Tools - Revision history

Raquell: Protected "Tools": Historical [edit=autoconfirmed:move=autoconfirmed]

2007-12-19T14:54:45Z

Protected "Tools": Historical [edit=autoconfirmed:move=autoconfirmed]

← Older revision

Revision as of 14:54, 19 December 2007

2007-07-30T23:45:38Z

← Older revision		Revision as of 23:45, 30 July 2007
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	==Other tools of interest==		==Other tools of interest==

-	JDesigner \| JigCell \| Excel \| MatLab	+	JDesigner \| JigCell \| Excel \| MatLab \| XPP

	===[http://sbw.kgi.edu/software/jdesigner.htm JDesigner]===		===[http://sbw.kgi.edu/software/jdesigner.htm JDesigner]===
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	===MCell===		===MCell===
		+
		+	===XPPAUT===

2007-07-30T23:41:00Z

[http://www.nrcam.uchc.edu/ Virtual Cell]

← Older revision		Revision as of 23:41, 30 July 2007
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-	===[http://www.~~nrcam~~.~~uchc.edu~~/ Virtual Cell]===	+	===[http://www.vcell.org/ Virtual Cell]===


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	'''Virtual Cell Software Guides'''		'''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]		[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==		==Other tools of interest==

2007-05-03T01:23:07Z

← Older revision		Revision as of 01:23, 3 May 2007
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	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.		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==		==Other tools of interest==

2007-05-03T01:11:11Z

← Older revision		Revision as of 01:11, 3 May 2007
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	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.		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.
-


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	===MatLab===		===MatLab===
		+
		+	===MCell===

2007-05-03T01:10:21Z

[http://jigcell.biol.vt.edu/ JigCell]

← Older revision		Revision as of 01:10, 3 May 2007
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	==Tools used during the workshop==		==Tools used during the workshop==

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	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.		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.

-	~~===[http://jigcell.biol.vt.edu/ JigCell]===~~
-
-	~~This modeling framework makes uses a spreadsheet interface, solves differential equations, allows users to enter their own rate constants and input conditional statements for the simulation.~~
-
-	Because the cell cycle underlies the growth, development, and reproduction of all living organisms, knowledge about its control is central to cell biology and has potential applications in the health care and pharmaceutical industries. We want to develop novel, computational tools, with user-friendly interfaces, for studying complex biochemical regulatory systems in general, and the cell cycle control system in particular.
-	~~- exerpted from the JigCell site.~~

-	~~Paper on the JigCell Model Builder (PDF)~~

	===Excel===		===Excel===

	===MatLab===		===MatLab===

2007-05-02T02:03:58Z

← Older revision		Revision as of 02:03, 2 May 2007
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-

	==Tools used during the workshop==		==Tools used during the workshop==
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	===MatLab===		===MatLab===
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-	~~===GenMapp===~~
-
-
-	~~The main features underlying GenMAPP are:~~
-
-	* Draw pathways with easy to use graphics tools
-	* Color genes on MAPP files based on user-imported genomic data
-	* Query genomic data against MAPPs and the GeneOntology with MAPPFinder
-
-	~~- excerpted from the GenMapp site.~~

2007-05-01T17:59:48Z

← Older revision		Revision as of 17:59, 1 May 2007
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-	~~Tools~~	+
-	~~_______________________________________________________~~	+

	==Tools used during the workshop==		==Tools used during the workshop==

2007-05-01T17:59:04Z

← Older revision		Revision as of 17:59, 1 May 2007
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	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.		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.

-	===JigCell===	+	===[http://jigcell.biol.vt.edu/ JigCell]===

	This modeling framework makes uses a spreadsheet interface, solves differential equations, allows users to enter their own rate constants and input conditional statements for the simulation.		This modeling framework makes uses a spreadsheet interface, solves differential equations, allows users to enter their own rate constants and input conditional statements for the simulation.

2007-05-01T17:58:05Z

← Older revision		Revision as of 17:58, 1 May 2007
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	[[Tools#Stella\|Stella]] \| [[Tools#Virtual Cell\|Virtual Cell]]		[[Tools#Stella\|Stella]] \| [[Tools#Virtual Cell\|Virtual Cell]]

-	===Stella===	+	===[http://www.hps-inc.com/softwares/Education/StellaSoftware.aspx Stella]===


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-	===Virtual Cell===	+	===[http://www.nrcam.uchc.edu/ Virtual Cell]===


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	JDesigner \| JigCell \| Excel \| MatLab		JDesigner \| JigCell \| Excel \| MatLab

-	===JDesigner===	+	===[http://sbw.kgi.edu/software/jdesigner.htm JDesigner]===