Leading Project for Biosimulation > Cell/Biodynamics Simulation > simBio

Feature Request ID FR-3: Implementation of 2D plots in Sarai et al, 2003 at simBio


To implement the 2D plots in Sarai et al, 2003 in the simBio project. The plots can be found in the SAnode project at a private repository.


It is not possible to just implement the plots in the simBio project because the classes call JSEntry. This will make a cycle in the build path of the simBio project because JavaSpaceClient depends on simBio.

It should be possible to run the XML-protocols in simBio without JavaSpaceClient. To run the XML-protocols in the Javaspace it is okay to be dependent on simBio, because JavaSpaceClient itself dependents on simBio.

System Design

Do the implementation in the same manner as the implementation of 2D plots in Sarai et al, 2006 at simBio. See Implementation of 2D plots in Sarai et al, 2006 at simBio for more information.


  1. To test that the system design works, run the implemented XML-files Fig.1.protocol.xml, Fig.2A.protocol.xml and Fig.2B.protocol.xml in the PC cluster.
  2. Test that all existing testcases in the simBio project still works.

Test Result

All the specified tests have been run with successful result.

Committed Files

The version has been tagged to SAnode in the simBio_mikael project. After the increment was accepted it was merged to the simBio project.