simBio

simBio 1.0PR2 released

Tue, 16 Jan 2007 20:55:22 +0900

A new release of simBio is now available at http://sourceforge.net/project/showfiles.php?group_id=146713 Changes from previous version are

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

For more information, see http://sourceforge.net/projects/simbio/

Please stay tuned

Thu, 02 Nov 2006 09:29:43 +0900

The volume regulation model has been published in Takeuchi et al. (2006) on 1st Nov. We are working hard to catch up The Journal of General Physiology, and the source code to reproduce the figures will be available in a few weeks. Ayako Takeuchi, Shuji Tatsumi, Nobuaki Sarai, Keisuke Terashima, Satoshi Matsuoka, and Akinori Noma, Ionic Mechanisms of Cardiac Cell Swelling Induced by Blocking Na⁺/K⁺ Pump As Revealed by Experiments and Simulation. The Journal of General Physiology, 128(5): 495-507, 2006. doi:10.1085/jgp.200609646

simBio 0.3.02 released.

Mon, 08 May 2006 18:28:03 +0900

A new release of simBio is now available at http://sourceforge.net/project/showfiles.php?group_id=146713 Changes from previous version are

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.
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
Add some tests.
A duplicated jar is deleted.
Some Javadoc comments are revised.
Bugs are fixed, such as Ist, Ito, GUI.

For more information, see http://sourceforge.net/projects/simbio/

simBio 0.3 released

Wed, 02 Nov 2005 09:01:41 +0900

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

LGPL is applied.
GUI has been improved.
The volume regulation model of the ventricular myocyte (Terashima et al, 2006, in press) is included.
Comments in xml files will be kept after calculation.

Available model list: http://www.sim-bio.org/docs/bio/ Download: http://sourceforge.net/projects/simbio/ Users' mailing list: http://sourceforge.net/projects/simbio/ 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. For more information, see Nobuaki Sarai, Satoshi Matsuoka and Akinori Noma simBio: a Java package for the development of detailed cell models Progress in Biophysics and Molecular Biology, 2005, in press

Eclipse Plug-in for simBio

Tue, 06 Sep 2005 01:31:43 +0900

Description

Execute simBio through pop-up menu of Eclipse Java Perspective. RunGUI, Composer, ResultGenerator, and XmlGenerator can be launched.

You can find latest information from http://www.sim-bio.org/.

License

This plugin is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1.

This plugin is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License (LGPL_2-1.txt) for more details.

The GNU Lesser General Public License can be found at http://www.gnu.org/copyleft/lesser.html

Requirements

Eclipse 3.x (this plugin has created on Eclipse 3.0.2.)
simBio (this plugin has created with simBio 0.2.2.)

Install

This plugin can be installed through update manager of Eclipse 3.x. Here the process with Eclipse 3.1 is described.

Select Eclipse menu: "Help" - "Software Updates" - "Find and Install"
Check "Search for new features to install", then "Next"
Click "New Remote Site"
Input "Name:" box as you like such as "simBio", and "URL:" box as "http://www.sim-bio.org/eclipse/update/", then "Finish"
"Updates" dialog will appear, so check simBio, then "Next".
Check "I accept the terms in the license agreement", then "Next"
Click "Finish"
"Verification" dialog will appear as not yet digitally signed.
Click "Install All".
"Install/Update" dialog will appear, You can choose either "Yes" or "Apply Changes".

Unpack simBio_eclipse_x.x.x.zip and put org.simBio.eclipse_* directory in Eclipse/plugins directory.

Usage

Run on GUI

Right click xml files for simBio, then pop-up menu will appear. Select [simBio] - [Run on GUI], then the XMLs are executed on GUI.

The Setting will be stored, then you can run it through the cool bottun.

You can also run the previous settings through the menu, Run - Run History.

Compose and Run

Right click an xml file for org.simBio.Composer, select [simBio] - [Compose and Run], then a model xml will be composed and be run on GUI. An "composed.xml" file will be created on the same directory, so you need to reflesh the view of Eclipse.

Run Protocol

Right click an model xml and an protocol xml, select [simBio] - [Run Protocol], then org.simBio.ResultGenerator will run the protocol.

Generate XML

Right click Reactors and/or Analyzers, select [simBio] - [Generate XML], then XML files for the specific class will be created.

Copyright

0.2.1

Mon, 06 Jun 2005 16:59:58 +0900

Dr. Alan Garny has made a function that can translate a model in CellML into the simBio style, on Cellular Open Resource　(COR).

Screen shots

xml/cor/hodgkin_huxley_squid_axon_1952_modified.xml xml/cor/vanderpol_model_1928.xml We made the latest version freely available. Download: File List at SourceForge.net Javadoc API has also updated. The matsuoka_et_al_2004 model has slightly updated.

API

Tue, 18 Jan 2005 18:35:29 +0900

Javadoc API is located at http://www.sim-bio.org/docs/api/.

Matsuoka et al., 2004

Tue, 18 Jan 2005 18:28:58 +0900

The excitation–contraction–metabolism coupling model from Matsuoka et al., 2004 is incorpolated. Download: File List at SourceForge.net Matsuoka S, Sarai N, Jo H, Noma A. Simulation of ATP metabolism in cardiac excitation-contraction coupling. Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):279-99.

download simBio_*.zip and extract all.
execute the simBio_*.jar included. (Java 2 Platform, Standard Edition, v 1.4.2 (J2SE) or later is needed, which is freely available from http://java.sun.com/.)
select [File]-[Open] and open xml/matsuoka_et_al_2004/exp/AnoxiaSimulation.xml.
select [Model]-[Start] to simulate anoxia.

LRd and Noble98 models

Tue, 16 Nov 2004 18:18:16 +0900

The guinea-pig ventricular cell models of Luo-Rudy and Noble98 are incorpolated. Faber GM, Rudy Y. Action potential and contractility changes in [Na⁺]_i overloaded cardiac myocytes: a simulation study. Biophy J 2000;78:2392-2404 Noble D, Varghese A, Kohl P, Noble P. Improved guinea-pig ventricular cell model incorporating a diadic space, IKr and IKs, and length- and tension-dependent processes. Can J Cardiol. 1998 Jan;14(1):123-34.

Matsuoka et al, 2003

Wed, 20 Oct 2004 12:00:00 +0900

We are proud of making simBio available. Download: File List at SourceForge.net This package can reproduce the results in Matsuoka et al, 2003, which is a guinea pig ventricular cell model, and Sarai et al, 2003, which is a sino-atrial node cell model. Please see docs folder included in the extracted files, for further information.

how to use

Wed, 20 Oct 2004 08:51:49 +0900

Requirements

Java2-SDK 1.4.x from http://Sun.com/.
The simBio is developed using Java2 SDK 1.4.2_01.

1st install java

Follow the instructions provided by http://Sun.com/.

2nd extract all

includes are

docs
lib
xml
simBio-0.2-*.jar

3rd run simBio

execute 'simBio-0.2-*.jar'. Double-click it or open DOS pronpt, and input

cd "simBio.0.2"
java -jar simBio-0.2-*.jar

Select xml/matsuoka_et_al_2003/ventricularCell_RK.xml from the menu 'File' - 'Open'.

4th calculate the model

click 'Model' - 'Start', the calculation will be done.
you can change the every value in the table.
If you want to calculate other model, please select proper xml such as "xml/hodgkin_huxley_1952/squid_axon.xml".

To use cool bar, select 'Tool' - 'Option', and drug and drop the buttons.

404 Not Found

Sun, 18 Jan 2004 19:34:43 +0900

The requested URL was not found on this server. The link seems to be wrong or outdated. Please inform the author of that page about the error. If you entered the URL manually please check your spelling and try again.

403 Forbidden

Sun, 18 Jan 2004 19:32:29 +0900

You don't have permission to access the requested directory or object. There is either no index document or the directory is read-protected. It is either read-protected or not readable by the server.

401 Unauthorized

Sun, 18 Jan 2004 19:30:53 +0900

This server could not verify that you are authorized to access the requested URL. You either supplied the wrong credentials (e.g., bad password), or your browser doesn't understand how to supply the credentials required. In case you are allowed to request the document, please check your user-id and password and try again.