Unsuccessful Pruning

[Wylan Wong]

Hi, I'm a beginner to this software and I am trying to prune and compress a Synechocystis PCC 6803 genome scale model to its central carbon metabolism using the Network Reducer. However, I cannot achieve the same results reported in the Erdrich et al. (2015) paper using the reduce_Synechocystis.m script provided by the paper. Please advise, thank you!

Wylan

[Wylan Wong]

P.S. By unsuccessful I mean that only 3 reactions were pruned from the 599-reaction model. The compression works.

[Steffen]

Hi Wylan,

we will test the script with the current CNA version and
then come back to you shortly. It might be that there have
been some changes in the NetworkReducer function that
are not  compatible anymore with the scripts from this paper.

Have you tested the E.coli compression scripts? Do they work?

Best,
Steffen.

[Steffen]

Hi Wylan,

We found the bug!

Please download CNA again and then try once more.

Note that some minor differences in the reduced networks are possible,
which depend on your system, MATLAB version etc. (this may lead to a
a different order of reaction removals; however, the set constraints will be
fulfilled in any case).

Please let us know whether this works now.

Best,
Steffen.

[Wylan Wong]

Hi Steffen,

Thank you for your quick response! I have reinstalled CNA and tried to use Network Reducer again and it worked as desired. Please ignore my message earlier about an error, that was simply because I did not activate CNA. Thanks again for your help.

Wylan