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Release Notes

simBio releases

simBio 1.0 released

Changes from the previous version are

  1. Debug: x axis of graph is renewed by exact duration set at min and max.
    See Bug ID S-28: Graph X Axis Problem Documentation.
  2. Revised Javadoc in English and in Japanese.
  3. A testcase org.simBio.XmlFilesTest.java was created to:
    1. Validate whether a calculation written in each XML can be started or not, i.e. executable test.
    2. Run a complete test of all the XML-files.

    See Feature Request ID FR-19: Testcase that test all XML-files
    and Feature Request ID FR-19R: Error detection for XmlFilesTest.

  4. CSV files generated from GUI menu and via CsvMaker became the same.
    See Bug ID S-32: Time Step Bug.
  5. Fix the paths of the generated files by protocol.
    See Bug ID S-36: Exchanger Path Bug.
  6. Speeded up org.simBio.sim.analyzer.graph.RelationGraph.
    See Bug ID S-4: RelationGraph Runs Slowly.
  7. Main site www.sim-bio.org has been updated using Forrest and MovableType.
  8. Exchangers for protocol were updated and added.
  9. Added 2D contour plot feature.
    See Feature Request ID FR-1:3: MS3 on how to release distributed computation packages.
  10. Updated jars. See NOTICE section in Readme*.txt for current version of used class libraries.
    See Feature Request ID FR-1:4: MS4 on how to release distributed computation packages.
  11. Revised code and XMLs according to Code Conventions
    See Code Convention.
  12. Added XMLs to reproduce Figs in Sarai et al (2003) and (2006), which need plotting feature.
    See Feature Request ID FR-2: Implementation of 2D plots in Sarai et al, 2006 at simBio
    and Feature Request ID FR-3: Implementation of 2D plots in Sarai et al, 2003 at simBio.
  13. Improved the error handle for the method that integrates the ordinary differential equation.
    See Bug ID S-16: Conductor.integrate Error Handling.
  14. Made it possible for simBio to run protocol XML-files using multithreads (randomizer threads="4").
    See Feature Request ID FR-14: randomizer threads="4".
  15. Made it possible to use tag xmlDir for simBio.
    See Feature Request ID FR-15: Implement xmlDir functionality.
  16. The beta stimulation model by Kuzumoto et al (2007) was included.
    See Instructions for kuzumoto_et_al_2007.
  17. A feature to produce separate English and Japanese API documentation was included.
    See Bilingual Feature.
  18. The distributed computation packages, JavaSpaces, JavaSpacesClient, and RemoteClient was included.
    See Feature Request ID FR-1:1: MS1 on how to release distributed computation packages,
    Feature Request ID FR-1:2: MS2 on how to release distributed computation packages,
    Feature Request ID FR-1:3: MS3 on how to release distributed computation packages
    and Feature Request ID FR-1:4: MS4 on how to release distributed computation packages.
  19. The beta stimulation model by Himeno et al (2008) was included.
    See Available Models.
  20. A project named packager was made to create all the release packages for simBio and simBio Eclipse plug-in from one place.
    See Feature Request ID FR-4: Create a release packager project.
  21. simBio Eclipse plug-in was updated.
    See Eclipse plug-in may need update.

simBio 1.0PR2 released

Changes from the previous version are

  1. The volume regulation model by Takeuchi et al (2006) was included.
  2. The calcium gate model of Gap junction by Oka et al (2006) was included.
  3. The analysis of NCX knockout by Sarai et al 2006 was included.
  4. The human ventricular cell models proposed by Kurata et al (2005) and by ten Tusscher et al (2004) were included.
  5. The Gap Junction model by Henriquez AP et al (2001) was included.
  6. The Japanese documents were separated to docs_ja project.
  7. The Documents were revised.

simBio 0.3.02 released

Changes from the previous version are

  1. The human cardiac cell model proposed by ten Tusscher et al (2004) is included at src/xml/tenTusscher_et_al_2004
  2. Being able to modify a model xml to change settings from control. See src/xml/matsuoka_et_al_2003/Fig.2.make.xml. Also, src/xml/kuratomi_et_al_2003.xml is deleted and the modification from matsuoka_et_al_2003 is written in kuratomi_et_al_2003.make.xml
  3. Some tests have been added.
  4. A duplicated jar has been deleted.
  5. Some Javadoc comments have been revised.
  6. Bugs have been fixed, such as Ist, Ito, GUI.

simBio 0.3.01 released

Changes from the previous version are

  1. commons-lang-2.1.jar is included in Class-Path of MANIFEST.MF to avoid an Exception.
  2. log4j.xml is located at lib/ in the bin.zip distribution.

simBio 0.3 released

LGPL is applied to the new version, GUI has been improved, and comments in xml files will be kept after calculation.

More information is available at http://www.sim-bio.org/

simBio Eclipse plug-in releases

simBio Eclipse plug-in 1.0.0 released

Changes from the previous version are

  1. The three pop-up menus [simBio]->[Run Protocol], [simBio]->[Compose and Run] and [simBio]->[Run on GUI] has been replaced with a new pop-up menu as [simBio]->[Run model] that call Entry.main().
  2. A new pop-up menu as [simBio]->[Run model on JavaSpaces] that call JSEntry.main() has been added to run models on simBio_JavaSpaces.
  3. The pop-up menu [simBio]->[Generate XML] remain as it was.

simBio Eclipse plug-in 0.2.1 released

First version of simBio Eclipse plug-in released on SourceForge.