insilicoIDE 0.1.1 Getting Started

Launch insilico IDE that you downloaded, then you will see blank white canvas (Fig. 1).

Load inisilicoML model / cellML model

Go into a directory named "samples" in the archive, and you will find several sample models written in insilico ML format. Drag and drop a file "hodgkin-huxley.xml" on the white canvas of insilico IDE. You find a yellow circle entitled "HodgkinHuxley". It represents a module (Fig. 2). If you again drag and drop another model file, then it will add on the canvas. In "File" menu, there are two ways to load model files. One is "Open New File..." and the other is "Add Another Model". You can treat cellML files in the same way.

By double clicking on the module you can browse modules in sub-layer of the module if the module has (Fig. 3). Lines between the module and modules in its substructure are called Edges. If you again double click the top module, the substructure will be hidden.

blank onemodule expanded
Fig. 1: Blank canvas Fig. 2: One module Fig. 3: Substructure of a module

Simulation

To perform numerical simulation on this model, once you need to export the model into C++ source code. Compile it by some means (g++ on cygwin, visual C++, etc) , and execute the binary file. You will have result.csv as result in which time series of every value involved in the model is written as a function of time. Since the data file is a text file, you can draw graphs by Excel, gnuplot and so on (whatever you want to use).

Select Export in File menu. Then a window opens (Fig. 4) and asks the method of numerical integration (Euler / 4th-order Runge-Kutta) , simulation time step (default 0.01 s), total duration of simulation (default 10,000 s) and rate of thinning out of the resultant time series to dump into a file. In addition to that, if you prefer to perform parallel computation on your cluster PC, by just marking in a check box of "Generate MPI Parallel Simulation", the generated C++ source code can work on PC cluster.

(for the package insilicoIDE0.1.1pg) You can use "draw graph" in a context menu appeared by right clicking on any modules to view the time profile of variables obtained by numerical integration. Before you select "draw graph" you need to select Ports that you want to observe by left click on the target Port. Shift + left click allow you to select several Ports to observe (Fig. 5).

source graph
Fig. 4: C++ source code generation Fig. 5: Graph drawing (only in insilicoIDE0.1.1pg)

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).

context makeEdge
Fig. 6: Context menu Fig. 7: Create an Edge

 

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