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documentation:faq [11:52 01.10.2013]
Walter [General]
documentation:faq [18:52 16.11.2017] (current)
Jörn Starruß [General]
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 ++++ More details | ++++ More details |
-** How it does what it does ** 
  
-See the documentation in the [[documentation:​tech_specs|tech specs]] for details on numerical methods and methods of model integration.+** More information ** 
 + 
 +For more information,​ refer to the [[documentation:​manual|user manual]].
  
 ** What it cannot do ** ** What it cannot do **
  
-See the [[documentation:​limitations|list of limitations]].+See the necessarily incomplete ​[[documentation:​limitations|list of limitations]].
  
 ++++ ++++
  
-++++ ''​morpheus''​ and ''​morpheus-gui''​ executables ​|+++++ Software structure ​|
  
-Morpheus consists of: +Morpheus ​is a self-contained application. Internally, it consists of two stand-alone executables
-  * Simulator called ​''​morpheus''​ +  * ''​morpheus''​: the simulator ​ 
-  * Graphical user interface (GUI) called ​''​morpheus-gui''​+  * ''​morpheus-gui''​: the graphical user interface (GUI) 
  
-Internally, ​these stand-alone applications ​are linked by the exchange of XML and XSD files:+The communication between ​these stand-alone applications ​is through ​XML and XSD files:
   * The GUI reads an XML Schema description (XSD) file that specifies rules for valid XML models.   * The GUI reads an XML Schema description (XSD) file that specifies rules for valid XML models.
   * The GUI start a simulation job by executing ''​morpheus''​ with a generated XML model as argument.   * The GUI start a simulation job by executing ''​morpheus''​ with a generated XML model as argument.
  
-The simulator ''​morpheus''​ can also be used as stand-alone program from the command line. +Note that both executable can also be used as stand-alone programs. ​The simulator ''​morpheus''​ can also be used as stand-alone program from the command line. And ''​morpheus-gui''​ may be used to control remote computing resources.
  
 [{{ :​morpheus-sim.png?​direct&​400 | ''​morpheus''​ simulator from the command line interface. }}] [{{ :​morpheus-sim.png?​direct&​400 | ''​morpheus''​ simulator from the command line interface. }}]
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 ** Source ** ** Source **
  
-The source code is not yet publicly available. ​Pending decisions on specific software license models and code documentation,​ the access to the SVN code repository is restricted to the developers and our collaborators+The source code publicly available ​at [[https://​gitlab.com/​morpheus.lab/​morpheus|GitLab]]
  
 ** Building from source **  ** Building from source ** 
  
-For developers/​collaborators with access to the [[http://​imc.zih.tu-dresden.de/​websvn/​listing.php?​repname=Morpheus|Morpheus SVN repository]],​ information ​on building Morpheus from source can be found [[devel:source|here]] ​(password protected).+Information ​on building Morpheus from source can be found [[https://​gitlab.com/​morpheus.lab/​morpheus/​blob/​master/​README.md|here]].
  
 ++++ ++++
  
 ++++ Where can I get help? | ++++ Where can I get help? |
-** Limited support **  
  
-Morpheus is distributed as-is and we have limited resources for support. Nevertheless,​ your experiences are essential for us to improve the software.\\+** User forum ** 
  
-** Questions ​**+Use the [[forum:​users|Morpheus user forum]] to get support from developers and other users. 
 + 
 +** User manual ​** 
 + 
 +The [[documentation:​manual|user manual]] is the primary source of information on usage of Morpheus.
  
-If you have a question that is not answered in the [[documentation:​faq|FAQ]],​ do not hesitate to [[walter.deback@tu-dresden.de|ask us]]. 
  
 ** Debug mode ** ** Debug mode **
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 [{{ :​faq_debug.png?​direct&​250 | Run a crashed simulation in ''​Debug''​ mode, and send us the log file ''​gdb.log''​.}}] [{{ :​faq_debug.png?​direct&​250 | Run a crashed simulation in ''​Debug''​ mode, and send us the log file ''​gdb.log''​.}}]
- 
- 
-** Bug reports ** 
- 
-If you experience reproducable crashes in a situation not covered in the [[documentation:​issues|Known Issues]] section, please send us a [[joern.starruss@tu-dresden.de|bug report]]. \\ 
- 
-In the bug report, include as much information as possible, such as: \\ 
- 
-  * How to reproduce the bug 
-  * XML model that produced the error 
-  * Morpheus version/​revision (see ''​Settings -> Local -> Check Simulation -> Test''​) ​ 
-  * Your operating system 
-  * Log file of the debugger (''​gdb.log''​) 
  
 ++++ ++++
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 ++++ Developers | ++++ Developers |
  
-The developers behind ​Morpheus ​are Jörn Starruß and [[http://​walter.deback.net|Walter de Back]].  +Morpheus ​is developed by Jörn Starruß and [[http://​walter.deback.net|Walter de Back]] at the [[http://​imc.zih.tu-dresden.de/​imc|IMC group]] headed by prof. [[http://​imc.zih.tu-dresden.de/​imc/​index.php?​page=members&​who=deutsch|Andreas Deutsch]]. ​
- +
-We work at the [[http://​imc.zih.tu-dresden.de/​imc|IMC group]] headed by prof. [[http://​imc.zih.tu-dresden.de/​imc/​index.php?​page=members&​who=deutsch|Andreas Deutsch]]. ​+
  
 We are part of the [[http://​tu-dresden.de/​die_tu_dresden/​zentrale_einrichtungen/​zih|Center for High Performance Computing]] at the [[http://​www.tu-dresden.de/​en|Technische Universität Dresden]], Germany. We are part of the [[http://​tu-dresden.de/​die_tu_dresden/​zentrale_einrichtungen/​zih|Center for High Performance Computing]] at the [[http://​www.tu-dresden.de/​en|Technische Universität Dresden]], Germany.
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 ++++ ++++
  
-++++ Comparison to similar software | 
  
-A number of other software packages exist that, similar to Morpheus, offer multiscale simulation of multicellular systems. Yet, these packages differ in the model formalisms they implement, and the way the features are exposed to the user (usability). ​ 
  
-** CompuCell3D ** 
- 
-[[http://​www.compucell3d.org/​|CompuCell3D]] is probably the most closely related simulation platform. CompuCell3D implements the cellular Potts model (CPM) and allows user to link cell-based models to ODEs and PDEs. Although Morpheus offers the same set of model formalism, it focuses less on cellular Potts models. 
-In fact, Morpheus is often used to simulate pure PDEs, ODE lattices or image-based modeling, without resorting to CPM-based modeling of motile cells. ​ 
- 
-Other differences lie in usability. CompuCell3D comes with an intuitive graphical user interface which allows users to parameterize and execute models and even provides real-time visualization of 2D and 3D simulations. However, this GUI does not allow full specification of models, part of which must be specified in python scripts (e.g. sets of differential equations). ​ 
-Although the GUI included in Morpheus does not offer the same advanced visualization capabilities,​ it does allow user to construct models within the GUI, without the need for scripting or programming,​ including specification of ODE and PDE models as expressions in infix notation. Morpheus also includes work flow features such as the opening multiple documents and a mySQL-based job archive. 
- 
-** Episim ** 
- 
-[[http://​tigacenter.bioquant.uni-heidelberg.de/​tissue-modelling.html|Episim]] ... vertex based models 
- 
-Usability... ​ 
-- automated model integration... ​ 
-- modeling in process diagrams 
- 
-** Chaste ** 
- 
-[[http://​www.cs.ox.ac.uk/​chaste/​|Chaste]] is arguably the most advanced simulation platform for multicellular systems. ​ 
- 
-- CPM and vertex based models 
- 
-Usability... C++ library... Pitched to advanced computational experts... 
- 
- 
-  
- 
- 
-++++ 
 ===== Modeling =====  ===== Modeling ===== 
  
documentation/faq.1380621146.txt.gz · Last modified: 11:52 01.10.2013 by Walter