Tools

From Computational Cell Biology

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		+	==Tools used during the workshop==
		+	[[Tools#Stella|Stella]] |  [[Tools#Virtual Cell|Virtual Cell]]
		+
		+	===[http://www.hps-inc.com/softwares/Education/StellaSoftware.aspx Stella]===
		+
		+
		+	This software uses the metaphor of flows and stocks for drafting models of dynamic systems. Model examples and tutorials can be downloaded from the company site.
		+
		+	This software is useful for Mapping and Modeling, Simulation and Analysis, and Communication
		+
		+
		+	===[http://www.vcell.org/ Virtual Cell]===
		+
		+
		+	Users create models through a graphical user interface or by generating mathematical descriptions using Virtual Cell Math Language. The tool is accessible via the web with user registration.
		+
		+	'''Virtual Cell Software Guides'''
		+	[http://www.vcell.org/login/VCell%20Quick%20Start%20Guide.pdf Quick tips][http://www.vcell.org/login/user_guide_4_1.pdf User Guide 4.1]
		+
		+	==Other tools of interest==
		+
		+	JDesigner | JigCell | Excel | MatLab | XPP
		+
		+	===[http://sbw.kgi.edu/software/jdesigner.htm JDesigner]===
		+
		+
		+	This application is used to draw biochemical networks and export the drawn network as SBML (Systems Biology Markup Language). It can be used as an interface for developing networks that run on Jarnac.
		+
		+
		+	===Excel===
		+
		+	===MatLab===
		+
		+	===MCell===
		+
		+	===XPPAUT===

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Latest revision as of 14:54, 19 December 2007

Contents 1 Tools used during the workshop 1.1 Stella 1.2 Virtual Cell 2 Other tools of interest 2.1 JDesigner 2.2 Excel 2.3 MatLab 2.4 MCell 2.5 XPPAUT

Tools used during the workshop

Stella | Virtual Cell

Stella

This software uses the metaphor of flows and stocks for drafting models of dynamic systems. Model examples and tutorials can be downloaded from the company site.

This software is useful for Mapping and Modeling, Simulation and Analysis, and Communication

Virtual Cell

Users create models through a graphical user interface or by generating mathematical descriptions using Virtual Cell Math Language. The tool is accessible via the web with user registration.

Virtual Cell Software Guides Quick tipsUser Guide 4.1

Other tools of interest

JDesigner | JigCell | Excel | MatLab | XPP

JDesigner

This application is used to draw biochemical networks and export the drawn network as SBML (Systems Biology Markup Language). It can be used as an interface for developing networks that run on Jarnac.

Excel

MatLab

MCell

XPPAUT