Productivity

holobiomicslab Skill

Use when when you have loaded aligned peak data (from a preceding molecular networking alignment task) as a structured table with peak intensity, m/z, retention time, and alignment quality metrics, and you need to reduce false positives, remove noise, or focus analysis on peaks above a.

holobiomicslab Skill

Use when you have peak/feature tables from one or more of MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to integrate them into a unified lipidomics workflow (e.g., LipidMatch).

holobiomicslab Skill

Use when you have untargeted LC/MS metabolomics data from stable isotope labeling experiments (e.g., 13C-glucose vs. 12C-glucose) already converted to mzXML format, and you need to systematically identify putatively incorporated metabolic features by comparing unlabeled and labeled sample groups.

holobiomicslab Skill

Use when before initiating a release branch workflow for a multi-module Maven project, particularly when the repository contains multiple pom.xml files at different directory levels and a release branch naming convention (e.g., 'release/X.Y.Z') is planned.

holobiomicslab Skill

Use when when converting pre-processed MS/MS spectra into fixed-length vector representations using Word2Vec embeddings for Spec2Vec similarity scoring. Specifically, apply this skill after you have represented individual peaks and neutral losses as words ('[redacted-email]', 'loss@xxx.

holobiomicslab Skill

Use when after ISF features have been identified and annotated in Part 4 of the ISFrag workflow, and you need to represent the structural relationships among ISF features and their parent ions hierarchically.

holobiomicslab Skill

Use when you have raw LC/MS data in mzML format and need to execute a complete non-targeted screening workflow to extract and annotate chemical features.

holobiomicslab Skill

Use when when preparing to execute the Nextflow4MS-DIAL workflow on raw LC-HRMS metabolomics data (.mzML or .

holobiomicslab Skill

Use when when you have access to the source code of a chemo-informatics tool (e.

holobiomicslab Skill

Use when when setting up a fresh clone of the ENPKG workflow repository or when onboarding to a new machine. Use this skill before attempting to run any workflow stages (data organization, taxonomical enhancement, MN generation, SIRIUS annotation, or graph building).

holobiomicslab Skill

Use when when you have a Spectra-based MS analysis workflow in R but need access to specialized spectral similarity, filtering, or normalization algorithms available only in Python libraries.

holobiomicslab Skill

Use when you have multiple metabolomic studies with aggregate summary statistics (p-values, fold-change estimates) and need to perform meta-analysis while harmonizing compound nomenclature across datasets. Use this skill when the underlying R package (e.

holobiomicslab Skill

Use when use when the workflow requires spectral-similarity-prediction-evaluation.

holobiomicslab Bundle

Use when you have a parent structure (drug, natural product, xenobiotic) and untargeted LC-MS/MS data and want to find its biotransformation products — predict plausible metabolites in-silico by rule-based expansion (BioTransformer mammalian/gut-microbial/ environmental rules, EnviPath microbial degradation, or MINE/Pickaxe combinatorial reaction-network generation), filter candidates to those detectable in the experimental mass range, then screen and rank them against the observed LC-MS/MS features to annotate which predicted biotransformation products were actually seen.

holobiomicslab Skill

Use when after running DESeq() on a DESeqDataSet and extracting results with results(dds), you have a results table with log₂ fold changes, p-values, and adjusted p-values (padj). Use this skill when you need to (1) identify genes meeting a significance threshold (e.g., padj < 0.

holobiomicslab Skill

Use when when you have raw mass spectrometry spectral data (peak intensities across m/z values) and need to feed it into MLP or GNN models for metabolite annotation, or when you need to generate LDA topic labels as auxiliary multi-task learning targets.

holobiomicslab Skill

Use when when you have centroided mzML files from LC-MS metabolomics and need to construct high-mass-resolution mass tracks for each sample before alignment. Apply this skill at the start of an untargeted metabolomics workflow, before building a cross-sample MassGrid.

holobiomicslab Skill

Use when you have LC-MS/MS data acquired in DDA mode from untargeted metabolomics experiments and need to remove chimeric (co-fragmented) MS/MS spectra that result from multiple precursor ions fragmented simultaneously.

holobiomicslab Skill

Use when immediately after peak detection in the IDSL.IPA workflow, when you have a list of candidate peaks extracted from EIC data and need to remove noise-dominated signals before downstream peak property evaluation and annotation.

holobiomicslab Skill

Use when you have a raw or Seurat object-backed scRNA-seq expression matrix and need to: (1) stabilize variance across genes with SCTransform normalization, (2) extract feature loadings in reduced dimensionality space via reverse PCA to use as input for GESECA or other coregulation-based enrichment.

holobiomicslab Skill

Use when use when the workflow requires background-distribution-significance-thresholding.

holobiomicslab Skill

Use when when you need to verify that a GitHub Actions workflow (e.g., main.yml) executes successfully on your local machine, reproduce a reported passing or failing CI build status, or debug why a workflow badge reports success/failure.

holobiomicslab Skill

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

holobiomicslab Skill

Use when when deploying a Streamlit workflow app in offline mode (online_deployment: false) or when Redis is unavailable in online mode, and you need to launch workflows as independent background processes while maintaining the ability to track, recover, or cancel them later by their PID.

holobiomicslab Skill

Use when when beginning a metabolomics analysis workflow in maplet, you have raw or preprocessed metabolomics data (assay measurements) and associated sample metadata (colData) or feature annotations (rowData), and you need to create a single, unified container that will hold data, intermediate.

holobiomicslab Skill

Use when analyzing RNA-seq count data from a DESeq2 workflow where you have fitted negative binomial generalized linear models and need to extract final results. Use it specifically when you want to identify genes with adjusted p-value below a predetermined significance threshold (e.g., α=0.

holobiomicslab Skill

Use when you have a multi-fold cross-validation training workflow that must run as parallel SLURM array jobs, each with its own GPU, and you need to ensure that all jobs can locate the same training data, code repository, container image, and results directory without hardcoded absolute paths or.

holobiomicslab Skill

Use when after implementing a shared-weight ResNet18 encoder module but before integrating it into the DeepION data augmentation and projection workflow.

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

LEX: Legal-Entity-X-ref workflow skill. Use this skill when the user needs Centralized 'Truth Engine' for cross-jurisdictional legal context (US, EU, CA) and contract scaffolding and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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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

Moyu workflow skill. Use this skill when the user needs > and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

AI.MD v4 — 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.

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Axiom — First-Principles Assumption Auditor / 第一性原理拆解器 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 × 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

Speed Reader workflow skill. Use this skill when the user needs Launch RSVP speed reader for text and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

diegosouzapw Bundle

SymPy - Symbolic Mathematics in Python workflow skill. Use this skill when the user needs SymPy is a Python library for symbolic mathematics that enables exact computation using mathematical symbols rather than numerical approximations and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.