Productivity

holobiomicslab Skill

Use when starting from raw LC-MS spectral files (mzML or mzXML format) in a global metabolomics study and you need to produce a complete, validated feature table with m/z, retention time, and intensity values across all samples.

holobiomicslab Skill

Use when when a user uploads a JSON project document to the Pairing Omics Data Platform, before accepting it into the repository or indexing it for search. Use this skill to catch missing required fields, incorrect field types, and constraint violations early in the submission workflow.

holobiomicslab Skill

Use when you need to verify that a GitHub Actions workflow (such as dev_build_release.yml) successfully completes end-to-end, especially after code changes or to confirm that automated build infrastructure is functioning correctly.

holobiomicslab Skill

Use when you have created a GNPS molecular network (classical or feature-based workflow) and separately run an MS2LDA experiment on the corresponding MGF file, and you want to associate each network node with its constituent substructural motifs and visualize which motifs are shared between.

holobiomicslab Skill

Use when when beginning a new mass spectrometry analysis workflow with raw spectral data files in mzML, mzXML, msp, MGF, or JSON format.

holobiomicslab Skill

Use when you need to support multiple plotting backends for the same data visualization task, and you want to centralize backend selection logic so that users can specify their preferred rendering engine (matplotlib, bokeh, or plotly) at call time without modifying the core plotting logic.

holobiomicslab Skill

Use when after applying one or more mpactr filters (mispicked, group, CV, or insource) to a peak table in a chained filtering workflow.

holobiomicslab Skill

Use when you have a GNPS task ID from a completed molecular networking workflow (METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING on GNPS1, or classical_networking_workflow / feature_based_molecular_networking_workflow on GNPS2) and need to access the resulting spectral.

holobiomicslab Skill

Use when after peak picking and sample alignment when you have an aligned feature table containing m/z and retention time coordinates. Use it when your untargeted LC-MS workflow needs to reduce feature redundancy caused by naturally occurring stable isotope patterns and common adduct formation.

holobiomicslab Skill

Use when after running in silico annotation tools (SIRIUS, ISDB) or spectral library matching on your feature table, when you need to retain only annotations meeting a minimum confidence threshold.

holobiomicslab Skill

Use when when you need to convert vendor-specific raw mass spectrometry files (.raw) to the open mzML format using imzML Writer, and msconvert is not yet installed or its location is not recognized by the system.

holobiomicslab Skill

Use when after installing a Python package or before running a computational workflow for the first time, to verify that the CLI entry point is properly configured, the Python environment is correctly set up, and to discover available command-line arguments and their defaults (e.

holobiomicslab Skill

Use when when you have a processed Bruker Solarix FT-ICR mass spectrum object (from ReadBrukerSolarix) and a reference peak list file (SRFA.

holobiomicslab Skill

Use when when you need to confirm that a Java project's GitHub Actions workflow (e.g., 'dev_build_release.yml') has completed successfully and generated usable build artifacts;

holobiomicslab Skill

Use when you have LC-MS/MS DDA metabolomics data (positive and/or negative ionization modes) and sample metadata (originating taxon) for one or more samples, and you need to generate a Wikidata-connected RDF knowledge graph for integrated natural products analysis, taxonomy-aware compound.

holobiomicslab Skill

Use when when evaluating whether an MS data processing platform (such as mzmine) supports the full range of separation/ionization techniques your laboratory uses, or when assessing whether gaps exist in the software architecture that would require external pre- or post-processing for specific.

holobiomicslab Skill

Use when after completing dereplication and cosine similarity clustering in the MolNotator workflow, when you have merged, dereplicated molecular and ion data (output from mode_merger and dereplicator steps) and need to assemble the final molecular network representation connecting predicted.

holobiomicslab Skill

Use when when you have raw LC-MS/MS spectral data in .

holobiomicslab Skill

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

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

Use when you need to determine the full scope of hardware and methodological compatibility for a bioinformatics tool before designing an analytical workflow.

holobiomicslab Skill

Use when you need to supply candidate metabolite structures for mass spectrometry annotation when working within an integrative metabolomics data analysis workflow (such as MAGMa).

holobiomicslab Skill

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).

holobiomicslab Skill

Use when when deploying a Nextflow workflow across multiple execution environments (local machines, HPC clusters) where tool versions, dependencies, or OS configurations may differ. Choose this skill specifically when you need to process LC-HRMS .mzML or .

holobiomicslab Skill

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

tools-only Bundle

Orchestrates the full kernel patch review workflow across multiple agents

tools-only Bundle

Prepare for meetings by gathering attendee context and related topics

tools-only Bundle

Annotate Airflow tasks with data lineage using inlets and outlets. Use when the user wants to add lineage metadata to tasks, specify input/output datasets, or enable lineage tracking for operators without built-in OpenLineage extraction.

tools-only Bundle

Manually trigger plan-sync to update downstream task specs after implementation drift

tools-only Bundle

Master coordinator for the Evaluate-Loop workflow v3. Supports GOAL-DRIVEN entry, PARALLEL execution via worker agents, BOARD OF DIRECTORS deliberation, and message bus coordination. Dispatches specialized workers dynamically, monitors via message bus, aggregates results. Uses metadata.json v3 for parallel state tracking. Use when: '/go <goal>', '/conductor implement', 'start track', 'run the loop', 'orchestrate', 'automate track'.

tools-only Bundle

Simulate a 5-member expert board deliberation for major decisions. Use when evaluating plans, architecture choices, feature designs, or any decision requiring multi-perspective expert analysis. Triggers: 'board review', 'get expert opinions', 'board meeting', 'director evaluation', 'consensus review'.

tools-only Bundle

Synchronizes downstream task specs after implementation. Spawned by flow-next-work after each task completes. Do not invoke directly.

tools-only Bundle

Phase-level implementation workflow for builder agents. Handles reading phase files, finding references, invoking domain skills, implementing all steps, and running verification (tests + typecheck). Preloaded into builder agents via skills: field — not user-invocable.

tools-only Bundle

Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.