Installing COBRA toolbox for MATLAB

2010-09-01T14:03:33Z

COBRA with SBML Toolbox v2::

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	== SBML Toolbox download and installation==		== SBML Toolbox download and installation==
-	The COBRA Toolbox is not fully compatible with version 3 of the SBML Toolbox. ~~We have been able~~ to ~~use it~~ with ~~either~~ version 2 (described [http://benheavner.com/systemsbio/index.php?title=Installing_COBRA_toolbox_for_MATLAB&action=submit#COBRA_with_SBML_Toolbox_v2: here]) or version 3.1.2 (described [http://benheavner.com/systemsbio/index.php?title=Installing_COBRA_toolbox_for_MATLAB&action=submit#COBRA_with_SBML_Toolbox_v3.1.2: here])	+	The COBRA Toolbox is not fully compatible with version 3 of the SBML Toolbox. Specifically, the functions relating to reading and writing SBML depend upon a certain data structure produced by the SBML Toolbox. This structure changed between versions 2 and 3 of the SBML Toolbox.
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		+	The COBRA Toolbox is fully compatible with SBML Toolbox version 2 (described [http://benheavner.com/systemsbio/index.php?title=Installing_COBRA_toolbox_for_MATLAB&action=submit#COBRA_with_SBML_Toolbox_v2: here]), but cannot import models in newer versions of SBML.
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		+	If you modify the necessary functions for converting the data structure from new versions of the SBML Toolbox, the COBRA Toolbox can also be used with version 3.1.2 of the SBML Toolbox (installation is described [http://benheavner.com/systemsbio/index.php?title=Installing_COBRA_toolbox_for_MATLAB&action=submit#COBRA_with_SBML_Toolbox_v3.1.2: here])


	=== COBRA with SBML Toolbox v2: ===		=== COBRA with SBML Toolbox v2: ===
-	SBML Toolbox Version 2 (including 2.0.2) is now old, but it's compatible with the COBRA toolbox. Since it's old, it doesn't read and write the latest versions of SBML. ~~Therefore~~, ~~'''using~~ Version 3.1.2 ~~is recommended'''~~. See the [http://sbml.org/Software/SBMLToolbox SBML Toolbox website] for more information about the SBML toolbox's functionality.	+	SBML Toolbox Version 2 (including 2.0.2) is now old, but it's compatible with the COBRA toolbox. Since it's old, it doesn't read and write the latest versions of SBML. You need to either save newer models in an old version of SBML (possibly losing information in the process), or modify portions of the COBRA toolbox to allow the use Version 3.1.2. See the [http://sbml.org/Software/SBMLToolbox SBML Toolbox website] for more information about the SBML toolbox's functionality.
	#Download '''version 2.0.2''' of the SBML Toolbox. The file you want is called "[http://sourceforge.net/projects/sbml/files/SBMLToolbox/2.0.2/SBMLToolbox-2.0.2-setup-win32.exe/download SBMLToolbox-2.0.2-setup-win32.exe]". If you download from [http://sourceforge.net/project/showfiles.php?group_id=71971&package_id=129013 Sourceforge], be sure to scroll down to get version 2.0.2, '''not''' version 3.		#Download '''version 2.0.2''' of the SBML Toolbox. The file you want is called "[http://sourceforge.net/projects/sbml/files/SBMLToolbox/2.0.2/SBMLToolbox-2.0.2-setup-win32.exe/download SBMLToolbox-2.0.2-setup-win32.exe]". If you download from [http://sourceforge.net/project/showfiles.php?group_id=71971&package_id=129013 Sourceforge], be sure to scroll down to get version 2.0.2, '''not''' version 3.
	#Double click the installer that you downloaded. By default, this will install the Toolbox to C:\Program Files\SBML\SBMLToolbox-2.0.2 This default is okay.		#Double click the installer that you downloaded. By default, this will install the Toolbox to C:\Program Files\SBML\SBMLToolbox-2.0.2 This default is okay.
	# Do not install the libsbml libraries to the system path. Leave the "Write libsbml libraries to 'C:\WINDOWS\system32'" box '''unchecked'''.		# Do not install the libsbml libraries to the system path. Leave the "Write libsbml libraries to 'C:\WINDOWS\system32'" box '''unchecked'''.
-	# After ~~th[http://www.example.com link title]e~~ install wizard finishes, in Matlab, navigate to C:\Program Files\SBML\SBMLToolbox-2.0.2\toolbox	+	# After the install wizard finishes, in Matlab, navigate to C:\Program Files\SBML\SBMLToolbox-2.0.2\toolbox
	# Add the SBML Toolbox to your Matlab PATH variable by typing "install"		# Add the SBML Toolbox to your Matlab PATH variable by typing "install"
	# Matlab will give you a warning that future versions will not work with .dll files. This is okay.		# Matlab will give you a warning that future versions will not work with .dll files. This is okay.
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	=== COBRA with SBML Toolbox v3.1.2: ===		=== COBRA with SBML Toolbox v3.1.2: ===
-	SBML Toolbox Version 3.1.2 is ~~(mostly)~~ compatible with the COBRA toolbox. As distributed, the COBRA Toolbox ~~function~~ "writeCbModel" ~~fails testing~~. You'll need to do some recoding to ~~fix~~ the ~~problem~~. ~~I haven't worked through~~ the ~~issue to troubleshoot it yet~~.	+	SBML Toolbox Version 3.1.2 is not compatible with reading and writing SBML files for use with the COBRA toolbox. As distributed, the COBRA Toolbox functions "readCbModel" and "writeCbModel" do not work. You'll need to do some recoding to translate from the SBML Toolbox data structure to the one expected by the COBRA Toolbox. However, the payoff for this effort is that you can use the COBRA Toolbox with newer models, such as the [http://www.comp-sys-bio.org/yeastnet/ Yeastnet Consensus Reconstruction].

	# The SBML Toolbox Version 3.1.2 requires that you install libsbml version 4.0.1 (or version 4.1.0) with matlab bindings first (SBML Toolbox Version 2.0.2 installs libSBML as part of the automated install procedure).		# The SBML Toolbox Version 3.1.2 requires that you install libsbml version 4.0.1 (or version 4.1.0) with matlab bindings first (SBML Toolbox Version 2.0.2 installs libSBML as part of the automated install procedure).

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Installing COBRA toolbox for MATLAB