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
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
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
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
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
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
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)
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/