Supplementary Release Note  -- insilicoIDE (ISIDE) 1.3  --

* Morphology related comments
On ISIDE, users can make a model including partial differential  
equations that are solved on a domain given by a morphological data.  
By this feature, users can simulate, for example, an action potential  
propagation on a 2D-sheet or a heart-shape object.

ISIDE 1.3 equips two new dialogs for editing morphology data. A single  
morphology can be defined in a single module. A morphology is composed  
of multiple geometries. For example, users can make a morphology  
containing a cylinder and two hemispheres located at both ends of the  
cylinder to make a morphology like a capsule (which might be a simple  
model of a cell body, for example). In this case, each of a cylinder  
and two hemispheres is a geometry. For each geometry, position and  
rotation can be defined in a local coordination defined on a module.  
These properties such as shape, position and rotation can be edited in  
a geometry dialog. Users can find this dialog from "Edit morphology" - 
 > "Geometry".

A segment is a part of a geometry which is used to define boundary  
conditions or initial conditions imposed on a morphology data. For  
example, an edge of a square-like morphology is defined as a segment,  
and a certain boundary condition is defined on the segment. Users can  
define several segments for each geometry. A segment edit dialog  
provides interfaces to edit segments.

These two dialogs, geometry and segment dialogs, allow users to edit  
morphology. Principally the morphology information edited on these  
dialogs are usable in solving PDEs. But for the moment, since the  
interfaces for setting boundary conditions or initial value conditions  
are not enough developed, the morphology information are not available  
yet in a solver of PDEs. This will be improved very soon.


* Template/Instance related comments
There is a framework called Template/Instance modeling in ISML. For  
example, when users want to create a neural network model including  
100 neurons which are the same type of neuron with slightly different  
parameter values, the template/instance framework is beneficial to be  
used in the modeling. At first users create a single neuron model and  
declare it as a template. Then 100 neurons are created as instances of  
the template. Then principally all instances are like copies of the  
template but since they are instances, once the template is modified  
somehow, the modifications are reflected to all instances immediately.

In the sample directly, there is a model  
ringed_Luo_Rudy_1991_model_with_instance.isml that includes the  
template/instance framework. This model can be simulated only by  
converting it into C++. ISSim has not yet supported template/instance  
framework. And ISIDE cannot edit template/instance yet. Hence this  
feature is still in stage of beta version. This kind of idea is  
inevitable for creating large scale models and this feature (template/ 
instance framework) will be also improved very soon.