Morpheus

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~~NOTOC~~
====== What's New ======

**Morpheus 2.0** is the 2nd major release that improves modeling flexibility, usability, and allowing extensibility. 

==== Open source ====
 
  * Morpheus is now **open source**.
    * Source code is available in the [[https://gitlab.com/morpheus.lab/morpheus|Git repository]].
    * Released under a permissive [[https://opensource.org/licenses/BSD-3-Clause|BSD license]]
  * Morpheus is an **extensible framework**
    * New modeling and analysis components can be added as plugins
      * Extend the Morpheus modeling language MorpheusML by your concept
      * Base your concept implementation into a plugin based on the stable C++ extension API and profit from
        * Simple integration of MorpheusML and implementation
        * Automated symbol dependency tracking and scheduling
        * Integration with other components via math expression
==== Simulator ====

== Modeling ==

  * **Expressions everywhere**
    * In addition to numerical values, plugin can now take mathematical expressions as inputs
    * Greatly improves modeling flexibility by coupling of submodels
    * CPM temperature can now also be function of time, e.g. to simulate annealing.

[{{ :download:math_expression_2.png?direct&150 |Parameters can given as math expressions, interpreted at run-time.}}]

  * **CPM surface scaling**
    * New correction terms for scaling of surface of CPM cells
    * Now calculated in accordance to the scaling rules as specified in [[http://bmcbiophys.biomedcentral.com/articles/10.1186/s13628-015-0022-x|Magno et al., BMC Biophysics, 2015]]


  * **MembraneProperties** 
    * Variables with spatial resolution, mapped to cell membrane
    * Uses circular (2D) or spherical (3D) approximation of cell shape
    * Allows spatially resolved registration of (neighboring) cell properties 
    * Enables reaction-diffusion of properties on membrane

[{{ :download:membrane_pde.png?direct&250 |MembraneProperties provide a scalar field mapped to the cell membrane on which reaction-diffusion systems can be simulated.}}]

  * **Reporters**
    * All ''Reporters'', plugins that generate statistics and mappings, have been revised and generalized. 
    * ''NeighborhoodReporter'' provides statistics (e.g.sum, mean) on properties of the cell's directly adjacent microenvironment
    * ''CellReporter'' provides statistics on properties of the cellular environment such as including the concentration of ''MembraneProperties'' and ''Fields''.

[{{ :download:reporters.png?direct&500 |NeighborhoodReporter counts the number of neighbors of the other cell type. Left: colors show two cell types. Middle: colors and labels show number of non-identical neighboring cells. Right: colors and labels show length of interface to non-identical neighboring cells}}]


  * A number of **new plugins** introduce new modeling features, including
    * ''AddCell'': add CPM cells during simulation based on a condition and a location specified by a probability density function.
    * ''ChangeCelltype'': change the cell type of a cell based on a condition. 
    * ''Protrusion'': actin-inspired feedback model that control shape and motility of CPM cells, as proposed by [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004280|Niculescu et al., 2015]].

[{{ :download:protrusion.png?direct&200 |The new Protrusion plugin models positive feedback of active membrane regions, inspired by actin dynamics.}}]


== Performance ==

  * **Performance optimization**
    * Automatic scheduling has been revised and optimized by subdividing according to spatial contexts. 
    * Tracking of CPM object properties has been moved to an adaptive tracker, tracking only the required information
    * All expressions are evaluated in thread-safe containers to optimize use of multithreading.

  * **Performance measurements and profiling**
    * Information on execution time (wall time, CPU time) and peak memory usage 
    * Execution times (wall time) are listed per plugin

[{{ :download:profiling.png?direct&500 |A performance profile is generated after each simulation.}}]

== Analysis ==

  * **TIFFPlotter**
    * Now writes OME-TIFF headers (Open Microscopy Environment) to facilitate visualization of 3D-5D image data with external such as [[http://fiji.sc/Fiji|Fiji]] or [[http://www.dimin.net/software/bioview3d/|BioView3D]]. 

[{{ :download:BioView3D.png?direct&250 | Morpheus' TIFFPlotter exports time-lapse multichannel TIFF stacks with OME-TIFF header can be easily visualized with external tools such as [[http://www.dimin.net/software/bioview3d/|BioView3D]]. }}]


  * **Logger** 
    * The completely revised ''Logger'' plugin provides generic tool for data export.
    * Data export: Periodically writes any combination of variables (Globals, Properties, Fields, etc.) to file in CSV or Matrix format.
    * Plotting: Logger also provides a versatile interface for generating data visualizations including time plots, phase diagrams, cell trajectory plot, spacetime plot, profile plots, surface plots etc.

[{{ :download:logger.png?direct&500 |The new ''Logger'' plugin provides a versatile interface for data export and data visualization.}}]
==== MorpheusML ====

  * **Scoping** 
    * Lexical scoping was introduced: symbols are only valid on the scope in which they are declared.
    * Improves intuitive character and consistency of model description language 
    * Allows multiple usages of symbols, setting global defaults, etc.   

  * **Globals**
    * New Globals section for global constants, variables and ''Fields''
    * Scalar field previously PDE/Layer are moved into Globals/Fields

  * **MorpheusML 2.0**
    * Restructured MorpheusML markup language
    * Allows better future integration with other formats such as SBML  
    * Fixboard can partially convert Morpheus 1.x models into new format.

==== GUI ====

  * **Documentation** 
    * Doxygen-generated in-app docs appear in HTML (using QtWebKit) 
    * Docs are both context-sensitive and can be searched (using QtHelp framework)
    * Docs can include latex-based maths (displayed using MathJax) 

[{{ :download:documentation.png?direct&400 |The new in-app documentation is context-sensitive, browsable, features Latex equations and XML examples.}}]


  * **Panel with addable plugins** 
    * New context-sensitive overview of addable plugins shows what plugins can be added


[{{ :download:plugin_panel.png?direct&300 |Plugins can now be added using a new panel that shows what can be added at the selected position.}}]


  * **Generate symbol graph**
    * Shows interdependencies between symbols and scopes

[{{ :download:symbol_graph.png?direct&400 |Symbol graphs show how Morpheus interprets the model. This can be used for model testing and tracing bugs.}}]


  * **Generate movies**
    * Images can be generatedfrom image sequences within GUI
    * Also generates multiple movies from ''ParamSweep''
    * Requires ''ffmpeg'' or ''avconv'' (download from [[https://www.ffmpeg.org/download.html|here]])

[{{ :download:create_movie.png?direct&400 |Create movies from images.}}]



  * **ImageTable**
    * Generate visual tables of ''ParamSweep'' results including images or movies (viewable in HTML5-enabled web browsers)


[{{ :download:image_table.png?direct&300 | The new ImageTable feature gives a quick overview of the results of a parameter sweep from a web browser.}}]
===== Version 1.2.1 =====
=== Changes === 
  * SBML support is built-in for Ubuntu 14.04+ as libSBML was removed from repositories.
  * Fixed rare GUI crashes on Mac OSX when moving model elements.

===== Version 1.2 =====

The changes in this version focus on improving modeling flexibility, but also include several improvements in automatic scheduling as well as a new preview panel in the user interface. Download version 1.2 [[download:download|here]].
=== Major changes === 
[{{ :download:preview_morpheus.png?direct&400 |New panel to preview images and text files in result browser.}}]
  * New **preview panel** in GUI in the result browser for images and plain text files.

  * New ''ChildID'' option for ''Proliferation''. This supports the representation of **asymmetric cell divisions** by providing a symbolic handle to treat daughter cells differently after cell division.
    * See new example [[examples:cellular_potts#Stem cells in the intestinal crypt|Crypt.xml]]

  * New ''ChangeCellType'' plugin to conditionally **change the cell type** of a cell. By default, cell properties are copied, but may be overridden using ''Triggers''.
    * See new example [[examples:cellular_potts#Stem cells in the intestinal crypt|Crypt.xml]]

  * New ''VectorRule'' to manipulate ''PropertyVector'', either in x,y,z or phi,theta,radius (spherical coordinates). This facilitates **vector computations** to e.g. control directed cell motility. 
    * See new example [[examples:cellular_potts#Run and Tumble|RunAndTumble.xml]]

  * New ''FlipCells'' plugin to represent **cell motility** in CA-like models. This plugin enables the conditional switching of positions with a random neighboring site. 
    * See new example [[examples:miscellaneous#Particle Aggregation: FlipCells|ParticleAggregation.xml]]

  * New ''PopulationReporter'' to collect **population-level statistics** on cell ''Properties''. This allows individual cell behavior to depend on population-level properties, or to collect population statistics to log and plot. 
    * See new examples [[examples:miscellaneous#Particle Aggregation: FlipCells|ParticleAggregation.xml]] and [[examples:cellular_potts#Stem cells in the intestinal crypt|Crypt.xml]]

  * New ''StopCondition'' to **terminate a simulation** upon a ''Condition'' before reaching ''StopTime''. This can significantly improve efficiency in e.g. parameter explorations or sensitivity analysis.
    * See new example [[examples:miscellaneous#Particle Aggregation: FlipCells|ParticleAggregation.xml]]

  * New ''trigger'' option for ''Event''. This provides a choice to **trigger events** (1) whenever the condition changes from false to true (as in SBML) or (2) whenever the condition is true.

  * Several fixes and many improvements to **automatic scheduling**.
    * Analysis tools are now scheduled according to input symbols if ''interval=0''

=== Minor changes === 

  * New ''InitCA'' plugin to populate CA-like models.
    * See examples [[examples:miscellaneous#Particle Aggregation: FlipCells|ParticleAggregation.xml]], [[examples:differential_equations#Coupled ODE lattice: Lateral signaling|LateralSignaling.xml]], [[examples:miscellaneous#Game of Life: Cellular Automata|GameOfLife.xml]] and [[examples:miscellaneous#French Flag: Morphogen gradient|FrenchFlag.xml]]

  * Fix ''InitRectangle'' on ''hexagonal'' lattices.

  * Support for $\alpha$-synchronous simulation.

  * Fixed issue with ''Delay'' properties.

  * ''HistogramLogger'' now supports logarithmic binning and plotting

=== Acknowledgments ===

Many of these new features are the result of requests from users. In particular, we thank //Maria Herberg// (Medical Faculty, TU Dresden), //Angelo Torelli// (Mannheim University of Applied Sciences) and //Ovidiu Pârvu// (Brunel University) for useful suggestions.
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===== Version 1.1.1 =====

=== Minor changes === 

  * Fix issue in Windows with SBML import feature.
  * Fix issue in GUI with displaying newly created elements.
  * Updated version for math expression parser ([[http://muparser.beltoforion.de/|muparser]]).

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===== Version 1.1 =====

=== Major changes === 

  * Added **SBML Import** feature that converts SBML-based models into equivalent intracellular models of differential equations in Morpheus description language. An [[examples:differential_equations#sbml_importmapk_signaling|example model]] is added.

  * Added ''DelayProperty'' that returns assigned values after a specified time lag which enables the simulation of **delay differential equations**. An [[examples:differential_equations#delay_differential_equationscell_cycle|example model]] is added.

  * A distinction is made between **''Equation''s and ''Rule''s** whereby the latter are equations within a ''System''. Unlike ''Equation''s, ''Rule''s may have recurrency and be part algebraic loops.

  * **''Event''s** are now triggered whenever the condition change from false to true, for SBML compatibility.

  * Sequential processes are now **scheduled** only as often as their input symbol can change. This avoids redundant processing and optimizes computational performance.   
=== Minor changes ===

  * Fixed issues with file dialogs and output folder button under Windows.
  * Fixed  libfreetype problems with Gnuplot.app under Mac OSX.
  * Reduced verbosity in standard output (''model.xml.out'').
  * Moved Examples menu to toolbar menu.
  * Various minor fixes.

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