BioBridge

Modelling and simulation tools for clinicians — Systems Medicine approach

BioBridge was one of the first Biomax projects initiating a Systems Medicine approach to patient care. Systems Medicine is a holistic approach that incorporates evidence-based medicine with the interactions between all components of health, disease, human genetics, environment and behavior.

At the time, efforts to implement information technology (computer analysis) to solve clinical problems used very limited data sets, despite the vast availability of data from various life science disciplines. By integrating genomic, proteomic and metabolomic data, Biomax demonstrated that such knowledge can be used to address practical clinical applications as well as wider healthcare and related challenges.

The BioBridge consortium brought together SMEs with complementary skills in the domains of semantic interoperability, heterogeneous data integration and simulation technologies to develop innovative tools to facilitate the interplay between omics data and clinical information.

Together with academic teams, they facilitated the translational analysis of a test case: nitroso-redox imbalance of the cardiovascular system. Nitroso-redox disequilibrium causes O2 transport – O2 utilization mismatching at the tissue level in highly prevalent chronic disorders (chronic health failure, chronic obstructive pulmonary disease and diabetes). It has been identified as a common pathway leading to systemic effects associated with poor prognosis and high use of healthcare resources. The produced simulation tools offer a new technique for clinicians to identify appropriate biomarkers for non-invasive monitoring.

Synergies between SMEs and academic teams as well as product quality assurance were assured through the generation of experimental data for model refinement and validation.

The BioBridge project focused on the application of simulation techniques on top of multilevel data to create models for understanding how molecular mechanisms are dynamically related to complex diseases at the systemic level.

By exploring and identifying gaps of information, the project developed standards to transfer and filter data from existing molecular biology databases as well as data generated from new high-throughput experiments such as microarray, in vivo metabolic profiling and proteomics into models of complex diseases. From the beginning, BioBridge members worked directly with SMEs to create protocols for commercial use that standardize the analysis of relevant aspects of disease.

  • Knowledge management for Systems Biology: a general and visually driven framework applied to translational medicine
    Maier D, Kalus W, Wolff M, Kalko S G, Roca J, et al. BMC Systems Biology 5:38 (2011)
    Abstract | Full text
  • Aus der Forschung an das Krankenbett (From research to bedside)
    Maier D (2010) Systembiologie.de Vol 02: 72-75
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  • Creating a Bridge between Modelica and the Systems Biology Community
    Brugard J, Hedberg D, Cascante M, Cedersund G, Gomez-Garrido A, Maier D, Nyman E, Selivanov V and Stralfors P (2009) Proceedings 7th Modelica Conference Como, Italy
    Abstract | Full text
  • Making use of integrated data — Knowledge management tutorial
    Maier D (2009) Talk at the Barcelona School on Biomedical Informatics 2009 in Barcelona, Spain
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  • Integration of transcriptomics data into systems biology modeling in the BioBridge portal
    Gómez–Garrido A, Márquez S, Hernández M, Selivanov V, Cascante M, Villà–Freixa J and Kalko S (2008) in Schriftenreihe Informatik 26. BIRD08 2nd International Conference on Bioinformatics Research and Development. pp. 75-81
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