Compression of reactions lower bound and upper bound

[Marina Kurtz]

Hi everyone,

I need to understand how are chosen the lower and upper bound in case of compression.

For example: reaction 1: lb=0 ub=1000 reaction 2: lb=-1000 ub=1000

after compression: reaction 1 + reaction 2: lb=0 ub= 2.5

But why? 

Best regards,

Marina

[klam...@googlemail.com]

Hi Martina,

in fact, in your example, the correct bounds of the compressed reaction

should be lb=0 and ub=1000.

Do you have a simple example where you get this 2.5?

Maybe there are even more reactions that are compressed in one reaction?

Normally, the lb of the compressed reactions should be the max of all lb's

and the ub the min of all ub's.

Best,
Steffen.

[Marina Kurtz]

Hi Steffen,

I would have expected these lower and upper bounds as well.

In most cases this is also true, but in some lumped reactions something goes wrong. I have two examples:

Ecample1:

Reaction1: NADP+[vc] + Isocitrate[vc] -> H+[vc] + NADPH[vc] + CO2[vc] + 2-Oxoglutarate[vc] lb= 0 ub= 1000

Reaction2: H2O[vc] + Acetyl-CoA[vc] + Oxaloacetate[vc] -> CoA[vc] + Citrate[vc] lb= 0 ub= 1000

Reaction3: Citrate[vc] <=> H2O[vc] + cis-Aconitate[vc] lb= -1000 ub= 1000

Reaction4: Isocitrate[vc] <=> H2O[vc] + cis-Aconitate[vc] lb= -1000 ub= 1000

R1+R2+R3+R4 lumped: NADP+[vc] + H2O[vc] + Acetyl-CoA[vc] + Oxaloacetate[vc] -> H+[vc] + NADPH[vc] + CO2[vc] + 2-Oxoglutarate[vc] + CoA[vc] 

lb= 2.5614 ub= 1000

Example 2:

Reaction1: UDP-glucose[vc] + D-Fructose 6-phosphate[vc] -> UDP[vc] + Sucrose 6'-phosphate[vc] lb= 0 ub= 1000

Reaction2: H2O[vc] + Sucrose 6'-phosphate[vc] -> Pi[vc] + Sucrose[vc] lb= 0 ub=1000

R1+R2 lumped: 7.6555 UDP-glucose[vc] + 7.6555 D-Fructose 6-phosphate[vc] + 7.6555 H2O[vc] -> 7.6555 UDP[vc] +  7.6555 Pi[vc] + 7.6555 Sucrose[vc] 

lb= 7.3363e-04 ub= 24.0668

Do the changed stoichiometric coefficients destroy the lower and upper bounds here?

I have no idea what's happening. But something goes wrong. Do you maybe have an explanation?

Best regards,

Marina

[klam...@googlemail.com]

Hi Martina,

no idea what goes wrong there ... will check this next week when I'm back

in the office.

Could you perhaps send me (via email) your network + script used

to compress the network?

Thanks,

Steffen.