Copasi - Revision history

Jwelker: /* Metabolic Control Analysis */

2019-07-01T20:53:55Z

Metabolic Control Analysis

2019-07-01T20:44:10Z

Helpful Tips

2019-07-01T20:42:40Z

Parameter Scanning and Sampling

2019-07-01T20:20:53Z

Reports

2019-07-01T18:54:07Z

2019-07-01T18:53:50Z

2019-07-01T18:53:33Z

2019-07-01T18:53:16Z

2019-07-01T18:52:49Z

Steady State

2019-07-01T18:52:38Z

Steady State

← Older revision		Revision as of 20:53, 1 July 2019
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	==Metabolic Control Analysis==		==Metabolic Control Analysis==

		+	Metabolic Control Analysis (MCA) is a mathematical framework used to assess how the control upon the steady state values of the system's variables is distributed among the different reactions.

		+	'''Calculating Control Coefficients'''
		+
		+	# Download the model on which you wish to run an MCA.
		+	# Click the triangle next to "Task" and select "Metabolic Control Analysis" then click "Run."
		+	# Select the Flux Control Coefficients Tab.
		+
		+	'''Flux Control Coefficients Tab'''
		+	* Rows represent the fluxes of the reactions.
		+	* Columns represent the enzymes that catalyze the reactions.
		+	* Flux control coefficients can be negative.
		+
		+	'''Concentration Control Coefficients'''
		+	* Columns represent the perturb of the enzymes.
		+	* Rows represent the species that were affected.

	==Helpful Tips==		==Helpful Tips==

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 * For Steady-State, if you only want to use one method, the other methods can be set to 0.
 * If the rates are not close to zero in the results of the steady state, then you need to adjust the method.
 ==References==
 [http://copasi.org/Support/Video_Tutorials/ Copasi Website]

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 ==Parameter Scanning and Sampling==
+# Click the triangle next to "Tasks" and select "Parameter Scan" from the drop down menu.
+# Choose the calculation you want to perform from the drop down menu.
 ==Metabolic Control Analysis==

← Older revision		Revision as of 20:20, 1 July 2019
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	==Reports==		==Reports==

		+	How to configure output text reports.

		+	# Load a model
		+	# Set up a task
		+	# Click "Output Assistant" and choose an option under "Reports."
		+	# Click the triangle next to "Output Specifications" then choose "Report Templates" your new template should have appeared.
		+	# Customize the template by deleting the parameters you are uninterested in.
		+	# Return to your task and click the "Report" button.
		+	# Select your report template, uncheck the "Append" box, rename the file, and click "OK."
		+	# Run the task.
		+	# Click "Yes" to the pop-up window.

		+	'''Opening the file in a spreadsheet software'''
		+
		+	* Separate by tabs.

	==Parameter Scanning and Sampling==		==Parameter Scanning and Sampling==

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 Finding a combination of methods that works may take some trial and error.
 You can check your steady state by making a plot and ensuring the lines are all completely horizontal.
 [[File:steadystate.png|400px|thumb|left|Figure 1. This graphic depicts the difference between a stable and unstable steady state. While both of these are steady states, only one is stable.]]

← Older revision		Revision as of 18:53, 1 July 2019
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	[[File:steadystate.png\|400px\|thumb\|left\|Figure 1. This graphic depicts the difference between a stable and unstable steady state. While both of these are steady states, only one is stable.]]		[[File:steadystate.png\|400px\|thumb\|left\|Figure 1. This graphic depicts the difference between a stable and unstable steady state. While both of these are steady states, only one is stable.]]
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← Older revision		Revision as of 18:53, 1 July 2019
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	Finding a combination of methods that works may take some trial and error.		Finding a combination of methods that works may take some trial and error.
	You can check your steady state by making a plot and ensuring the lines are all completely horizontal.		You can check your steady state by making a plot and ensuring the lines are all completely horizontal.
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−	~~[[File:steadystate.png\|400px\|thumb\|left\|Figure 1. This graphic depicts the difference between a stable and unstable steady state. While both of these are steady states, only one is stable.]]~~
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		+	[[File:steadystate.png\|400px\|thumb\|left\|Figure 1. This graphic depicts the difference between a stable and unstable steady state. While both of these are steady states, only one is stable.]]

← Older revision		Revision as of 18:53, 1 July 2019
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	[[File:steadystate.png\|400px\|thumb\|left\|Figure 1. This graphic depicts the difference between a stable and unstable steady state. While both of these are steady states, only one is stable.]]		[[File:steadystate.png\|400px\|thumb\|left\|Figure 1. This graphic depicts the difference between a stable and unstable steady state. While both of these are steady states, only one is stable.]]
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	==Reports==		==Reports==

← Older revision		Revision as of 18:52, 1 July 2019
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	Finding a combination of methods that works may take some trial and error.		Finding a combination of methods that works may take some trial and error.
	You can check your steady state by making a plot and ensuring the lines are all completely horizontal.		You can check your steady state by making a plot and ensuring the lines are all completely horizontal.
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