Morpheus

Morpheus

Multicellular Simulation

TU Dresden

Morpheus

A modeling and simulation environment for the study of multi-scale and multicellular systems.

Some of its 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.
  • public model repository: share your models with citable persistent identifier and authorship credit.
  • data integration: FitMultiCell toolbox for efficient parameter estimation from experimental data.
  • easy to get started: free online courses, context-sensitive in-app documentation, rich in-app examples menu, interactive model graph display.

Morpheus is developed by Jörn Starruß (repo), Walter de Back (repo) and Lutz Brusch at the Center for Information Services and High Performance Computing, TU Dresden, Germany.

Screenshot of two overlapping Morpheus windows.
Morpheus' modeling (top) and simulation (bottom) interfaces.

Funding

Morpheus development is supported by

  • DFG Research Software Sustainability programme (project 391070520)
  • BMBF e:Med Systems Medicine network
  • BMBF Computational Life Sciences

Events

Meet us and Morpheus at these talks, workshops and courses

Harmony 2023
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community …
ICSB 2022
Summit on global systems life science challenges in the post-pandemic world.

Examples

…of what you can do with Morpheus

Explore a huge variety of Morpheus models, including contributed and published models, in our extensive model repository.

Ordinary differential equations
Reaction-diffusion systems
Cellular Potts models
Multi-scale models

Courses

We’ve developed a set of courses that take you from installation to expert topics in small steps, fully illustrated with screenshots, stuffed with tips & tricks and further exercises.

Getting Started

Getting Started

Take a first glance at Morpheus. We will take a look at the user interface and run some example models.

SBML import

SBML import

Morpheus supports almost all of the SBML core standard. And has been validated on the extensive SBML test suite.

Multiscale models

Multiscale models

How to create a minimal multiscale model combining ODE, PDE and CPM models.

From PDE to tissue

From PDE to tissue

Convert a 1D PDE model into 2D and 3D multiscale tissue models.

Drawing cell genealogies

Drawing cell genealogies

How to export the cell division history and using external analysis tools.

User Map

Morpheus Users Worldwide

Have a look at the places where Morpheus is cited.

Selected Publications

For a complete list of more than 220 articles citing Morpheus, click here.

Support

Docs, FAQ, Help and Contact

In-app Docs

Morpheus has documentation right within the graphical user interface:

Screenshot of the Morpheus in-app documentation window
In-app documentation
  • plugin docs: describes function and attributes of plugin
  • supports: $\LaTeX$ math and <XML/> code usage examples
  • context-sensitive: shows the docs for the currently selected plugin
  • browsing: browse through all docs
  • dockable: drag panel to make into a window

Getting More Help

Source Type of support
FAQ
  • In case you have a question, the answer may already be in the Frequently asked questions. So check here first.
Wiki
  • User manual
  • Developer’s guide
User Forum
  • Modeling questions
  • User interface issues
Issue Tracker
  • Bug reports
  • Feature requests
  • Support for (plugin) developers
Twitter
@morpheus_lab
  • Urgent modeling issues
  • Announcements