MATLAB Computational Biology Tools - Revision history

Henning Schmidt at 08:41, 29 May 2008

2008-05-29T08:41:34Z

←Older revision		Revision as of 08:41, 29 May 2008
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	'''<font color="blue">This is the OWW entry page for the MATLAB Computational Biology Tools discussion page (improve these pages with impunity)</font>'''		'''<font color="blue">This is the OWW entry page for the MATLAB Computational Biology Tools discussion page (improve these pages with impunity)</font>'''
-
-	~~==Bioinformatics Toolbox==~~
-
-	~~==SimBio Toolbox==~~

	==Systems Biology Toolbox 2==		==Systems Biology Toolbox 2==
Line 16:		Line 12:
	* Statistics (clustering, percentiles, boxplots, etc.)		* Statistics (clustering, percentiles, boxplots, etc.)
	* Global and local optimization algorithms		* Global and local optimization algorithms
		+	* Signal processing functions
		+	* Statistical functions
	* etc.		* etc.

-	The SBPD extension package for the Systems Biology Toolbox 2 adds high-speed simulations, combination of models, experiments, and measurement data in so called projects. Functions are available that support the complete model building process (modeling, simulation, identifiability analysis, model reduction, parameter estimation (multiple experiment and multiple measurement fitting), validation, etc.). The projects are a powerful construct that allows to keep a perfect overview over your modeling task at any time. Graphical user interfaces support the workflow.	+	The SBPD extension package for the Systems Biology Toolbox 2 adds:

		+	* High-speed simulations
		+	* Combination of models, experiments, and measurement data in so called projects
		+	* Functions supporting the whole model building process
		+	* Modeling, simulation
		+	* Identifiability analysis
		+	* Model reduction
		+	* Parameter estimation (multiple experiment and multiple measurement fitting)
		+	* Statistical analysis
		+	* Graphical user interfaces supporting the workflow
		+
		+	The projects are a powerful construct that allows to keep a perfect overview over your modeling task at any time.

	http://www.sbtoolbox2.org/		http://www.sbtoolbox2.org/

	[[doi:10.1093/bioinformatics/bti799]]		[[doi:10.1093/bioinformatics/bti799]]
		+
		+	==Bioinformatics Toolbox==
		+
		+	==SimBio Toolbox==
		+
		+

	==General MATLAB Topics==		==General MATLAB Topics==

Henning Schmidt: /* Systems Biology Toolbox 2*/

2008-01-21T14:06:25Z

Systems Biology Toolbox 2

←Older revision		Revision as of 14:06, 21 January 2008
Line 5:		Line 5:
	==SimBio Toolbox==		==SimBio Toolbox==

-	==Systems Biology Toolbox==	+	==Systems Biology Toolbox 2==
-	The Systems Biology Toolbox for MATLAB offers systems biologists an open and user extensible environment, in which to ~~explore ideas, prototype and share new algorithms, and~~ build ~~applications for the analysis and simulation~~ of biological systems. It features a wide ~~range~~ of ~~functions:~~	+	The Systems Biology Toolbox 2 for MATLAB offers systems biologists a powerful, open, and user extensible environment, in which to build models of biological systems. Experiments can be performed on models, just like in real lab life but in silico. The representation of models, experiments, and measurement data is intuitive and easy to use. The toolbox features a wide variety of specialized analysis tools and MATLAB adds to that by a large number of inbuilt functions and a high level scripting language, allowing the user to quickly and efficiently add new functionality. Inbuild simulation and analysis tools include:
-	* Modeling (based on ODEs and ~~chemical reaction equations)~~	+
-	* Handling of ~~measurement data~~	+
-	* Import of SBML models	+
-	* Simulation (deterministic and ~~stochastic)~~	+
	* Steady-state and stability analysis		* Steady-state and stability analysis
-	* ~~Determination of the stoichiometric matrix~~	+	* Stoichiometry
	* Parameter sensitivity analysis		* Parameter sensitivity analysis
-	* Network identification
-	* Parameter estimation
	* Determination of moiety conservations		* Determination of moiety conservations
-	* Simple model reduction
	* Bifurcation analysis		* Bifurcation analysis
	* Localization of mechanisms leading to complex behaviors		* Localization of mechanisms leading to complex behaviors
-	* ~~Optimization~~ algorithms	+	* Statistics (clustering, percentiles, boxplots, etc.)
-	* and ~~some specialized functions~~ ...	+	* Global and local optimization algorithms
-	http://www.~~sbtoolbox~~.org/	+	* etc.
		+
		+	The SBPD extension package for the Systems Biology Toolbox 2 adds high-speed simulations, combination of models, experiments, and measurement data in so called projects. Functions are available that support the complete model building process (modeling, simulation, identifiability analysis, model reduction, parameter estimation (multiple experiment and multiple measurement fitting), validation, etc.). The projects are a powerful construct that allows to keep a perfect overview over your modeling task at any time. Graphical user interfaces support the workflow.
		+
		+
		+	http://www.sbtoolbox2.org/

	[[doi:10.1093/bioinformatics/bti799]]		[[doi:10.1093/bioinformatics/bti799]]

Koeris at 15:22, 19 June 2006

2006-06-19T15:22:37Z

←Older revision		Revision as of 15:22, 19 June 2006
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	* and some specialized functions ...		* and some specialized functions ...
	http://www.sbtoolbox.org/		http://www.sbtoolbox.org/
		+
		+	[[doi:10.1093/bioinformatics/bti799]]

	==General MATLAB Topics==		==General MATLAB Topics==

Koeris: Added the very cool systems bio toolbox. Citation to follow. Mike

2006-06-19T15:10:54Z

Added the very cool systems bio toolbox. Citation to follow. Mike

←Older revision		Revision as of 15:10, 19 June 2006
Line 4:		Line 4:

	==SimBio Toolbox==		==SimBio Toolbox==
		+
		+	==Systems Biology Toolbox==
		+	The Systems Biology Toolbox for MATLAB offers systems biologists an open and user extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological systems. It features a wide range of functions:
		+	* Modeling (based on ODEs and chemical reaction equations)
		+	* Handling of measurement data
		+	* Import of SBML models
		+	* Simulation (deterministic and stochastic)
		+	* Steady-state and stability analysis
		+	* Determination of the stoichiometric matrix
		+	* Parameter sensitivity analysis
		+	* Network identification
		+	* Parameter estimation
		+	* Determination of moiety conservations
		+	* Simple model reduction
		+	* Bifurcation analysis
		+	* Localization of mechanisms leading to complex behaviors
		+	* Optimization algorithms
		+	* and some specialized functions ...
		+	http://www.sbtoolbox.org/

	==General MATLAB Topics==		==General MATLAB Topics==

Ty M. Thomson at 20:40, 2 May 2006

2006-05-02T20:40:32Z

←Older revision		Revision as of 20:40, 2 May 2006
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-	'''<font color="blue">This is the OWW entry page for the ~~MathWorks~~ Computational Biology Tools discussion page (improve these pages with impunity)</font>'''	+	'''<font color="blue">This is the OWW entry page for the MATLAB Computational Biology Tools discussion page (improve these pages with impunity)</font>'''

	==Bioinformatics Toolbox==		==Bioinformatics Toolbox==
Line 5:		Line 5:
	==SimBio Toolbox==		==SimBio Toolbox==

-	==General ~~Matlab~~ Topics==	+	==General MATLAB Topics==
-	[[MATLAB\|~~Matlab~~ user tips]] <br>	+	[[MATLAB\|Basic MATLAB user tips]] <br>

	==OpenWetWare Resources==		==OpenWetWare Resources==

Ty M. Thomson: MathWorks Computational Biology Tools moved to MATLAB Computational Biology Tools

2006-05-02T20:39:12Z

MathWorks Computational Biology Tools moved to MATLAB Computational Biology Tools

←Older revision

Revision as of 20:39, 2 May 2006

Ty M. Thomson at 20:17, 2 May 2006

2006-05-02T20:17:05Z

←Older revision		Revision as of 20:17, 2 May 2006
Line 1:		Line 1:
	'''<font color="blue">This is the OWW entry page for the MathWorks Computational Biology Tools discussion page (improve these pages with impunity)</font>'''		'''<font color="blue">This is the OWW entry page for the MathWorks Computational Biology Tools discussion page (improve these pages with impunity)</font>'''

		+	==Bioinformatics Toolbox==

		+	==SimBio Toolbox==

-	==~~Resources~~==	+	==General Matlab Topics==
-	[[MATLAB\|Matlab tips]] <br>	+	[[MATLAB\|Matlab user tips]] <br>
-	[[Bioinformatics Discussion Group]]	+
-	[[Computing\|OWW Computing Resources]]	+	==OpenWetWare Resources==
-	[[Community\|Using OpenWetWare]]	+	[[Bioinformatics Discussion Group]] <br>
		+	[[Computing\|OWW Computing Resources]] <br>
		+	[[Community\|Using OpenWetWare]] <br>

Ty M. Thomson: /* Resources */

2006-05-02T20:14:52Z

Resources

←Older revision		Revision as of 20:14, 2 May 2006
Line 6:		Line 6:
	[[MATLAB\|Matlab tips]] <br>		[[MATLAB\|Matlab tips]] <br>
	[[Bioinformatics Discussion Group]]		[[Bioinformatics Discussion Group]]
		+	[[Computing\|OWW Computing Resources]]
		+	[[Community\|Using OpenWetWare]]

Ty M. Thomson at 20:12, 2 May 2006

2006-05-02T20:12:43Z

←Older revision		Revision as of 20:12, 2 May 2006
Line 4:		Line 4:

	==Resources==		==Resources==
-	[[~~Matlab~~\|Matlab tips]]	+	[[MATLAB\|Matlab tips]] <br>
	[[Bioinformatics Discussion Group]]		[[Bioinformatics Discussion Group]]

Ty M. Thomson at 20:12, 2 May 2006

2006-05-02T20:12:10Z

New page

'''<font color="blue">This is the OWW entry page for the MathWorks Computational Biology Tools discussion page (improve these pages with impunity)</font>'''

==Resources==
[[Matlab|Matlab tips]]
[[Bioinformatics Discussion Group]]