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LPEMs ?

More constraint scaning ?

Link to the model archive [[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/P6.zip|here]]
 = Introduction to LPEMs =
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Instructions '''Instructions'''
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3. A new directory called '''P6''' will be created. From the terminal, cd to the `P6/model` directory. 3. A new directory called '''P6''' will be created. From the terminal, cd to the `P6/Analysis `directory.
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6. Add `Analysis` directory to path and import necessary modules 6. Read Model

{{{#!python
 m = ScrumPy.Model('../model/A.woodii.spy')
}}}
7. Import the BuildLP module that will help us create LP problem.
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import sys
sys.path.append('../Analysis')
import lpems
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7. We will now create a LP problem from this model. We would make the LP such that its objective function is minimization of total fluxes and there is no demand on biomass production. However, we will set a demand on the production of acetate and ethanol with a fixed value 1. 8. We will now create a LP problem from this model. We would make the LP such that its objective function is minimization of total fluxes and there is no demand on biomass production. However, we will set a demand on the production of acetate and ethanol with a fixed value 1.
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lp.SetFixedFlux({'ACET_bp_tx': -1}) 		 lp.SetFixedFlux({'ACET_bp_tx': -1})
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8. Solve the LPEMs. We have written a small function that will solve the above lp and apply the LPEM algorithm on the solution and return you the LP solution (`sol`) and the LPEMS result (`modes`).		 9. We will solve this LP problem and calculate the LPEMs for the solution. We have written a small function that will solve the above lp and apply  the LPEM algorithm on the solution and return you the LP solution (`sol`) and the LPEMS result (`modes`).
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import lpems
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10. Print the transport reactions active in the solution. Hint: The transport reaction ids have `_tx` in them.
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9. Print the transport reactions active in the solution. Hint: The transport reaction ids have `_tx` in them. 11. How many reaction are active in the solution?
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10. How many reaction are active in the solution? Did you find any common reactions from Practical 4? 12. How many LPEM modes did you get?
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11. How many LPEM modes did you get? To print the modes use following command
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To print the modes use following command print(modes.Stos()) print(modes.Stos())

Introduction to LPEMs

LPEM algorithm decomposes the steady state flux vector into weighted elemetary modes such that the sum of these elementary modes is the original flux vector.

Here we will apply LPEM algorithm to genome scale metabolic model (GSM) of Acetobacter woodii. As seen in practical 4, the organism is capable of assimilating CO2, CO and H2 and produce acetate and ethanol. We will use the GSM of A. woodii to investigate the LPEMs utilized for the production of acetate and ethanol. We will see if the organism utilizes CO and H2.

Instructions

1. Download the required model and python code file from here. This is a zip file.

2. Copy the downloaded zip file in the workshop directory on your system and extract the zip file.

3. A new directory called P6 will be created. From the terminal, cd to the P6/Analysis directory.

4. Start ScrumPy from this directory.

5. Read model. The name of the main model file is A.woodii.spy. Recall from previous practicals and read this model.

6. Read Model 

   1  m = ScrumPy.Model('../model/A.woodii.spy')

7. Import the BuildLP module that will help us create LP problem. 

   1 import BuildLP

8. We will now create a LP problem from this model. We would make the LP such that its objective function is minimization of total fluxes and there is no demand on biomass production. However, we will set a demand on the production of acetate and ethanol with a fixed value 1. 

   1 lp = BuildLP.NoBiomassLP(m)
   2 lp.SetFixedFlux({'ACET_bp_tx': -1})
   3 lp.SetFixedFlux({'ETOH_bp_tx': -1})

9. We will solve this LP problem and calculate the LPEMs for the solution. We have written a small function that will solve the above lp and apply the LPEM algorithm on the solution and return you the LP solution (sol) and the LPEMS result (modes). 

   1 import lpems
   2 sol, modes = lpems.GetLPEMs(m,lp)

10. Print the transport reactions active in the solution. Hint: The transport reaction ids have _tx in them.

11. How many reaction are active in the solution?

12. How many LPEM modes did you get?

To print the modes use following command 

   1 print(modes.Stos())

None: Meetings/Nottingham2024/Prac6 (last edited 2024-12-12 10:32:52 by trunil)