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HolobiomicsLab

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1. ▌
   Mrm Transition Extraction · holobiomicslab

   Use when you have raw LC-MS/MS data in MRM acquisition mode and need to systematically identify and catalog all precursor m/z and corresponding product m/z values for each transition monitored during data collection.
   9 installs
2. ▌
   Ms Ms Spectrum Prediction · holobiomicslab

   Use when you have MS/MS spectra (in MGF format) with required metadata fields (TITLE, PRECURSOR_MZ, PRECURSOR_TYPE, COLLISION_ENERGY) and need to predict candidate molecular formulas ranked by confidence.
   9 installs
3. ▌
   Ms2 Spectra Tic Filtering · holobiomicslab

   Use when after concatenating replicate MS/MS spectra for each precursor feature (m/z and retention time), use this skill when you have multiple replicate scans per feature and need to reduce spectral count while preserving the highest-intensity, most-reliable spectra.
   8 installs
4. ▌
   Ms2lda Feature Annotation · holobiomicslab

   Use when after creating a GNPS mass spectral molecular network and running an MS2LDA experiment, use this skill when you want to identify and visualize which substructural motifs (Mass2Motifs) are shared across clustered spectra, particularly to highlight fragmentation pattern similarities between.
   11 installs
5. ▌
   Multi Tool Schema Mapping · holobiomicslab

   Use when you have peak/feature table outputs from one or more peak-picking tools (MZmine, XCMS, MS-DIAL, Compound Discoverer) with different column names and metadata structures, and you need to ingest them into LipidMatch or another unified lipidomics pipeline that requires consistent column.
   8 installs
6. ▌
   Pathway Score Aggregation · holobiomicslab

   Use when you have a metabolite intensity matrix (samples × metabolites) or gene expression matrix (samples × genes) with corresponding pathway definitions (pathway IDs mapped to feature sets), and you need to rank pathways by activity level to identify which biological processes are most affected.
   8 installs
7. ▌
   Peptide Spectrum Matching · holobiomicslab

   Use when when you have high-resolution tandem mass spectrometry data (in mzML or mzXML format) and a spectral library, and need to identify peptides including those with post-translational modifications.
   9 installs
8. ▌
   Proteome Dataset Handling · holobiomicslab

   Use when you have a collection of MS/MS spectra in MGF format and need to prepare them for GPU-based clustering. Dataset size and available GPU memory are critical: use GTX 1080Ti for smaller proteome datasets; use GTX 3090 for datasets like PXD000561 that exceed GTX 1080Ti capacity.
   11 installs
9. ▌
   Python Workflow Scripting · holobiomicslab

   Use when you have raw mass spectrometry spectral data in common formats (MGF, MSP, mzML, mzXML, JSON) that requires standardized metadata cleaning, validation, and peak filtering before comparative analysis. Use this skill when you need to encode data quality constraints (e.
   13 installs
10. ▌
    R Workflow Implementation · holobiomicslab

    Use when you have raw mass spectrometry data in mzXML, mzML, or netCDF format from untargeted LC/HRMS analysis that has been pre-processed by IDSL.
    11 installs
11. ▌
    Resolver Url Construction · holobiomicslab

    Use when when you have a USI string (comprising dataset identifier, spectrum index, and optional library reference) and need to generate a stable, machine-readable link that resolves to interactive spectrum visualization or programmatic access.
    10 installs
12. ▌
    Retention Time Prediction · holobiomicslab

    Use when you have MS1-formatted mass spectrometry files from a liquid chromatography–mass spectrometry (LC-MS) experiment and need to predict the retention time of peptide ions without relying on spectral libraries, empirical models, or manual feature engineering.
    14 installs
13. ▌
    Schema Compliance Testing · holobiomicslab

    Use when when uploading or ingesting a new paired omics project JSON document into the Pairing Omics Data Platform, or when programmatically submitting projects via the OpenAPI interface. Apply this skill before persisting the document to disk or indexing it for search.
    12 installs
14. ▌
    Siamese Network Inference · holobiomicslab

    Use when you have a collection of cleaned MS/MS spectra (in formats like mzML, mgf, msp, mzxml, or json) and need to predict molecular structural similarities between spectrum pairs without pre-computing RDKit fingerprints.
    12 installs
15. ▌
    Smiles Parsing Validation · holobiomicslab

    Use when when you have a dataset of molecular structures encoded as SMILES strings that will be processed downstream (e.
    11 installs
16. ▌
    Sparse Matrix Computation · holobiomicslab

    Use when clustering large collections of high-resolution MS/MS spectra (thousands to millions) and you have already converted spectra to low-dimensional vectors via feature hashing.
    12 installs
17. ▌
    Spectral Data Exploration · holobiomicslab

    Use when you have completed msFeaST pipeline preprocessing and generated a JSON output file (dashboard_data.
    11 installs
18. ▌
    Spectral Data Integration · holobiomicslab

    Use when you have three distinct mass spectrometry data sources (quantification table, metadata table, and spectral data from an MS library or reference dataset like omsw_pleurotus_ms2deepscore) and need to combine them into a single JSON output that preserves all three modalities for interactive.
    9 installs
19. ▌
    Spectral Library Matching · holobiomicslab

    Use when you have one or more MS/MS spectra in .mgf format (or USI identifiers) and need to: (1) identify unknowns by searching against domain-curated reference data; (2) assign Level 2 metabolomics annotations via GNPS library matches; (3) aggregate matches across organism lineages (e.
    11 installs
20. ▌
    Spectrum Metadata Parsing · holobiomicslab

    Use when a user submits one or more MS/MS spectra (via .mgf file, USI list, or direct upload) and the downstream analysis requires dispatching to a specific domain-specific MASST tool (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST, or metadataMASST).
    14 installs
21. ▌
    Spectrum Query Formatting · holobiomicslab

    Use when you have parsed LC-MS/MS spectral data (precursor m/z, ionization mode, collision energy, and a list of fragment m/z and intensity pairs) and need to submit it to the CSI:FingerID web service for molecular fingerprint prediction as part of a metabolite identification workflow.
    8 installs
22. ▌
    Survival Data Preparation · holobiomicslab

    Use when when you have clinical survival outcomes (event status and follow-up time) and high-dimensional metabolomic or expression data, and you need to feed them into Cox-PH or Cox-nnet prognosis models.
    7 installs
23. ▌
    Suspect Database Matching · holobiomicslab

    Use when you have LC-MS peak/feature data, a curated suspect compound database with known m/z, retention time, and fragment ion coordinates, and you observe that traditional peak extraction algorithms have failed to detect ions corresponding to suspected contaminants or chemicals of interest.
    11 installs
24. ▌
    Thermo Raw Format Parsing · holobiomicslab

    Use when when you have LC-MS data in Thermo .raw format (a proprietary binary output from Thermo mass spectrometers) and need to load it into a 3D LC-MS viewer or extract structured spectral metadata (retention time, m/z values, intensities, scan number, MS level) for visualization or quantitative.
    12 installs
25. ▌
    Tree To Query Translation · holobiomicslab

    Use when you have a shallow decision tree trained on ChemEcho feature vectors (peak or neutral loss formulas) and need to deploy it as an executable query against tandem mass spectrometry data.
    11 installs
26. ▌
    Vendor Format Abstraction · holobiomicslab

    Use when you have mass-spectrometry raw data files from multiple vendors (e.g., Thermo, Waters, Bruker, Sciex) and/or mixed standard formats (mzML, mzXML) that must be processed by a single analysis pipeline.
    12 installs
27. ▌
    Accuracy Metric Computation · holobiomicslab

    Use when after running inference on a trained structure prediction model with one or more input modalities (1H NMR, 13C NMR, or combined), you have generated predicted molecular formulas and connectivity graphs that need to be compared against known ground truth structures.
    13 installs
28. ▌
    Compound Identifier Mapping · holobiomicslab

    Use when after filtering a peak table to remove mispicked ions, group contaminants, and low-replicability features, you have a curated feature list with m/z, retention time, and MS/MS spectra ready for annotation.
    10 installs
29. ▌
    JSON Response Serialization · holobiomicslab

    Use when when a backend service receives structured prediction results from an external API (e.g., nmrshiftdb peak predictions) and must return them to a client application via HTTP POST response.
    12 installs
30. ▌
    Metabolite Score Projection · holobiomicslab

    Use when you have Nightingale Health 1H-NMR metabolomics assay output (metabolite concentrations in a samples × features matrix) and you want to compute a published metabolic risk score or surrogate biomarker (mortality risk, metabolic age, cardiovascular event risk, type-2 diabetes risk, COVID-19.
    11 installs
31. ▌
    Mixture Spectrum Comparison · holobiomicslab

    Use when you have an observed NMR mixture spectrum and one or more candidate reconstructed spectra (each formed by summing weighted single-compound spectra), and need a continuous, transportable distance metric to score how well the reconstruction approximates the observed mixture.
    11 installs
32. ▌
    Nmr Peak JSON Serialization · holobiomicslab

    Use when you have proton (1H) and carbon-13 (13C) NMR peak measurements from a molecular sample and need to classify the molecule using the SMART 3 deep learning API. The peaks must be reformatted from their native instrument output into JSON before submission to the /api/smart3/search endpoint.
    8 installs
33. ▌
    Nmr Spectrum Peak Detection · holobiomicslab

    Use when you have a loaded INADEQUATE NMR spectrum file (after referencing via basic shifting) and need to identify individual peak positions and intensities as input to downstream peak network clustering or metabolite matching.
    8 installs
34. ▌
    Smiles Structure Annotation · holobiomicslab

    Use when you have LC–QTOF mass spectra from real environmental or biological samples (e.g., wastewater, complex mixtures) and need to assign molecular structures to spectra where traditional library matching fails or reference compounds are unavailable.
    12 installs
35. ▌
    Spectral Peak Deconvolution · holobiomicslab

    Use when you have a raw 1D NMR spectrum (FID or processed format) from urine, worm, or other biological samples and need to extract peak positions, intensities, and linewidths as a tabular peak list.
    8 installs
36. ▌
    Atac Seq Peak Annotation · holobiomicslab

    Use when after differential peak analysis (tl.diff_test) has identified peaks that differ in accessibility across cell types or conditions.
    6 installs
37. ▌
    Bam To Bigwig Conversion · holobiomicslab

    Use when after running TOBIAS ATACorrect to generate bias-corrected signal tracks from aligned ATAC-seq reads. Use this skill when you have corrected cutsite signal (as .
    8 installs
38. ▌
    Barcode Fragment Mapping · holobiomicslab

    Use when you have a coordinate-sorted BAM file from a single-cell ATAC-seq experiment (especially 10X Genomics platforms) and need to extract per-fragment information including cell barcodes, fragment coordinates, and quality metrics for downstream analysis in SnapATAC2 or compatible tools.
    8 installs
39. ▌
    Bigwig Signal Processing · holobiomicslab

    Use when after bias correction of ATAC-seq reads (via ATACorrect) when you have a bias-corrected bigWig file and need to measure transcription factor footprint strength within defined accessible regions (peaks, motif sites, or called footprint boundaries).
    8 installs
40. ▌
    Dmr Detection Bumphunter · holobiomicslab

    Use when you have preprocessed, normalized beta-value matrices from EPIC or 450k methylation arrays with at least two sample groups (case/control, treatment/untreated, or similar contrasts) and seek to identify regions of coordinated differential methylation rather than individual CpG sites.
    11 installs
41. ▌
    Fragment File Validation · holobiomicslab

    Use when after invoking pp.make_fragment_file to convert a coordinate-sorted BAM file (e.g., from 10X ATAC or standard alignment) into a compressed fragment file.
    8 installs
42. ▌
    Sparse Matrix Validation · holobiomicslab

    Use when after generating a count matrix from fragment data using pp.add_tile_matrix, pp.make_peak_matrix, or pp.make_gene_matrix in SnapATAC2.
    11 installs
43. ▌
    API Contract Validation · holobiomicslab

    Use when integrating with an external API (such as TensorFlow Serving) where changes to the response schema could break dependent code, or when model metadata must be extracted and verified before being used in downstream analysis steps.
    11 installs
44. ▌
    Build System Monitoring · holobiomicslab

    Use when when you need to capture a snapshot of a research software project's health metrics from multiple CI/CD and repository services (Travis CI, Landscape.
    9 installs
45. ▌
    Ccs Bias Quantification · holobiomicslab

    Use when you have IM-MS lipidomics data acquired on samples spiked with fully labeled U13C lipid standards (e.g., U13C yeast extract), and you need to assess whether systematic CCS deviation exists between your instrument's measured values and the DT CCS N2 reference library for U13C labeled lipids.
    12 installs
46. ▌
    Data Summary Statistics · holobiomicslab

    Use when you have a curated relational dataset (structure-organism pairs) and need to quantify how structures distribute across a categorical variable (e.g., organism prevalence).
    14 installs
47. ▌
    Docker Image Management · holobiomicslab

    Use when when you need to confirm that a published Docker image (e.g., hosted on Docker Hub) can be pulled and instantiated successfully, and when the target tool has a defined entry point or CLI interface.
    12 installs
48. ▌
    Multiquant File Parsing · holobiomicslab

    Use when you have Sciex Multiquant text export files from one or more metabolomics or lipidomics analytical sequences and need to identify and locate QCpool (pooled quality control) samples that should have been injected at regular intervals, or when you must validate that the study design's.
    11 installs
49. ▌
    Spectral Peak Filtering · holobiomicslab

    Use when you have imported raw mass spectrometry data in formats such as MGF, MSP, mzML, or mzXML and need to clean the spectral data prior to similarity comparisons, metadata validation, or export.
    11 installs
50. ▌
    Twim Ms Data Processing · holobiomicslab

    Use when you have TWIM-MS data (arrival time and m/z values) from a multi-omic sample and need to: (1) establish a CCS calibration curve from known standards, (2) assign unidentified features to biomolecular classes (e.
    10 installs
51. ▌
    Workflow Reconstruction · holobiomicslab

    Use when when you have a partially documented or undocumented MS analysis pipeline and need to verify its correctness, trace data provenance through multiple processing stages, integrate tools via unified parameter handling (CTD scheme), or ensure the workflow adheres to community standards for.
    12 installs
52. ▌
    Analysis Type Selection · holobiomicslab

    Use when preparing to run LipidMatch-4.2 and you need to determine which analysis mode should execute. Specifically: when your input data consists of lipid standards or lipid-rich samples (set Lipid analysis mode); when you are analyzing Tween surfactant-containing samples (set Tween-positive mode);
    13 installs
53. ▌
    Batch Record Processing · holobiomicslab

    Use when when you have a repository containing hundreds or thousands of structured records (e.g., MassBank records in standardized format) that must be validated for correctness before release or merge.
    9 installs
54. ▌
    Cdf File Format Parsing · holobiomicslab

    Use when when you have multiple CDF files from mass spectrometry imaging experiments (e.g., root tissue MALDI-MS data) that need to be ingested into Matlab for linear imaging analysis. Trigger: presence of .
    11 installs
55. ▌
    Command Line Invocation · holobiomicslab

    Use when after completing a BiG-SLiCE clustering analysis and needing to access the pre-calculated BGC and GCF cluster assignments in tabular format for spreadsheet analysis, statistical testing, or integration with other bioinformatics pipelines.
    12 installs
56. ▌
    Data Frame Augmentation · holobiomicslab

    Use when after assign_hierarchy has added KEGG compound identifiers and hierarchical metadata to your metabolomics count data frame, and you need to link metabolites to their functional orthologs (KO numbers) and gene names for pathway or functional enrichment analysis.
    7 installs
57. ▌
    Docker Image Deployment · holobiomicslab

    Use when when you have a containerized scientific tool available on Docker Hub (e.
    10 installs
58. ▌
    Docker Network Creation · holobiomicslab

    Use when when deploying a multi-container application stack using docker-compose where containers need reliable hostname-based service discovery and isolation from the host network.
    11 installs
59. ▌
    Drugbank Format Parsing · holobiomicslab

    Use when when you have obtained a DrugBank release file (requiring access credentials) and need to extract drug records with standardized fields (names, structures, identifiers, classification) for integration into a metadata enrichment or cleanup workflow that queries multiple drug/natural product.
    11 installs
60. ▌
    Entry Status Tabulation · holobiomicslab

    Use when you need to assess the curation completeness and status distribution of a MIBiG JSON dataset—for instance, to identify how many entries are in 'active', 'retired', or 'pending' states, or to audit changes in entry status over time.
    12 installs
61. ▌
    Feature Matrix Assembly · holobiomicslab

    Use when when you have a set of chemical structures (SMILES, SDF, mol, mol2, or hin files) and need to convert them into a tabular feature representation for retention time prediction, metabolite annotation, or other quantitative structure–property modeling tasks.
    8 installs
62. ▌
    Fold Change Calculation · holobiomicslab

    Use when after completing statistical tests (t-test, Mann–Whitney U, or ANOVA) on matched lipid abundances grouped by experimental condition or sample category, and before compiling final results tables.
    7 installs
63. ▌
    Graph Topology Analysis · holobiomicslab

    Use when you have (1) a set of input metabolites (e.
    12 installs
64. ▌
    Gwas Result Integration · holobiomicslab

    Use when you have independent metabolomic GWAS results (metabolite p-values, effect sizes, metabolite IDs) and separate meta-genome GWAS results (variant p-values, effect sizes, genomic variant IDs) from similar diseases or phenotypes, and you want to discover novel metabolite–gene associations and.
    12 installs
65. ▌
    Hpc Job Parallelization · holobiomicslab

    Use when you have a filtered set of conformers (100s–1000s) from ASE-ANI that each require independent quantum calculations via QUICK, and you have access to HPC resources with multiple cores or nodes. Parallelization is necessary when serial execution would exceed practical time budgets (e.
    6 installs
66. ▌
    Lipid Database Querying · holobiomicslab

    Use when you have acquired full-scan mass spectrometry imaging data (e.g., from a mouse bladder or tissue section) with detected m/z features and want to assign chemical identities to those features by querying a structured lipid database.
    8 installs
67. ▌
    Matlab Script Execution · holobiomicslab

    Use when you have located MATLAB scripts in a Codes-Explained folder with accompanying Read-Me.
    14 installs
68. ▌
    Model Residual Analysis · holobiomicslab

    Use when after fitting a linear model to normalized metabolomics featuredata using LinearModelFit(), to validate model assumptions (homogeneity of variance, normality), detect influential observations, and confirm that the model's coefficient and p-value estimates are reliable for downstream.
    10 installs
69. ▌
    Mz Binning And Indexing · holobiomicslab

    Use when immediately after parsing mzML files into (m/z, scan_number, intensity) tuples when you need to build mass tracks from raw MS1 spectra. Use it when working with high-resolution instruments (e.
    8 installs
70. ▌
    Peak Collision Flagging · holobiomicslab

    Use when you have extracted a peak list from MSI data and need to annotate matrix-related signals, but overlapping peaks or isobaric ions (ions with identical or near-identical m/z values) risk being misclassified.
    12 installs
71. ▌
    Psm Record Augmentation · holobiomicslab

    Use when your PSM input file (e.g., from MaxQuant or other search engines that do not report fixed modifications) lacks modification annotations for residues that were chemically modified during sample preparation (e.g., carbamidomethylation of cysteines, TMT labeling of lysines and N-termini).
    11 installs
72. ▌
    Pubchem API Integration · holobiomicslab

    Use when when you have raw chemical structures in diverse input formats (SMILES, SDF, or other molecular representations) from multiple sources and need to produce a uniform, canonicalized representation before molecular descriptor calculation, fingerprinting, or retention time modeling.
    11 installs
73. ▌
    Qc Signal Normalization · holobiomicslab

    Use when your metabolomic dataset contains dedicated QC samples (pooled or standard reference material injected at intervals throughout the analytical sequence) and you observe intensity drift, batch effects, or systematic signal variation correlated with run order or acquisition time rather than.
    16 installs
74. ▌
    Sbml Model Manipulation · holobiomicslab

    Use when when you have consensus metabolic reconstructions in SBML format for individual community members and need to resolve metabolic gaps by leveraging cross-member dependencies and community-level constraints before phenotypic validation or flux analysis.
    10 installs
75. ▌
    Smiles Mol File Parsing · holobiomicslab

    Use when when you have molecular structures encoded as SMILES strings or MOL files from an in-house database or spectroscopy repository, and need to convert them into node-edge graph representations with explicit atom features (atomic number, degree, formal charge, hybridization) and bond features.
    13 installs
76. ▌
    Tabular Data Validation · holobiomicslab

    Use when after curating and integrating structure-organism pairs from multiple sources when you need to produce a high-confidence subset suitable for publication or computational validation.
    9 installs
77. ▌
    Tensor Embedding Design · holobiomicslab

    Use when when you need to represent discrete chemical formulae (e.
    11 installs
78. ▌
    Type Coercion To String · holobiomicslab

    Use when when converting intermediate JSON records to output dictionaries via matrix directives and all field values must be serialized as strings for downstream format compatibility (e.g., mwTab format or other repository-specific formats that expect string-typed metadata fields).
    7 installs
79. ▌
    Unit Test Design Pytest · holobiomicslab

    Use when after implementing a custom Filter subclass (e.g., Tanimoto threshold filter) in minedatabase/filters.py and before integrating it into a pickaxe_run.py workflow.
    11 installs
80. ▌
    Volcano Plot Generation · holobiomicslab

    Use when you have CSV files containing fold-change estimates and statistical p-values from a differential expression analysis (e.
    11 installs
81. ▌
    Word2vec Model Training · holobiomicslab

    Use when when you have a collection of mass spectra (e.
    10 installs
82. ▌
    Qc Failure Event Detection · holobiomicslab

    Use when rapid QC-MS is actively monitoring LC-MS data acquisition and a QC check result (e.g., internal standard retention time drift, m/z deviation, or intensity threshold breach) returns a fail status.
    12 installs
83. ▌
    Breath Biomarker Discovery · holobiomicslab

    Use when you have GC–MS data from human breath samples and need to identify marker metabolites for disease diagnosis, phenotyping, or biomarker discovery without a predefined target list. Your data is noisy or conventional peak picking has produced high false-positive rates.
    13 installs
84. ▌
    Metabolomics Nmr Router · holobiomicslab

    Use when a task needs a skill from ASB Metabolomics — NMR — search this unit's 276 evidence-grounded skills, then apply and optionally ground the one that fits.
    13 installs
85. ▌
    Metabolomics Ce Ms Router · holobiomicslab

    Use when a task needs a skill from ASB Metabolomics — CE-MS — search this unit's 114 evidence-grounded skills, then apply and optionally ground the one that fits.
    8 installs
86. ▌
    Metabolomics Gc Ms Router · holobiomicslab

    Use when a task needs a skill from ASB Metabolomics — GC-MS — search this unit's 367 evidence-grounded skills, then apply and optionally ground the one that fits.
    10 installs
87. ▌
    Metabolomics Lc Ms Router · holobiomicslab

    Use when a task needs a skill from ASB Metabolomics — LC-MS — search this unit's 2,621 evidence-grounded skills, then apply and optionally ground the one that fits.
    10 installs
88. ▌
    Masster · holobiomicslab

    Use when you need to run the Zamboni-lab Masster (MASSter) workflow for untargeted LC-MS metabolomics data analysis. NONCOMMERCIAL tool — confirm permitted use before applying (see License notice).
    11 installs
89. ▌
    Metabolomics Collection Router · holobiomicslab

    Use when an agent needs to find and apply a computational-metabolomics / LC-MS-MS skill from this collection, and optionally ground it against the source paper via Perspicacité before acting.
    10 installs
90. ▌
    Metabolomics Ms Generic Router · holobiomicslab

    Use when a task needs a skill from ASB Metabolomics — mass-spectrometry — search this unit's 804 evidence-grounded skills, then apply and optionally ground the one that fits.
    9 installs
91. ▌
    Metabolomics Ms Imaging Router · holobiomicslab

    Use when a task needs a skill from ASB Metabolomics — MS-imaging — search this unit's 292 evidence-grounded skills, then apply and optionally ground the one that fits.
    11 installs
92. ▌
    Metabolomics Ion Mobility Router · holobiomicslab

    Use when a task needs a skill from ASB Metabolomics — ion-mobility-MS — search this unit's 390 evidence-grounded skills, then apply and optionally ground the one that fits.
    12 installs
93. ▌
    Msp File Parsing · holobiomicslab

    Use when you have a Mass Spectrum Point (MSP) file containing electron ionization mass spectral records with header fields and peak intensity pairs, and you need to load it into an R data structure for library searching, format validation, or round-trip conversion.
    11 installs
94. ▌
    Mgf File Parsing · holobiomicslab

    Use when you have raw or MZmine-processed MGF files (containing MS/MS spectra with m/z values, intensities, and precursor masses) that need to be segmented by sample, deduplicated, or prepared for fragment annotation and adduct analysis in the MolNotator pipeline.
    12 installs
95. ▌
    Jcamp File Parsing · holobiomicslab

    Use when you receive uploaded spectral data in JCAMP format (jcamp) as input to the /api/v1/chemspectra/file/convert endpoint, or when you need to extract and validate metadata and peak information from an existing JCAMP file before converting to another format or performing spectral analysis.
    9 installs
96. ▌
    Mwtab File Parsing · holobiomicslab

    Use when you have mwTab format files (Mass Spectrometry or Nuclear Magnetic Resonance experimental data from Metabolomics Workbench) that need to be loaded into Python for downstream analysis, validation, conversion to JSON, or programmatic manipulation of metadata and data sections.
    11 installs
97. ▌
    Asb Contribute · holobiomicslab

    Use when an ASB skill proved wrong, stale, missing or wasteful in practice — its steps failed, no skill covered the task, the leaves existed but nothing composed them, or the tool has changed. Turns that friction into a redacted, dedupable report the user approves before anything is filed.
    6 installs
98. ▌
    Metabolomics Direct Infusion Router · holobiomicslab

    Use when a task needs a skill from ASB Metabolomics — direct-infusion-MS — search this unit's 97 evidence-grounded skills, then apply and optionally ground the one that fits.
    12 installs
99. ▌
    Ms2 Dereplication · holobiomicslab

    Use when you have MS2 tandem mass spectrometry data in .mzML format and need to match unknown spectra against a reference library (GNPS, HMDB, MassBank) to identify which known compounds are present in your sample.
    13 installs
100. ▌
     Mzml File Parsing · holobiomicslab

     Use when you have raw LC- or GC-HRMS data from vendor instruments (ESI or APCI ionization) that needs to be converted to a vendor-neutral format for non-target screening, or you already have mzML files that require loading into a Python environment for downstream feature detection and MS2 spectral.
     11 installs