Frequently Asked Questions

insilicoIDE 1.0
insilicoIDE 0.3

- insilicoIDE 1.0 -
Q. I tried to simulate an ISML model on insilicoSim, but display an error window. How should I handle this?

A. There are some bugs in the ISML model. Check these items.

  • All ports are linked by edges.
  • All output-pots in functional-unit modules refer physical-quantity.
  • Types of physical-quantity are corret.
  • All state physical-quantity have initial-value setting.
  • Direction of forwarding edge is correct (check tail-module-id and head-module-id).

If you cannot resolve your problem, please send your ISML file with your comments to admin(at)physiome.jp. We would like to try to do our best to find the problem, and will suggest you possible ways to resolve it.

- insilicoIDE 1.0 -
Q. What kinds of MathML elements does insilicoSim support?

A. Here are supported MathML elements.

plus, minus, times, divide, power, sin, cos, tan, sec, csc, cot, sinh, cosh, tanh, sech, csch, coth, arcsin, arccos, arctan, arcsec, arccsc, arccot, arcsinh, arccosh, arctanh, arcsech, arccsch, arccoth, exp, ln, log, abs, root, floor, eq, lt, gt, geq, leq, neq, and, or, diff, partialdiff, inverse, transpose, outerproduct, vectorproduct, scalarproduct, grad, divergence, laplacian

- insilicoIDE 0.3 -
Q. I tried to simulate a model on ISIDE by selecting a "show simulated waveforms" menu, but no waveforms appear. How should I handle this?

A. There are several possible causes for this situation.

  1. No output port has not been selected. In this case, please make a left click at least one of the output port, making the color of the port green. Then select a "show simulated waveforms" menu.

  2. The time discretization step may not be appropriate. Since the current version of ISIDE has not yet support variable time step algorithm, we should ask the user to set an appropriate time step for numerical integration. Please make a right click on the Clock module located on the top-left corner, and then select "Edit module" menu. The windows for integration conditions will appear. Please try to set another, possibly smaller time step for integration.

  3. When "show simulated waveforms" menu is used, ISIDE uses Visual C++ compiler located at "C:\Program Files\Microsoft Visual Studio8\VC\bin\cl.exe" or "C:\Program Files\Microsoft Visual Studio9.0\VC\bin\cl.exe". Thus users need to install Visual C++ 2005 or 2008. The user can download Visual C++ 2005 express edition (for free) from here, and 2008 express edition (for free) from here. If you will not use Visual C++ compiler, you will use File-->Export to generate C++ source file, and you can compile it using your favorite C++ compiler instead. However in this case "show simulated waveforms" menu cannot be used.

If you cannot resolve your problem, please send your ISML file with your comments to admin(at)physiome.jp. We would like to try to do our best to find the problem, and will suggest you possible ways to resolve it.

- insilicoIDE 0.3 -
Q. I have saved my ISML model on IDE as CellML file with its extension.cellml, and tried to simulate on PCEnv0.4. But PCEnv judged the exported file as incorrect. How should I handle this?

A. First, please confirm that your ISML model can be simulated correctly on ISIDE. If the model runs properly on ISIDE but not on PCEnv, the most probable cause is the use of incorrest physical unit in your model. The ISML model may use incorrect physical unit. Although the current ISIDE check the consistency of physical units of input and output ports when two modules are connected, if the user ignore the warning telling you the inconsistency of the physical unit, ISIDE does not care about the inconsistency. Thus, if the user would like to simulate your model on PCEnv, please make sure that all physical unit is set appropriately.

- insilicoIDE 0.3 -
Q. I downloaded a morphology model of human skeletal system (MPID000008) from the Morphology Database, and also associated dynamic model of bipedal gait (DBID410:Yamasaki_2DBiped7Link_2003_withSkeletalHumanModel) from the insilicoDB (ISDB). After importing the dynamic model to the insilicoIDE (ISIDE), I simulated the dynamic model using the popup menu item "Show Morpho-Dynamics". After tens of seconds, a window named structure dailog appears, but I could not see any visualization of the simulated result. How can I get a walking motion of the skeletal model?

A. Please make sure that you have a folder with the name "VisualModel" at the same directory where you placed the ISML file of the dynamic model. The VisualModel folder should include VSML files for the morphology model of human skeletal system. To see if these files and the folder are located correctly, select the popup menu item "Show Morphology Data" before performing the item "Show Morpho-Dynamics" and make sure that you have a static visualization of the skeletal system model.If this is confirmed, "Show Morpho-Dynamics" should now work properly.