte window, or reduce file size for faster processing.
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53. ▌
    Rule Set Ranking And Selection · holobiomicslab

    Use when when you have a large set of generalized reaction rules (e.
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54. ▌
    S4 Class Extension Development · holobiomicslab

    Use when you need to create a new backend for the Spectra package that provides MS data from a new source (file format, database, or computational resource) not covered by existing backends (MsBackendMzR, MsBackendMemory, MsBackendSql, etc.).
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55. ▌
    Sdf Compound Structure Parsing · holobiomicslab

    Use when when you have fragment records (experimental or predicted) with compound identifiers or cross-reference fields that need to be validated against a reference compound database in SDF format.
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56. ▌
    Simulation Result Reproduction · holobiomicslab

    Use when when you have access to a study's source repository containing executable simulation code in a Jupyter notebook, and you need to validate that the reported ORA results can be regenerated from the provided Python implementation.
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57. ▌
    Smiles Adduct Form Enumeration · holobiomicslab

    Use when when you have SMILES structures of small organic molecules and need to predict CCS values for metabolite annotation in untargeted mass spectrometry workflows. Specifically, apply this skill when the same chemical entity may appear in multiple ionization states (e.
    0 installs
58. ▌
    Software Mode Routing Dispatch · holobiomicslab

    Use when you are preparing to run LipidMatch or FluoroMatch and need to select the correct analysis mode for your sample type: lipid profiling, Tween-positive surfactant analysis, or PFAS (per- and polyfluoroalkyl substances) analysis.
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59. ▌
    Source Code Repository Cloning · holobiomicslab

    Use when you need to obtain the full source code of a scientific tool (such as LipidSpace) to build it locally, verify cross-platform compilation, inspect the codebase structure, or set up a development environment.
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60. ▌
    Spatial Overlap Quantification · holobiomicslab

    Use when you have two co-registered LA-ICP-MS element channel images and need to determine whether their spatial distributions are correlated.
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61. ▌
    Spectral Peak Fitting Gaussian · holobiomicslab

    Use when you have 1D MS signal data (extracted ion chromatograms, arrival time distributions, or intensity profiles) and need to resolve overlapping or closely-spaced peaks with accurate position, height, and width estimates.
    0 installs
62. ▌
    Spectral Similarity Validation · holobiomicslab

    Use when after training a Word2vec model on tokenized mass spectra and converting reference spectra into fixed-length embedding vectors, use this skill to confirm that the embedding space preserves spectral similarity before deploying it for spectrum matching.
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63. ▌
    Statistical Test Configuration · holobiomicslab

    Use when after data transformation, normalization, and filtering are complete, and you have assigned experimental groups (main effects, covariates, pairing structure).
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64. ▌
    Structured Data Table Creation · holobiomicslab

    Use when you have obtained a raw reference library file (such as the DTCCS_N2 library for U13C labeled lipids) and need to validate its structure, verify that all expected lipid entries are present, and ensure CCS values fall within physically plausible ranges (typically 50–300 Ų for small lipids).
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65. ▌
    Suspect List Format Conversion · holobiomicslab

    Use when you have generated a set of transformation products (TPs) from one or more parent compounds using generateTPs (via BioTransformer, CTS, or PubChemLite library algorithms) and need to screen for these TPs in your LC-HRMS feature data.
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66. ▌
    Technical Variation Assessment · holobiomicslab

    Use when when you have a preprocessed metabolomics matrix (log2-scaled, CSV format with batch identifiers in the first column) and need to determine whether technical variation is present, which correction model (ber, ber-bagging, parametric ComBat, or non-parametric ComBat) performs on your.
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67. ▌
    Tissue Background Segmentation · holobiomicslab

    Use when you have loaded a laser ablation ICP-MS image into pew² and need to distinguish tissue signal from instrument background or non-ablated substrate.
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68. ▌
    Topic Modeling Lda Application · holobiomicslab

    Use when you have redundancy-filtered, tokenized BGCs (each gene represented as a Pfam domain or subPfam combination) and you want to identify fine-grained gene sub-clusters whose membership is driven by co-occurrence patterns of protein domains rather than statistical significance alone.
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69. ▌
    Vendor Format Routing Dispatch · holobiomicslab

    Use when you have a collection of raw mass spectrometry data files from multiple instrument vendors (Agilent, Bruker, Thermo) and/or mzML exports that need to be converted to a standardized, cross-platform format for downstream software development, AI research, or multi-vendor meta-analysis.
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70. ▌
    Vocabulary Coverage Validation · holobiomicslab

    Use when after merging separate vocabularies for distinct data modalities (e.g., spectral tokens for m/z values and intensities, structural tokens for SMILES or graphs) and before deploying the unified vocabulary in a language model.
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71. ▌
    Workflow Configuration Parsing · holobiomicslab

    Use when you have a workflow.csv file co-located with sequence.csv in a SmartPeak session directory and need to load a default or custom workflow configuration into an executable command sequence.
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72. ▌
    Feature Based Molecular Networking And Propagation Workflow · holobiomicslab bundle

    Use when you have untargeted LC-MS/MS MS2 data and want to spread a handful of confident annotations across whole molecular families — build a feature-based molecular network, seed it with spectral-library and SIRIUS/CANOPUS annotations, then propagate compound classes and analogue annotations across network components (MolNetEnhancer / network annotation propagation) so unannotated nodes inherit chemically-plausible identities.
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73. ▌
    Pathway Functional Analysis Workflow · holobiomicslab bundle

    Use when you have an LC-MS metabolomics feature list (m/z, optionally p-values/fold changes) and want biological interpretation without prior identification — feature preparation, mummichog functional analysis from m/z, pathway/enrichment analysis, and pathway-level interpretation.
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74. ▌
    Anndata Object Manipulation · holobiomicslab

    Use when you have single-cell RNA-seq count matrices or processed expression data and need to store them alongside cluster assignments (e.g., leiden cluster labels), cell metadata, and computed analysis results (e.
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75. ▌
    Factor Design Specification · holobiomicslab

    Use when when setting up a DESeqDataSet from count matrices or transcript quantification, you must specify a design formula before running DESeq() if your experiment has batch effects, multiple treatment groups, or multi-factor designs.
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76. ▌
    Rna Seq Count Normalization · holobiomicslab

    Use when you have transcript-level abundance estimates and inferred counts from salmon/kallisto/Sailfish (with or without Gibbs/bootstrap replicates) that must be summarized to gene or transcript level, and you plan to use count-based differential expression tools (edgeR, DESeq2, limma-voom).
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77. ▌
    Transcript Event Extraction · holobiomicslab

    Use when you have a genome annotation GTF file and need to identify all transcript-level alternative splicing events (exon skipping, intron retention, alternative splice sites, mutually exclusive exons, alternative first/last exons) before quantifying their inclusion levels (PSI) across samples or.
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78. ▌
    Cosine Similarity Ranking Metrics · holobiomicslab

    Use when when you have pre-computed spectral embeddings (vectors) for both query spectra and a reference library, and you need to measure retrieval performance by ranking reference compounds by similarity to each query.
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79. ▌
    Derivatizing Matrix Configuration · holobiomicslab

    Use when you have a derivatizing matrix (e.g., TAHS or other publicly documented reagent) with known composition and ionization behavior that you want to use in Met-ID for metabolite annotation, and the matrix is not yet configured in your Met-ID installation.
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80. ▌
    Effective Mobility Transformation · holobiomicslab

    Use when you have raw CE-MS data (mzML or netCDF format) with migration time measurements and need to establish a reproducible compound-specific axis that is independent of run-to-run electroosmotic flow fluctuations.
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81. ▌
    Lcms Metabolomics Data Processing · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in .mzML or .
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82. ▌
    Msi Feature Metadata Preservation · 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.
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83. ▌
    Carbon Oxidation State Assessment · holobiomicslab

    Use when after molecular formula assignment from FT-ICR MS peak data, when you need to classify metabolites by their redox state to predict bioavailability or lability, or when generating thermodynamic indices for chemodiversity analysis and environmental metabolomic interpretation.
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84. ▌
    Cheminformatics Database Querying · holobiomicslab

    Use when you have a list of identified or suspected chemical compound names (e.g., from GC-MS Match.
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85. ▌
    Chromatography Data Preprocessing · holobiomicslab

    Use when you have raw spectra files from a liquid chromatography experiment (in-house or external database) and need to adapt a pretrained GNN-RT model to predict retention times for your molecules. Preprocessing is the mandatory first step before any model training or transfer learning can proceed.
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86. ▌
    Empirical Compound Pre Annotation · holobiomicslab

    Use when after feature detection from mzML files (e.g., via Asari) when you have a feature table with m/z, retention time, and intensity columns, and before MS1 or MS2 annotation.
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87. ▌
    Ftms Raw Data Loading And Parsing · holobiomicslab

    Use when you have received raw FT-ICR transient data from Bruker Solarix or ThermoFisher instruments and need to perform signal processing, apodization, calibration, or molecular formula assignment in CoreMS. The data must be in native vendor format (.d directory with ser/fid files, or .
    0 installs
88. ▌
    Image Processing For Metabolomics · holobiomicslab

    Use when you have GC–MS or LC–MS data represented as a two-dimensional map (m/z vs retention time) and need to identify analyte signals and marker features while minimizing false peak detections.
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89. ▌
    Isotope Labeling Data Integration · holobiomicslab

    Use when you have LC-MS peak tables from parallel unlabeled and labeled (isotope-traced) sample cohorts, sample metadata defining groups and conditions, and you seek to identify metabolic intermediates that accumulate differentially in a perturbed system (e.
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90. ▌
    Mass Spectrometry Data Formatting · holobiomicslab

    Use when you have raw GC-MS output exported as CSV (containing columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
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91. ▌
    Ms Instrument Type Classification · holobiomicslab

    Use when when evaluating or designing a mass spectrometry data analysis platform, and you need to verify that every supported separation/ionisation technique (LC, GC, IMS, MS Imaging) is covered by at least one processing module.
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92. ▌
    Peak Extraction Rescue Algorithms · holobiomicslab

    Use when traditional peak extraction algorithms have produced a feature table that you suspect is incomplete or missing known suspects from your target database (e.g., T3DB).
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93. ▌
    Peak Picking Algorithm Comparison · 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.
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94. ▌
    Retention Time Feature Clustering · holobiomicslab

    Use when after chromatographic peak detection (findChromPeaks) when you have a processed XcmsExperiment object with detected peaks and need to perform initial feature grouping. Use it when features of the same compound are expected to co-elute within a narrow retention-time window (e.
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95. ▌
    Adduct Specific Model Fine Tuning · holobiomicslab

    Use when when you have access to annotated MS/MS spectra from a specific ionization mode (e.g., negative ESI) or adduct class (e.
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96. ▌
    Backend Merging And Concatenation · holobiomicslab

    Use when when you have two or more MsBackend objects (e.g., multiple MsBackendMemory, MsBackendDataFrame, or MsBackendMzR instances) containing distinct sets of MS spectra and you need to consolidate them into a single backend for downstream analysis, parallel processing, or export.
    0 installs
97. ▌
    Beam Search Decoding Optimization · holobiomicslab

    Use when using Casanovo for de novo peptide sequencing on high-stakes datasets (immunopeptidomics, paleoproteomics, or monoclonal antibody discovery) where missing the correct sequence in the top-1 prediction is costly.
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98. ▌
    C Sharp Wrapper Invocation From R · holobiomicslab

    Use when when you need to read proprietary or binary data formats (e.g., Thermo Fisher .raw files) from R but the native implementation is in .NET/C#, and direct language bindings are unavailable or impractical. Use this when the target assembly requires Windows/.
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99. ▌
    Ccs Calibration Tunemix Execution · holobiomicslab

    Use when you have positive-mode tune mix reference data (e.g., example_tune_pos.h5) with known CCS values spanning a wide m/z range (e.g., 118.086–1522 m/z) and need to establish a CCS calibration model to convert experimental drift times or collision cross sections for downstream analysis.
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100. ▌
     Composite Mass Track Construction · holobiomicslab

     Use when when processing a multi-sample LC-MS metabolomics project after mass-track extraction and retention-time calibration have been applied to all individual samples, and you need to detect peaks across the entire cohort.
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