Integrations & APIs

holobiomicslab Skill

Use when when you have a GNPS molecular networking job archive (downloaded as a .zip or compressed archive) and need to prepare metabolomics spectra and molecular family data for NPLinker integration.

holobiomicslab Skill

Use when you have MS data in a new format or storage system (e.g., a custom database, HDF5 file, or proprietary raw file) and need to make it accessible to Spectra-based analysis workflows without forking the Spectra package itself.

holobiomicslab Skill

Use when when you have mwTab-formatted Mass Spectrometry or Nuclear Magnetic Resonance experimental data from the Metabolomics Workbench that must be converted to JSON for API integration, data sharing across systems, or validation against a defined JSON schema.

holobiomicslab Skill

Use when when annotating .msp files with metadata from multiple external web services and you need to monitor which services are slow or unreliable.

holobiomicslab Skill

Use when you have multiple mzML or HDF5 feature tables from the same study acquired on the same or similar instruments and need to align feature coordinates across samples to correct for systematic shifts in mass-to-charge, drift time, or retention time caused by instrumental drift, column aging.

holobiomicslab Skill

Use when when you need to construct a POST endpoint that ingests raw spectral data files from multiple vendor formats (jcamp, RAW, mzML) and must standardize them for downstream processing.

holobiomicslab Skill

Use when when extending an existing neural network class (e.g., SiameseModel) that lacks user-configurable regularization, and you need to prevent overfitting on moderate-sized training datasets (e.

holobiomicslab Skill

Use when after loading centroided .mzML LC–MS runs and before executing full peak detection and integration.

holobiomicslab Skill

Use when when building a multi-backend visualization library where users specify both a plot type (spectrum, chromatogram, peakmap) and a backend (matplotlib for static output, Bokeh or Plotly for interactive), and you need to avoid code duplication across backends while keeping the user-facing API.

holobiomicslab Skill

Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or file-level headers programmatically—e.

holobiomicslab Skill

Use when after converting mass-spectrometry data from an existing format (mzML, mzXML, or vendor-specific formats) into mzPeak using command-line tools or API calls.

holobiomicslab Skill

Use when after MS2LDA has inferred a motifset and you need to visualize and export the relationships between discovered Mass2Motifs for post-processing exploration, comparative annotation, or integration with external tools. Use this skill when you have motifset.json or motifset_optimized.

holobiomicslab Skill

Use when after batch effect removal and sample integration, when you have a normalized feature-by-sample abundance matrix (finalData) with corresponding sample group labels (finalLabel), and need to identify which metabolites discriminate between biological conditions or phenotypes for focused.

holobiomicslab Skill

Use when you have generated a GNPS molecular network (classical or feature-based workflow) and possess chemical class annotations (from GNPS library matching, ClassyFire, or other structural classifiers) that you wish to propagate onto network nodes and edges to enable chemical family-level.

holobiomicslab Skill

Use when after running tardisPeaks() in screening mode or peak detection mode, when you need to visually confirm that target compounds are visible in the expected m/z and retention time windows, verify that peak integration boundaries are correct, diagnose whether sawtooth artefacts are present.

holobiomicslab Skill

Use when you have R Spectra objects and need to apply Python-only MS algorithms (e.

holobiomicslab Skill

Use when after Blueshift or Gravity processing has produced a feature abundance table with annotations, but before final reporting or integration with sample/injection metadata.

holobiomicslab Skill

Use when when you have NMR peak assignments (1H and 13C chemical shift values) and need to submit them to the /api/smart3/search endpoint for automated structure classification. Use this skill before making API calls to ensure peak data conforms to the expected JSON schema.

holobiomicslab Skill

Use when when you have Thermo Fisher Scientific Orbitrap .raw files (e.g., from Q Exactive HF instruments) and need to extract spectral, chromatographic, or metadata directly into R for downstream statistical analysis, benchmarking, or integration with Bioconductor workflows.

holobiomicslab Skill

Use when you have completed batch spectral searches against multiple domain-specific MASST tools (via Fast Search API or individual domain searches) and need to combine and visualize the aggregated match results in a format compatible with metadataMASST web interface or downstream analysis.

holobiomicslab Skill

Use when after statistical analysis (e.g., MB-PLS with permutation testing) has identified a subset of significant LC-MS features (p < 0.05 or similar threshold) that require structural interpretation.

holobiomicslab Skill

Use when when you have raw LC-HRMS metabolomics data in .mzML or .

holobiomicslab Skill

Use when you have measured intracellular metabolite concentrations (e.g., via LC–MS/MS) across multiple cell lines or samples and want to predict which metabolic reactions are substrate-limited versus transcriptionally regulated.

holobiomicslab Skill

Use when when a tool like TARDIS extends its API to accept multiple input types (e.g., both file paths and MsExperiment objects), and you need to confirm that screening-mode diagnostic outputs (e.g., EIC plots, peak detection metrics) are identical regardless of which invocation pattern is used.

holobiomicslab Skill

Use when when you have LC/MS feature data (m/z, retention time, intensity) that must be annotated against a metabolic database and you have access to (or can construct) knowledge about biochemical reaction networks, expected isotope patterns, and instrument-specific adduct formation rules.

tools-only Bundle

Orchestrates a full morning sweep of pending items (email, tasks, Slack, WhatsApp, X). Use when the user asks for a sweep, morning routine, inbox sweep, or all pending items.

tools-only Bundle

Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts. Use when filtering compounds for drug-likeness or prioritizing leads by predicted safety.

tools-only Bundle

Build declarative AI Services with LangChain4j using interface-based patterns, annotations, memory management, tools integration, and advanced application patterns. Use when implementing type-safe AI-powered features with minimal boilerplate code in Java applications.

tools-only Bundle

Kalshi prediction markets — events, series, markets, trades, and candlestick data. Public API, no auth required for reads. US-regulated exchange (CFTC). Covers soccer, basketball, baseball, tennis, NFL, hockey event contracts. Use when: user asks about Kalshi-specific markets, event contracts, CFTC-regulated prediction markets, or candlestick/OHLC price history on sports outcomes. Don't use when: user asks about actual match results, scores, or statistics — use the sport-specific skill: football-data (soccer), nfl-data (NFL), nba-data (NBA), wnba-data (WNBA), nhl-data (NHL), mlb-data (MLB), tennis-data (tennis), golf-data (golf), cfb-data (college football), cbb-data (college basketball), or fastf1 (F1). Don't use for general "who will win" questions unless Kalshi is specifically mentioned — try polymarket first (broader sports coverage). Don't use for news — use sports-news instead.

tools-only Bundle

PGA Tour, LPGA, and DP World Tour golf data via ESPN public endpoints — tournament leaderboards, scorecards, season schedules, golfer profiles/overviews, and news. Zero config, no API keys. Use when: user asks about golf scores, tournament leaderboards, scorecards, PGA Tour schedule, golfer profiles, golfer season stats, LPGA results, or golf news. Don't use when: user asks about other sports — use football-data (soccer), nfl-data (NFL), nba-data (NBA), wnba-data (WNBA), nhl-data (NHL), mlb-data (MLB), tennis-data (tennis), cfb-data (college football), cbb-data (college basketball), or fastf1 (F1). For betting odds use polymarket or kalshi. For news use sports-news.

tools-only Bundle

Query protein-protein and gene interaction databases including STRING, BioGRID, and IntAct via their REST APIs and Python clients. Retrieve interaction networks, confidence scores, and functional enrichment. Use when building protein interaction networks, contextualizing gene lists with known interactions, or retrieving pathway-level interaction data.

tools-only Bundle

Enable Obsidian integration and migrate existing vault to wiki links

tools-only Bundle

Create structured build plans from feature requests or Flow IDs. Use when planning features or designing implementation. Triggers on /flow-next:plan with text descriptions or Flow IDs (fn-1-add-oauth, fn-1-add-oauth.2, or legacy fn-1, fn-1.2, fn-1-xxx, fn-1-xxx.2).

tools-only Bundle

MarkItDown API Reference

tools-only Bundle

Football (soccer) data across 13 leagues — standings, schedules, match stats, xG, transfers, player profiles. Zero config, no API keys. Covers Premier League, La Liga, Bundesliga, Serie A, Ligue 1, MLS, Champions League, World Cup, Championship, Eredivisie, Primeira Liga, Serie A Brazil, European Championship. Use when: user asks about football/soccer standings, fixtures, match stats, xG, lineups, player values, transfers, injury news, league tables, daily fixtures, or player profiles. Don't use when: user asks about American football (NFL), basketball (NBA), baseball, or any non-soccer sport. Don't use for live/real-time scores — data updates post-match. Don't use get_season_leaders or get_missing_players for non-Premier League leagues (they return empty). Don't use get_event_xg for leagues outside the top 5 (EPL, La Liga, Bundesliga, Serie A, Ligue 1).

tools-only Bundle

Provides repeatable CRUD workflows for Spring Boot 3 services with Spring Data JPA and feature-focused architecture. Use when modeling aggregates, repositories, controllers, and DTOs for REST APIs.