LPEMs ?

More constraint scaning ?

Link to the model archive here

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/model directory.

4. Start ScrumPy from this directory.

5. Add Analysis directory to path and import necessary modules

• import sys
• sys.path.append('../Analysis')
• import lpems
• import BuildLP

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

7.