Coding & Dev Tools

holobiomicslab Skill

Use when immediately after importing raw peak tables and metadata from MS preprocessing software (e.g., Progenesis, MS-DIAL, Bruker Metaboscape).

holobiomicslab Skill

Use when after data merging and cleanup (blank removal) and before univariate or multivariate statistical analysis, when your merged feature table (samples as columns, metabolite features as rows) contains samples processed in different MS batches or instrumental runs that may introduce systematic.

holobiomicslab Skill

Use when you have aligned fragment ion pairs from two MS/MS spectra (via maximum weight matching or other methods) and need to assign p-values or Z-scores to each matched pair to distinguish true biological/chemical relationships from random noise.

holobiomicslab Skill

Use when when you have a peak intensity matrix (rows = metabolite features, columns = samples) with corresponding compound annotations (peak ID → KEGG/ChEBI ID mapping), and you need to rank pathways or metabolite set groupings (KEGG pathways, Reactome pathways, GNPS Molecular Families, MS2LDA.

holobiomicslab Skill

Use when after correlation testing has validated putative parent–adduct ion pairs (e.g., via corrPairsMSI() on a massdiff object annotated with adductMatch results), use this skill to annotate and visualize the mass spectrum plot to confirm that identified pairs exhibit expected overlap—e.

holobiomicslab Skill

Use when when you have raw or processed FT-ICR MS peak-abundance .

holobiomicslab Skill

Use when you have centroided mzML LC–MS data, a curated list of target compounds (with theoretical m/z, expected retention time, and polarity), and you need to confirm target presence and extract quantitative metrics (area under curve, max intensity, signal-to-noise ratio, peak correlation, point.

holobiomicslab Skill

Use when you have centroided LC- or GC-HRMS data (in mzML format, ideally from data-dependent acquisition) and need to identify potential PFAS candidates from a large feature list.

holobiomicslab Skill

Use when when correcting LC-MS fractional abundances of measured isotopologues (FAM) from isotope labeling experiments where instrument resolution (e.

holobiomicslab Skill

Use when you have a filtered MS-DIAL peak list (post-generic filtering) containing m/z, retention time, and peak intensity metrics, and you need to group LC-MS features into clusters to reduce redundancy before parental signal extraction.

holobiomicslab Skill

Use when when you have a training set of MS2 spectra with known chemical structures (e.

holobiomicslab Skill

Use when you have a chemical structure (as SMILES string or identifier) and need to discover matching records across specialized natural product databases.

holobiomicslab Skill

Use when you have paired microbiome and metabolomic abundance tables (samples × features) with relative abundance or raw count values, and you are preparing data for downstream regression or neural network modeling of microbe-metabolite relationships.

holobiomicslab Skill

Use when when you have extracted ion chromatograms (XICs), ion mobilograms (IMs), or mass spectra from diaPASEF or other DIA workflows and need to visualize them interactively to inspect peak boundaries, compare MS1 vs MS2 traces, validate feature identifications, or communicate results.

holobiomicslab Skill

Use when you are preparing to apply Probability Product Kernel–based scoring to MS2 spectra for genomic–metabolomic linking, and you need to establish a reference set of ion peaks that represent robust spectral diversity without overfitting to any single study.

tools-only Bundle

Strategic objectives for the upcoming quarter

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Scan ScreenPipe data for uncommitted asks and promises, match to projects/people, and offer to create tasks.

tools-only Bundle

John Carmack-level implementation review via RepoPrompt or Codex. Use when reviewing code changes, PRs, or implementations. Triggers on /flow-next:impl-review.

tools-only Bundle

Epic completion review - verifies all epic tasks implement spec requirements. Triggers on /flow-next:epic-review.

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Migrates Honcho Python SDK code from v1.6.0 to v2.0.0. Use when upgrading honcho package, fixing breaking changes after upgrade, or when errors mention AsyncHoncho, observations, Representation class, .core property, or get_config methods.

tools-only Bundle

Migrates Honcho TypeScript SDK code from v1.6.0 to v2.0.0. Use when upgrading @honcho-ai/sdk, fixing breaking changes after upgrade, or when errors mention removed APIs like .core, getConfig, observations, or snake_case properties.

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Find CCSPlayer_ItemServices_GiveNamedItem

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Mandatory verification steps for all code reviews to reduce false positives. Load this skill before reporting ANY code review findings.

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Mandatory verification steps for all code reviews to reduce false positives. Load this skill before reporting ANY code review findings.

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Forces hypothesis-driven scientific reasoning for complex problems. Use when debugging, investigating root causes, solving problems with unknowns, dealing with repeated errors, designing architecture, or performing complex refactoring. Activate whenever the situation involves uncertainty, unknowns, or failed attempts — not for trivial or well-defined tasks.

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APPS evaluates AI agents on 10,000 coding problems collected from open-access programming platforms, spanning introductory, interview, and competition difficulty levels.

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MATH benchmark for mcpbr - 12,500 competition mathematics problems from AMC, AIME, and other competitions across 7 subjects and 5 difficulty levels.

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Make map animations with Mapbox

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Checks lore.kernel.org for prior discussion and unaddressed review comments

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Real-time weather forecast with 7-14 day predictions, temperature,...

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Genera la newsletter semanal de DevExpert recopilando contenido de X, YouTube, Postiz y bookmarks. Crea borrador en Listmonk para revisión.

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创建语音转文本请求

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Start, stop, pause, or mark moments in screen recordings with organized file...

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Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.

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Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. Use when generating figures for repertoire comparisons, clonal dynamics, or V(D)J gene usage.

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Discovers periodic signals of unknown period in time-series omics data using Lomb-Scargle periodograms (scipy), autocorrelation, and wavelet time-frequency decomposition (pywt). Identifies dominant frequencies, handles irregularly sampled data, and detects transient periodicity. Use when searching for periodic patterns of unknown period length, analyzing cell cycle oscillations, or processing unevenly spaced time-series. Not for testing known 24-hour rhythms (see temporal-genomics/circadian-rhythms).