Heterogeneous biological network visualization system

Case study in context of medical image data

Erno Lindfors, Jussi Mattila, Peddinti Gopalacharyulu, Antti Pesonen, Jyrki Lötjönen, Matej Oresic

    Research output: Chapter in Book/Report/Conference proceedingChapter or book articleScientificpeer-review

    Abstract

    We have developed a system called megNet for integrating and visualizing heterogeneous biological data in order to enable modeling biological phenomena using a systems approach. Herein we describe megNet, including a recently developed user interface for visualizing biological networks in three dimensions and a web user interface for taking input parameters from the user, and an in-house text mining system that utilizes an existing knowledge base. We demonstrate the software with a case study in which we integrate lipidomics data acquired in-house with interaction data from external databases, and then find novel interactions that could possibly explain our previous associations between biological data and medical images. The flexibility of megNet assures that the tool can be applied in diverse applications, from target discovery in medical applications to metabolic engineering in industrial biotechnology.
    Original languageEnglish
    Title of host publicationAdvances in Systems Biology
    EditorsIgor I. Goryanin, Andrew B. Goryachev
    PublisherSpringer
    Chapter5
    Pages95-118
    ISBN (Electronic)978-1-4419-7210-1
    ISBN (Print)978-1-4419-7209-5
    DOIs
    Publication statusPublished - 2012
    MoE publication typeA3 Part of a book or another research book

    Fingerprint

    User interfaces
    Visualization
    Metabolic engineering
    Medical applications
    Biotechnology

    Cite this

    Lindfors, E., Mattila, J., Gopalacharyulu, P., Pesonen, A., Lötjönen, J., & Oresic, M. (2012). Heterogeneous biological network visualization system: Case study in context of medical image data. In I. I. Goryanin, & A. B. Goryachev (Eds.), Advances in Systems Biology (pp. 95-118). Springer. https://doi.org/10.1007/978-1-4419-7210-1_5
    Lindfors, Erno ; Mattila, Jussi ; Gopalacharyulu, Peddinti ; Pesonen, Antti ; Lötjönen, Jyrki ; Oresic, Matej. / Heterogeneous biological network visualization system : Case study in context of medical image data. Advances in Systems Biology. editor / Igor I. Goryanin ; Andrew B. Goryachev. Springer, 2012. pp. 95-118
    @inbook{053a71a77f244b36a86f442d3694c7a7,
    title = "Heterogeneous biological network visualization system: Case study in context of medical image data",
    abstract = "We have developed a system called megNet for integrating and visualizing heterogeneous biological data in order to enable modeling biological phenomena using a systems approach. Herein we describe megNet, including a recently developed user interface for visualizing biological networks in three dimensions and a web user interface for taking input parameters from the user, and an in-house text mining system that utilizes an existing knowledge base. We demonstrate the software with a case study in which we integrate lipidomics data acquired in-house with interaction data from external databases, and then find novel interactions that could possibly explain our previous associations between biological data and medical images. The flexibility of megNet assures that the tool can be applied in diverse applications, from target discovery in medical applications to metabolic engineering in industrial biotechnology.",
    author = "Erno Lindfors and Jussi Mattila and Peddinti Gopalacharyulu and Antti Pesonen and Jyrki L{\"o}tj{\"o}nen and Matej Oresic",
    year = "2012",
    doi = "10.1007/978-1-4419-7210-1_5",
    language = "English",
    isbn = "978-1-4419-7209-5",
    pages = "95--118",
    editor = "Goryanin, {Igor I. } and Goryachev, {Andrew B.}",
    booktitle = "Advances in Systems Biology",
    publisher = "Springer",
    address = "Germany",

    }

    Lindfors, E, Mattila, J, Gopalacharyulu, P, Pesonen, A, Lötjönen, J & Oresic, M 2012, Heterogeneous biological network visualization system: Case study in context of medical image data. in II Goryanin & AB Goryachev (eds), Advances in Systems Biology. Springer, pp. 95-118. https://doi.org/10.1007/978-1-4419-7210-1_5

    Heterogeneous biological network visualization system : Case study in context of medical image data. / Lindfors, Erno; Mattila, Jussi; Gopalacharyulu, Peddinti; Pesonen, Antti; Lötjönen, Jyrki; Oresic, Matej.

    Advances in Systems Biology. ed. / Igor I. Goryanin; Andrew B. Goryachev. Springer, 2012. p. 95-118.

    Research output: Chapter in Book/Report/Conference proceedingChapter or book articleScientificpeer-review

    TY - CHAP

    T1 - Heterogeneous biological network visualization system

    T2 - Case study in context of medical image data

    AU - Lindfors, Erno

    AU - Mattila, Jussi

    AU - Gopalacharyulu, Peddinti

    AU - Pesonen, Antti

    AU - Lötjönen, Jyrki

    AU - Oresic, Matej

    PY - 2012

    Y1 - 2012

    N2 - We have developed a system called megNet for integrating and visualizing heterogeneous biological data in order to enable modeling biological phenomena using a systems approach. Herein we describe megNet, including a recently developed user interface for visualizing biological networks in three dimensions and a web user interface for taking input parameters from the user, and an in-house text mining system that utilizes an existing knowledge base. We demonstrate the software with a case study in which we integrate lipidomics data acquired in-house with interaction data from external databases, and then find novel interactions that could possibly explain our previous associations between biological data and medical images. The flexibility of megNet assures that the tool can be applied in diverse applications, from target discovery in medical applications to metabolic engineering in industrial biotechnology.

    AB - We have developed a system called megNet for integrating and visualizing heterogeneous biological data in order to enable modeling biological phenomena using a systems approach. Herein we describe megNet, including a recently developed user interface for visualizing biological networks in three dimensions and a web user interface for taking input parameters from the user, and an in-house text mining system that utilizes an existing knowledge base. We demonstrate the software with a case study in which we integrate lipidomics data acquired in-house with interaction data from external databases, and then find novel interactions that could possibly explain our previous associations between biological data and medical images. The flexibility of megNet assures that the tool can be applied in diverse applications, from target discovery in medical applications to metabolic engineering in industrial biotechnology.

    U2 - 10.1007/978-1-4419-7210-1_5

    DO - 10.1007/978-1-4419-7210-1_5

    M3 - Chapter or book article

    SN - 978-1-4419-7209-5

    SP - 95

    EP - 118

    BT - Advances in Systems Biology

    A2 - Goryanin, Igor I.

    A2 - Goryachev, Andrew B.

    PB - Springer

    ER -

    Lindfors E, Mattila J, Gopalacharyulu P, Pesonen A, Lötjönen J, Oresic M. Heterogeneous biological network visualization system: Case study in context of medical image data. In Goryanin II, Goryachev AB, editors, Advances in Systems Biology. Springer. 2012. p. 95-118 https://doi.org/10.1007/978-1-4419-7210-1_5