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# Morpheus
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Morpheus is a modeling and simulation environment for the study of multiscale and multicellular systems.
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For further information look at https://morpheus.gitlab.io .
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Morpheus has been developed by Jörn Starruß and Walter de Back at the Center for High Performance Computing at the TU Dresden, Germany as well as other [contributors](#contributors).
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<img src="https://gitlab.com/morpheus.lab/morpheus/uploads/3a7c4af0d6f9507f6143a67720d629e1/Morpheus.png" width="60%"/>

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# Looking for latest stable release?
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If you are looking for the latest stable release of Morpheus (v2), and do not necessarily need the source code, please download the precompiled packages for MS Windows, Mac OSX and Linux are available on the [download page](https://morpheus.gitlab.io/#download). 
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# Resources
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Morpheus is actively supported and provides help for users and developers:

- [User forum](https://groups.google.com/forum/#!forum/morpheus-users): Questions and answers on modeling with Morpheus
- [Issue tracker](https://gitlab.com/morpheus.lab/morpheus/issues): Bug reports and feature requests
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Documentation for users as well as plugin developers here found on the [gitlab wiki](https://gitlab.com/morpheus.lab/morpheus/wikis/home) and on the on the [old wiki](https://imc.zih.tu-dresden.de/wiki/morpheus):
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- [User manual](https://gitlab.com/morpheus.lab/morpheus/wikis/user-manual) (under construction)
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- [Plugin dev guide](https://gitlab.com/morpheus.lab/morpheus/wikis/dev-guide) (under construction)
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These docs may not reflect the latest state and are currently being updated.

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To find out more about Morpheus, please take a look at the home page:

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- [Homepage](https://morpheus.gitlab.io): Blog, events and downloads.
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# Building
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build tools required:
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  - g++ (>= 5.0)
  - cmake (>= 3.1)
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  - cmake-curses-gui (for ccmake, optional)
  - xsltproc
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  - xmllint (optional)
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  - doxygen
  - git

Libraries required (debian package notation):
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  - zlib1g-dev libtiff-dev graphviz-dev libboost-dev
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  - qttools5-dev libqt5sql5-sqlite libqt5svg5-dev (qtwebengine5-dev | libqt5webkit5-dev)
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  - optional: libsbml5-dev
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Runtime dependencies:
  - gnuplot

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```
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  git clone https://gitlab.com/morpheus.lab/morpheus.git morpheus
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  cd morpheus
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  mkdir build
  cd build
  cmake ..
  make && sudo make install
```

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## Building on Debian based systems

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Updates    
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To install all dependencies on Ubuntu 16.04 and 18.04 run:
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```  
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sudo apt-get install g++ cmake cmake-curses-gui xsltproc libxml2-utils doxygen git zlib1g-dev libboost-dev libtiff5-dev libsbml5-dev qttools5-dev libqt5svg5-dev qtwebengine5-dev libqt5sql5-sqlite gnuplot  
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```

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To install all dependencies on Ubuntu 20.04 run:
```  
sudo apt-get install g++ cmake cmake-curses-gui xsltproc libxml2-utils doxygen git zlib1g-dev libboost-dev libtiff5-dev libsbml5-dev qttools5-dev libqt5svg5-dev qtwebengine5-dev libqt5sql5-sqlite libsbml5-dev gnuplot  
```

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## Building/Installing on other systems
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On other distributions package names vary slightly. Consult the respective repositories to find corresponding package names that provide the libraries and their headers.
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# How to cite Morpheus
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Please use this reference when citing 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. https://doi.org/10.1093/bioinformatics/btt772

Additionaly, use the Morpheus [Research Resource Identifier (RRID)](https://scicrunch.org/resources) ([SCR_014975](https://scicrunch.org/browse/resources/SCR_014975)) in your method section.
Include the version number or commit hash for reproducability. Valid examples are:

> Morpheus, RRID:SCR_014975  
> Morpheus, v1.9.2, RRID:SCR_014975  
> Morpheus, e45739bc, RRID:SCR_014975

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# Contributors

- Jörn Starruß, TU Dresden, Germany
- Walter de Back, TU Dresden, Germany
- Fabian Rost, MPI PKS, Dresden, Germany
- Gerhard Burger, Leiden University, the Netherlands
- Margriet Palm, Leiden University, the Netherlands
- Emanuel Cura Costa, IFLySiB, La Plata, Argentina
- Osvaldo Chara, IFLySiB, La Plata, Argentina