insilicoIDE 0.2.0-0.2.4 Getting Started
Edit Models
You can delete modules and create new modules as children of a module or as a root module. A child module can be connected to its parent module by "Constituent" or "Include" edge that represents types of hierarchical structure. When you delete a model, edges linked to the module and modules in the lower layer of the module are also deleted automatically.
Create and Delete Modules
Right click on a module shows a popup context menu (Fig. 6). To create a child, select "Make Child Module" in the menu and also choose the type of connectivity between newly created child module and the parent module. If you select "Delete Module", the module pointed by mouse cursor will be removed from the canvas.
Create and Delete Edges
If you right-click on a edge, the popup menu shows two items, i.e. "Delete Link" and "Change Link Relation". To remove the edge, you use this menu. To create a new edge between two modules, you drag mouse cursor from a Output Port on a source model to a Input Port on a destination model (Fig. 7).
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| Fig. 6: Context menu | Fig. 7: Create an Edge |
Edit Module
A module is characterized by States, Parameters, Functions, which represent dynamical variables, static values and functions, respectively. There are two ways to use States in this version of insilico IDE. One is to use in ordinary differential equations. Thus Sates are accompanied by mathematical expression defining the vector field. Anothere way to use States is to express status of agent in a rule-based simulation. In this case, time evolusion rule must be define on the States.
To edit these properties, select "Edit Module" in a popup context menu appeared by right click on a module. Then a property editor appears (Fig. 8). In this editor there are several tabs corresponding to States, Parameters, Functions and Input Ports. To defin States and Functions, users need to describe equations. In a case of States, at first you need to select on state in a list, and click "Edit State Update Rule". Then window shown in Fig. 9 appears. In a panel at lower right, using a popup menu by right click on "ROOT" or equations, you can edit them. The equation must describe as like C programming. Users can use IF structure to make conditional equations. Only parameters, functions and input ports that are already defined are allowed to be used in equations.
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| Fig. 8: Porperty editor | Fig. 9: Equation editor |
Geometrical Information
A module also can be characterized by geometrical information, such as morphological data, position and direction. Morphological data can be assigned by commands "Set Patch" and "Set Voxel Data" in the popup context menu appeared by the right click on a module.
After setting Patch or Voxel data, you can view the model with morphological data by "View Structure" in the popup context menu (FIg. 10). Morphological data files must be located in a directory "VisualModel" which is at the same directory with the insilicoML model. In the example directory, you will find "musculoskeletal" directory. A model "Strove_1999_neuromusculoskeletalSystem.xml" is in the directory. Users can view a caricature of the skeletal system.
If users select "Show morpho-dynamics" from the context menu at the root module, an animation of body dynamics will play.
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| Fig. 10: Morphologicl data view |