denbi toolkit

MdOA Toolbox – Multi-Dimensional-Omics tools

The MdOA toolbox is a collection of browser-based applications that support end-to-end analysis and interpretation of omics datasets—from mass-spectrometry metaproteomics to feature selection for biomarker panels and interpretable clinical risk modeling. All tools run in the browser (supported by de.NBI Cloud); no local installation is required.

Key Features

  • Web-first access: Use the tools directly in your browser; no setup on local machines.

  • Purpose-built apps: Each app tackles a concrete task (MS/MS metaproteomics analysis, molecule/feature panel selection, interpretable sepsis risk prediction).

  • Transparent & interpretable outputs: Interactive visuals (PCA/cluster plots, model metrics, SHAP explanations) to aid result interpretation.

  • Hosted on German research infrastructure with clear ownership/contact

Tools

  • MPA Cloud – MetaProteomeAnalyzer Cloud – Web version of the MetaProteomeAnalyzer for metaproteomics/proteomics MS/MS data processing and visualization. Ideal for taxonomic/functional insights from complex communities. (Funded by de.NBI)
  • Prophane - Provides a tailored and fully automated workflow for metaproteomics analysis with special focus on metaprotein taxonomic and functional annotation. For the annotations you can choose between different databases and algorithm. (Funded by DFG)
  • OMEx – Omics Molecule Extractor – Open-source web app for selecting molecules and multi-marker panels from large omics tables using a stepwise, ML-based feature-selection workflow; includes interactive plots and performance metrics. (Funded by Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V.)
  • SBC-SHAP – A lightweight clinical utility app for real-time sepsis risk prediction using only age, sex, and complete blood count (CBC); provides SHAP-based explanations. (Funded by OVGU Magdeburg)

Applications

    • Metaproteomics & proteomics: Process and explore high-resolution MS/MS datasets; derive community composition and functional signals (MPA Cloud).
    • Biomarker discovery & panel building: Identify reproducible multi-marker panels for classification tasks in omics studies (OMEx).
    • Interpretable clinical modeling (research use): Rapid, explainable risk scoring from routine lab values to support methodological exploration and education (SBC-SHAP).

Target Audience

  • Researchers in microbiome/metaproteomics and translational omics needing browser-based analysis/selection tools.
  • Method developers & educators demonstrating interpretable ML on clinical-style lab data (with clear non-diagnostic disclaimers).
  • Training & workshops within the de.NBI ecosystem (e.g., metaproteomics courses highlighting MPA Cloud). The Applied Metaproteomics Workshop takes places yearly in Magdeburg, for further information take a look at our training course calendar.

For more information, please visit the official website:

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Funding: Development and maintenance partially funded by de.NBI