recon 2 proton balance

[Lake-Ee Quek]

Anyone has problem with Recon 2's proton balance?
As the proton balance is key in the calculation of ATP yield, I thought the following would be a good demonstration of the potential problems in Recon 2

R_NDPK1    1 M_atp_c + 1 M_gdp_c + 3 M_h_c = 1 M_adp_c + 1 M_gtp_c
R_NDPK1m    1 M_atp_m + 1 M_gdp_m = 1 M_adp_m + 1 M_gtp_m + 1 M_h_m

R_NDPK1m, I believe, is the correct representation, if we follow Recon 2's system:
M_atp_xxx: C10H13N5O13P3
M_adp_xxx: C10H12N5O10P2
M_gtp_xxx: C10H12N5O14P3
M_gdp_xxx: C10H12N5O11P2

There are two problems with R_NDPK1.
The rxn equation is not balanced. Where is "3 M_h_c" going to?

Any ideas? Perhaps I am missing something.

I am highlighting this problem, mostly in the bid to attract authors of Recon 2 to suggest a solution. Is this possible a programming bug when exporting the SBML model from your database?

[Ines Thiele]

Hi

Yes this is indeed a bug when exporting from the database. We will post the updated version asap. If interested you can find the correct reactions (but not downloadable for the moment) at humanmetabolism.org.

Please also make sure that you use recon2_model.xml not recon2.xml as it has reaction bounds as used for modeling in the paper. 

Ines

--
 
---
You received this message because you are subscribed to the Google Groups "COBRA Toolbox" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cobra-toolbo...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--

Ines Thiele, Ph.D.

Associate Professor in Systems Biomedicine

Head of the Molecular Systems Physiology Group

Luxembourg Centre for Systems Biomedicine 

UNIVERSITY OF LUXEMBOURG

CAMPUS BELVAL

7, avenue des Hauts-Fourneaux

L-4362 Esch-sur-Alzette

Luxembourg

www.lcsb.lu 

thielelab.eu 

GoogleScholarProfile

--

This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.

[Lake-Ee quek]

Hi Ines,

Thank you for the fast reply. I fully appreciate your groups’ effort in maintaining Recon X and making these resources freely available.

 

Regards,

Lake-Ee

[Lake-Ee Quek]

Recon 2.02 is up!. Thanks Ines and group for releasing the update.

Could you also provide a more detailed change log as well? I was wondering what were the other changes.

Thanks in advance.

Lake-Ee

[Ines Thiele]

Dear Lake-Ee

I have uploaded the log file to humanmetabolism.org. Recon 2.02 fixes the issue that you discovered. Thanks for your feedback! We aim to make Recon 2 even better with the help of the community.

Best Ines

--

 
---
You received this message because you are subscribed to the Google Groups "COBRA Toolbox" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cobra-toolbo...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.