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simBio / News: Recent posts

simBio Eclipse plug-in 1.0.0 released

This feature execute simBio through pop-up menu of Eclipse Java Perspective. Run model, Run model on JavaSpaces and Generate XML can be launched.

For more information, see http://www.sim-bio.org/

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.
Posted by Mikael Wing 2008-03-28

simBio 1.0 released

simBio is a simulator for biological systems such as cardiac cells, epithelial cells and pancreatic β cells. simBio is written in Java, uses XML and can solve ordinary differential equations.

For more information, see http://www.sim-bio.org/

Changes from previous version are

  1. Debug: x axis of graph is renewed by exact duration set at min and max.
    See http://www.sim-bio.org/specification/bugs/s028.html
  2. Revised Javadoc in English and in Japanese.
  3. A testcase org.simBio.XmlFilesTest.java was created to:
    A. Validate whether a calculation written in each xml can be started or not, i.e. executable test.
    B. Run a complete test of all the xml-files.
    See http://www.sim-bio.org/specification/featurerequests/fr019.html
    and http://www.sim-bio.org/specification/featurerequests/fr019r.html
  4. csv files generated from GUI menu and via CsvMaker became the same.
    See http://www.sim-bio.org/specification/bugs/s032.html
  5. Fix the paths of the generated files by protocol.
    See http://www.sim-bio.org/specification/bugs/s036.html
  6. Speeded up org.simBio.sim.analyzer.graph.RelationGraph.
    See http://www.sim-bio.org/specification/bugs/s004.html
  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 http://www.sim-bio.org/specification/featurerequests/fr001_3.html
  10. Updated jars. See NOTICE section in Readme*.txt for current version of used class libraries.
    See http://www.sim-bio.org/specification/featurerequests/fr001_4.html
  11. Revised code and xmls according to Code Conventions
    See http://simbio.wiki.sourceforge.net/Code+Convention
  12. Added xmls to reproduce Figs in Sarai et al (2003) and (2006), which need plotting feature.
    See http://www.sim-bio.org/specification/featurerequests/fr002.html
    and http://www.sim-bio.org/specification/featurerequests/fr003.html
  13. Improved the error handle for the method that integrates the ordinary differential equation.
    See http://www.sim-bio.org/specification/bugs/s016.html
  14. Made it possible for simBio to run protocol XML-files using multithreads (randomizer threads="4").
    See http://www.sim-bio.org/specification/featurerequests/fr014.html
  15. Made it possible to use tag xmlDir for simBio.
    See http://www.sim-bio.org/specification/featurerequests/fr015.html
  16. The beta stimulation model by Kuzumoto et al (2007) was included.
    See http://www.sim-bio.org/model/kuzumoto_et_al_2007.html
  17. A feature to produce separate English and Japanese API documentation was included.
    See http://www.sim-bio.org/features.html
  18. The distributed computation packages, JavaSpaces, JavaSpacesClient, and RemoteClient was included.
    See http://www.sim-bio.org/specification/featurerequests/fr001_1.html,
    http://www.sim-bio.org/specification/featurerequests/fr001_2.html,
    http://www.sim-bio.org/specification/featurerequests/fr001_3.html
    and http://www.sim-bio.org/specification/featurerequests/fr001_4.html
  19. The beta stimulation model by Himeno et al (2008) was included.
    See http://www.sim-bio.org/model/index.html
  20. A project named packager was made to create all the release packages for simBio and simBio Eclipse plug-in from one place.
    See http://www.sim-bio.org/specification/featurerequests/fr004.html
  21. simBio Eclipse plug-in was updated.
    See https://sourceforge.net/tracker/?func=detail&atid=768226&aid=1827335&group_id=146713... read more
Posted by Mikael Wing 2008-03-28

simBio 1.0PR2 released

simBio is a simulator for biological systems such as cardiac cells, epithelial cells, and pancreatic β cells.

Changes from 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 and messages were revised.

simBio is written in Java, uses XML and can solve ordinary differential equations. In an attempt to mimic biological functional structures, a cell model is, in simBio, composed of independent functional modules called Reactors, such as ion channels and the sarcoplasmic reticulum, and dynamic variables called Nodes, such as ion concentrations. The interactions between Reactors
and Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Reactors are prepared in a hierarchical order, in analogy to the biological classification. Each Reactor can be composed or improved independently, and can easily be reused for different models.... read more

Posted by Nobuaki Sarai 2007-01-16

simBio 0.3.02 released

A new release of simBio 0.3.02 is now available at http://sourceforge.net/project/showfiles.php?group_id=146713

Changes from 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, see http://www.sim-bio.org/docs/bio/ for other models.
2. Be able to modify a model xml to change settings from control. see src/xml/matsuoka_et_al2003/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. Add some tests.
4. A duplicated jar is deleted.
5. Some Javadoc comments are revised.
6. Bugs are fixed, such as Ist, Ito, GUI.

simBio is a simulator for biological systems such as cardiac cells, epithelial cells, and pancreatic β cells. simBio is written in Java,
uses XML and can solve ordinary differential equations.

In an attempt to mimic biological functional structures, a cell model is, in simBio, composed of independent functional modules called Reactors,
such as ion channels and the sarcoplasmic reticulum, and dynamic variables called Nodes, such as ion concentrations. The interactions between Reactors and Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Reactors are prepared in a hierarchical order, in analogy to the biological classification. Each Reactor can be composed or improved independently,
and can easily be reused for different models.... read more

Posted by Nobuaki Sarai 2006-05-08

simBio 0.3.01 released

simBio is a simulator for biological systems such as cardiac cells, epithelial cells, and pancreatic β cells. simBio is written in Java, uses XML and can solve ordinary differential equations.

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

In an attempt to mimic biological functional structures, a cell model is, in simBio, composed of independent functional modules called Reactors, such as ion channels and the sarcoplasmic reticulum, and dynamic variables called Nodes, such as ion concentrations. The interactions between Reactors and Nodes are described by the graph theory and the resulting graph represents a blueprint of an intricate cellular system. Reactors are prepared in a hierarchical order, in analogy to the biological classification. Each Reactor can be composed or improved independently, and can easily be reused for different models.... read more

Posted by Nobuaki Sarai 2005-11-04

simBio 0.3 is released.

simBio is a simulator for biological systems such as cardiac cells, epithelial cells, and pancreatic beta cells. simBio is written in Java, uses XML and can solve ordinary differential equations.

Changes from previous version are
1. LGPL is applied,
2. GUI has been improved,
3. The volume regulation model of the ventricular myocyte (Terashima et al, 2006) is included.
4. Comments in xml files will be kept after calculation.... read more

Posted by Nobuaki Sarai 2005-11-01

Users' mailing list is open

simBio users' mailing list is now open.
Please subscribe at http://lists.sourceforge.net/lists/listinfo/simbio-users (ML in English) or at http://lists.sourceforge.net/lists/listinfo/simbio-users_ja (ML in Japanese)

Posted by Nobuaki Sarai 2005-09-07

Home Page redirect to www.sim-bio.org

The Home Page link is redirected to the http://www.sim-bio.org/
The documents in Japanese will be found at http://jp.sim-bio.org/

Posted by Nobuaki Sarai 2005-09-07