Differences

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--- download:whatsnew [22:18 29.02.2016] – [Open source] Walter
+++ download:whatsnew [15:35 22.10.2018] (current) – [Open source] Jörn Starruß
@@ Line 6: / Line 6: @@
 ==== Open source ====
-  * Morpheus 2 is the first open source release.
+  * Morpheus is now **open source**.
-    * Source code is available in the [[https://gitlab.com/users/sign_in|Git repository]].
+    * 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 2 is an **extensible framework**
+  * Morpheus is an **extensible framework**
-    * Modeling and analysis tools can be customized or added as plugins
+    * New modeling and analysis components can be added as plugins
-    * A stable C++ API has been developed for plugin development
+      * Extend the Morpheus modeling language MorpheusML by your concept
-      * Simple integration of XML and implementation
+      * Place your concept implementation into a plugin based on the stable C++ extension API and profit from
-      * Automated symbol dependency tracking and scheduling
+        * Simple integration of MorpheusML and implementation
+        * Automated symbol dependency tracking and scheduling
+        * Integration with other components via math expression
+      * Integrate external simulation code into Morpheus by using the Symbol interface
 ==== Simulator ====
@@ Line 19: / Line 22: @@
   * **Expressions everywhere**
-    * In addition to numerical values, plugin can now take mathematical expressions as inputs
+    * In addition to numerical values, plugin parameters 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]]
@@ Line 41: / Line 49: @@
-  * A bunch of new plugins including
+  * 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.
@@ Line 49: / Line 57: @@
+== Performance ==
-== Simulation ==
+  * **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 now in thread-safe containers to optimize use of multithreading.
-  * **Performance measurements**
+  * **Performance measurements and profiling**
     * Information on execution time (wall time, CPU time) and peak memory usage
-  * **Profiling plugin performance**
     * Execution times (wall time) are listed per plugin
@@ Line 63: / Line 73: @@
   * **TIFFPlotter**
-    * Now writes OME-TIFF headers (Open Microscopy Environment) to facilitate visualization of 3D-5D image data with external such as Fiji, ImageJ or BioView3D.
+    * 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**
@@ Line 71: / Line 84: @@
 [{{ :download:logger.png?direct&500 |The new ''Logger'' plugin provides a versatile interface for data export and data visualization.}}]
 ==== MorpheusML ====
   * **Scoping**
-    * Symbol are only defined for the scope in which they are declared.
+    * 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 and variables
+    * New Globals section for global constants, variables and ''Fields''
-    * PDEs moved into Globals/Fields
+    * Scalar field previously PDE/Layer are moved into Globals/Fields
   * **MorpheusML 2.0**