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 (), Walter de Back (), Lutz Brusch (), Cedric Unverricht (), Robert Müller () and Diego Jahn () at the Center for Information Services and High Performance Computing, TU Dresden, Germany.
Funding
Morpheus development is supported by
- DFG Research Software Sustainability programme (project 391070520)
- BMBF e:Med Systems Medicine network
- BMBF Computational Life Sciences
Recent Posts
Events
Meet us and Morpheus at these talks, workshops and courses
Download
Get Morpheus package or build from source
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
Take a first glance at Morpheus. We will take a look at the user interface and run some example models.
SBML import
Morpheus supports almost all of the SBML core standard. And has been validated on the extensive SBML test suite.
Multiscale models
How to create a minimal multiscale model combining ODE, PDE and CPM models.
From PDE to tissue
Convert a 1D PDE model into 2D and 3D multiscale tissue models.
Drawing cell genealogies
How to export the cell division history and using external analysis tools.
Main Publication
Please cite this reference when you used Morpheus in your work and to support the further development of Morpheus.
J. Starruß, W. de Back, L. Brusch and A. Deutsch. Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology. Bioinformatics, 30 (9): 1331-1332, 2014.
User Map
Morpheus Users Worldwide
Have a look at the places where Morpheus is cited.
Selected Publications
For a complete list of more than 240 articles citing Morpheus, click here.
Support
Docs, FAQ, Help and Contact
In-app Docs
Morpheus has documentation right within the graphical user interface:
- 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 |
|
| Wiki |
|
| User Forum |
|
| Issue Tracker |
|
Twitter@morpheus_lab |
|