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IMC
ZIH
TU Dresden
Dept. for Innovative
Methods of Computing
 

Morpheus

Morpheus is a free and open source modeling and simulation environment for the study of multi-scale and multicellular systems. For full details and software download see the Morpheus homepage https://morpheus.gitlab.io.

Key features are:

  • multi-scale simulation: simulate multi-scale multicellular systems coupling ODEs, PDEs and cellular Potts models in 2D or 3D.
  • declarative modelling: construct models by describing them in a GUI instead of programming code.
  • MorpheusML language: easily share model description files with collaborators and copy/paste model parts.
  • SBML support: import SBML models (e.g. from BioModels database) into selectable cell types of a multicellular model, over 80% of SBML L3V2 and package comp are supported, validated.
  • workflow: tools for data export, visualization and parameter scans.
  • automatic scheduling: efficient simulation based on computed model dependency graph and adaptive solvers.
  • extensible: customize and extend features by developing your own plugins.
  • open-source: source code at gitlab under BSD license.
  • installers: are provided for Linux, Windows and macOS such that you do not need to compile and are set within minutes.
  • easy to get started: free online courses, context-sensitive in-app documentation, rich in-app examples menu.
  • parameter estimation: integrated in the FitMultiCell toolbox.
  • reproducibility: Morpheus and its declarative modeling language MorpheusML serve as technology carrier for the development of modeling standards like MultiCellML.

Morpheus GUI

Graphical User Interface (GUI) of Morpheus (from: Starruß et al., Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology, Bioinformatics 30, 1331-1332, 2014 [DOI]).

Cooperations:

Prof. Jan Hasenauer (Universität Bonn, Germany)
Dr. Frederik Graw (BioQuant, University of Heidelberg, Germany)
PD Dr. Wolfgang Müller, Dr. Martin Golebiewski (Heidelberg Institute for Theoretical Studies, Germany)

Key Publications:

  • J. Starruß, W. de Back, L. Brusch, A. Deutsch
    Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
    Bioinformatics, 30, 1331-1332, 2014 [DOI]

  • K. Meyer, H. Morales-Navarrete, S. Seifert, M. Wilsch-Braeuninger, U. Dahmen, E. M. Tanaka, L. Brusch, Y. Kalaidzidis, M. Zerial
    Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration
    Molecular Systems Biology 16 (2), e8985, 2020 [DOI]

  • E. Kolbe, S. Aleithe, C. Rennert, L. Spormann, F. Ott, D. Meierhofer, R. Gajowski, C. Stöpel, S. Hoehme, M. Kücken, L. Brusch, M. Seifert, W. von Schoenfels, C. Schafmayer, M. Brosch, U. Hofmann, G. Damm, D. Seehofer, J. Hampe, R. Gebhardt, M. Matz-Soja
    Mutual Zonated Interactions of Wnt and Hh Signaling Are Orchestrating the Metabolism of the Adult Liver in Mice and Human
    Cell Reports 29, 4553–4567.e7, 2019 [DOI]

  • H. T.-K. Vu, S. Mansour, M. Kuecken, C. Blasse, C. Basquin, J. Azimzadeh, E. W. Myers, L. Brusch, J. C. Rink
    Dynamic Polarization of the Multiciliated Planarian Epidermis between Body Plan Landmarks
    Developmental Cell 51(4), 526-542.e6, 2019 [DOI]

  • W. de Back, R. Zimm, L. Brusch
    Transdifferentiation of pancreatic cells by loss of contact-mediated signaling
    BMC Syst. Biol., 7, 77, 2013 [DOI]

  • W. de Back, J.X. Zhou, L. Brusch
    On the role of lateral stabilization during early patterning in the pancreas
    J. R. Soc. Interface, 10, 20120766, 2012 [DOI]

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