Productivity

holobiomicslab Skill

Use when when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/Yao_Streptomyces/roseosporus/0518_s_BuOH.

holobiomicslab Skill

Use when after peak detection in a nontargeted LC-MS workflow when you have a feature table with detected peaks and need to filter low-quality features or understand why certain features have inconsistent intensity or poor annotation confidence.

holobiomicslab Skill

Use when you have a lipid identification or library-generation task that requires you to define a target chemical space bounded by lipid classes (e.g., phosphatidylcholine, triglyceride) and fatty acid composition ranges (e.g., C14–C22 with 0–6 degrees of unsaturation).

holobiomicslab Skill

Use when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/... or mzspec:MSV000084951:AH22) and need to extract the corresponding mass spectrum peak list (m/z and intensity pairs) for downstream analysis, visualization, or cross-repository comparison.

holobiomicslab Skill

Use when when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-...

holobiomicslab Skill

Use when a web application receives mass spectrometry data through heterogeneous identifier formats and must automatically determine which loader (Task ID, USI, or FBMN) should process the input.

holobiomicslab Skill

Use when you have located a workflow definition file (YAML or JSON) from a versioned release and need to confirm that all mandatory workflow metadata fields (name, version, inputs, outputs, steps) are declared, properly formatted, and cross-references are resolved before validation or execution.

holobiomicslab Skill

Use when you have .mzML or .abf LC-HRMS metabolomics raw data files and need to perform peak detection, feature identification, and chromatogram alignment reproducibly across different compute environments (local workstations, HPC clusters).

holobiomicslab Skill

Use when you need to bootstrap a tool workflow by generating a version- or instrument-specific default configuration file (e.g., for MS-DIAL 4 vs. 5), execute an analysis on formatted input files (e.g., MS-DIAL export .txt files), or capture tool output for downstream validation.

holobiomicslab Skill

Use when you have a versioned workflow definition file (YAML or JSON) from a specific release commit and need to verify it conforms to the project's schema specification, validate the presence of all required metadata fields (name, version, inputs, outputs, steps), and detect syntax errors or.

holobiomicslab Skill

Use when you encounter a published scientific article or software paper that makes claims about data processing, analysis, or results, but the reproducibility context is unclear, artifacts are scattered, or the connection between claims and outputs is not immediately evident.

holobiomicslab Skill

Use when when you have pre-computed dense embeddings for query spectra (unknown compounds) and reference spectra (spectral library), and you need to rank library entries by similarity to each query for compound identification or structural similarity retrieval.

holobiomicslab Skill

Use when you have raw lipidomic and metabolomic data files generated by the Multi-ABLE barocycler-based concurrent multiomics method and need to perform integrative preprocessing (spectral normalization and alignment across samples) followed by multivariate analysis to identify differential lipids.

holobiomicslab Skill

Use when when you have a SummarizedExperiment containing metabolomic abundances and a corresponding vector of quality metrics (e.g., coefficient of variation computed across QC samples), and you need to filter to retain only features meeting a reproducibility threshold (e.g., CV ≤ 0.

holobiomicslab Skill

Use when after peak picking, sample alignment, and isotopologue/adduct grouping steps have been completed in an untargeted LC-MS workflow.

holobiomicslab Skill

Use when you have raw mass spectrometry outputs (peak areas/heights across samples and fragmentation spectra) that need to be formatted and validated before running the tima taxonomically informed annotation workflow.

holobiomicslab Skill

Use when you have a GitHub repository containing scientific records (e.

holobiomicslab Skill

Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal standards.

holobiomicslab Skill

Use when after completing feature annotation and reaction assignment in an untargeted metabolomics workflow, specifically when you have a feature-by-sample intensity matrix aligned with metabolite identities and want to communicate cluster structure, reaction pathway groupings, and feature.

holobiomicslab Skill

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

holobiomicslab Skill

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

holobiomicslab Skill

Use when when you have deposited or archived biosynfoni fingerprint vectors (such as from Zenodo 10.5281/zenodo.14822624) and need to ingest them into a Python workflow to compute distributional statistics, bit-frequency profiles, sparsity metrics, or pairwise similarity coefficients.

holobiomicslab Skill

Use when you have raw or partially processed metabolomics data (mzML/mzXML format) from LC-MS or GC-MS runs and need to apply standardized feature detection, alignment, and intensity normalization as part of a reproducible workflow.

holobiomicslab Skill

Use when you have UPLC-HRMS data from ThermoFisher, Agilent, or other vendor instruments (converted via MSConvert if needed), organized as batch-processed files ready for MSThunder input, and you need to identify unknown organic pollutants with deep learning-assisted structure prediction and.

holobiomicslab Skill

Use when when you have aligned peak-alignment data from a preceding molecular networking task (structured as a table with peak intensity, m/z, retention time, and alignment quality metrics) and need to visualize and interactively filter peaks across multiple spectra to support comparative mass.

holobiomicslab Skill

Use when when you need to benchmark multiple encoder types (e.g., FFN vs. GNN) on the same predictive task and require evidence that performance differences reflect genuine architectural trade-offs rather than suboptimal tuning.

holobiomicslab Skill

Use when you receive mass spectrometry data through heterogeneous identifier formats—specifically when the input could be a GNPS Task ID, a Universal Spectrum Identifier (USI), or a Feature-Based Molecular Networking (FBMN) identifier—and you need to programmatically determine which format was.

holobiomicslab Skill

Use when when setting up a new computational workflow (e.g., ENPKG) that depends on pinned versions of Python packages and system libraries, or when collaborating across machines where package availability or versions may differ.

holobiomicslab Skill

Use when when you have received chemical annotations from GNPS spectral library matching workflow and need to assess their reliability before downstream analysis (e.g., chemical explorer visualization, sample filtering, or comparative metabolomics).

holobiomicslab Skill

Use when when a Python package is being relocated to a new GitHub organization (e.

holobiomicslab Skill

Use when your task requires a pretrained convolutional encoder (ResNet18) to produce fixed-size representation vectors of a specific dimensionality (e.g., 512 dimensions) rather than the default output size.

diegosouzapw Bundle

LibreOffice Base workflow skill. Use this skill when the user needs Database management, forms, reports, and data operations with LibreOffice Base and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Cirq - Quantum Computing with Python workflow skill. Use this skill when the user needs Cirq is Google Quantum AI's open-source framework for designing, simulating, and running quantum circuits on quantum computers and simulators and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

AI.MD v4 \u2014 The Complete AI-Native Conversion System workflow skill. Use this skill when the user needs Convert human-written CLAUDE.md into AI-native structured-label format. Battle-tested across 4 models. Same rules, fewer tokens, higher compliance and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

Axiom \u2014 First-Principles Assumption Auditor / \u7b2c\u4e00\u6027\u539f\u7406\u62c6\u89e3\u5668 workflow skill. Use this skill when the user needs First-principles assumption auditor. Classifies each hidden assumption (fact / convention / belief / interest-driven), ranks by fragility \u00d7 impact, and rebuilds conclusions from verified premises. Bilingual: auto-detects Chinese or English and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

c-pro workflow skill. Use this skill when the user needs Write efficient C code with proper memory management, pointer and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.