Productivity

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

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).

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

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.

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 starting any task with the ASB Metabolomics skill collection — read this meta-skill first. It explains good practice (search -> apply -> ground), enforces the license-tier acknowledgment for non-open tools, then hands off to the _router skill for actual skill selection.

holobiomicslab Skill

Use when you have received raw CE-MS or LC-MS output files in vendor-specific formats from a mass spectrometry instrument and need to process them through an untargeted metabolomics workflow (e.g., AriumMS) that requires standardized, interoperable file formats.

holobiomicslab Skill

Use when you have raw mzML files from a mass spectrometry instrument and need to begin a preprocessing workflow in xcms. This is the essential first step before any peak detection (centWave, MSWParam) or feature grouping can occur.

holobiomicslab Skill

Use when when beginning a metabolomics annotation workflow with raw MS2 spectral data in .mzML format. This step is necessary when you have vendor-converted or standard .

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 when you need to retrieve mass spectrometry spectrum data from a metabolomics repository but only have a USI string (e.g., 'mzspec:GNPS:TASK-c95481f0c53d42e78a61bf899e9f9adb-spectra/specs_ms.mgf:scan:1943' or 'mzspec:MASSBANK::accession:SM858102').

holobiomicslab Skill

Use when a user has a whole metabolomics analysis GOAL (e.g. "annotate my untargeted LC-MS/MS data", "find biomarkers", "where else has this molecule been seen") rather than a single step — select the right end-to-end composite workflow super-skill, then run its stages, grounding each against its source papers.

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 you have a GitHub repository with published CI workflow badges (e.g., unit test or package test badges in the README) and need to independently verify that the workflows execute successfully, reproduce the pass/fail status, and collect structured test results.

holobiomicslab Skill

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

holobiomicslab Skill

Use when you have developed an R-based workflow (e.g., data processing, peak detection, quality review) that is complex enough to warrant interactive parameter tuning and visual feedback, and you need to distribute it to collaborators or end-users who prefer a graphical interface over scripting.

holobiomicslab Skill

Use when you have acquired imaging mass spectrometry (IMS) data stored in imzML format (accompanied by an .ibd ion binary data file) and need to load it into a Python-based spatial metabolomics workflow.

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 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.

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

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.

holobiomicslab Skill

Use when when you have a USI string (e.g., 'mzspec:GNPS:TASK-abc123:scan:1943') and need to retrieve the underlying spectrum data from its native repository without knowing a priori which backend stores it.

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 when you have trained multiple machine learning regressors on the same prediction task (e.

holobiomicslab Skill

Use when you have built a reusable workflow function (e.g., a Shiny app launcher, automated analysis routine) within an R package and need to make it available to package users.

holobiomicslab Skill

Use when after invoking a Nextflow workflow via `make run` or equivalent command, to confirm the workflow executed without errors and generated expected output files.

holobiomicslab Skill

Use when you have a target molecule (e.g., acetaminophen, a drug candidate, or a xenobiotic) whose structure you need to encode for metabolite prediction, reaction rule matching, or other structure-based cheminformatics workflow.

holobiomicslab Skill

Use when you have a library of natural product compounds (encoded as SMILES strings) and wish to rank them by predicted bioactivity or fitness for a downstream task.

holobiomicslab Skill

Use when you have received a peak/feature table from an unknown or variable upstream peak-picking tool and need to ingest it into LipidMatch or a similar unified workflow. The input file format, column naming, or metadata structure is tool-specific (e.

holobiomicslab Skill

Use when you have downloaded a GNPS molecular networking job archive and need to extract its contents (spectra.mgf, molecular_families.tsv, annotations.tsv, file_mappings) but do not know which GNPS workflow version produced it, preventing correct file naming and downstream computational analysis.