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SysBioChalmers / Kluyveromyces_marxianus-GEM

The consensus GEM for Kluyveromyces marxianus
https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM
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Help: For intergrating the TSS seq of 30D, 30DS, and 45D into the K. marxianus model #7

Closed wenjuanmo closed 4 years ago

wenjuanmo commented 4 years ago

As described in the paper, 'The TSS-seq data was used to turn off the gene-associated reactions without transcriptional evidence while leaving the constraints for other reactions intact. ... This was done by firstly fixing the lower and upper bounds for the biomass reaction to the 90% of the maximal growth rate and then maximizing the production for the biomass components of interest'. We followed this instruction and performed the simulation in the 30D condition for maximizing the production of protein. However, the simulation cannot be successfully calculated. Matlab commands are provided in the following.

model=importExcelModel('12859_2019_3134_MOESM2_ESM.xlsx',false); model=setParam(model,'eq',{'r_1913'},[0.54]);

set the maximal growth rate as 0.6, then its 90% is 0.54. This could also be achieved by setting

model=setParam(model,'lb',{'r_1913'},[0.540.9999]); model=setParam(model,'ub',{'r_1913'},[0.541.0001]); model=setParam(model,'obj',{'r_1906'},1); # maximizing the production for protein model30D= model; model30D=setParam(model30D,'eq',{'r_0346'},0); model30D=setParam(model30D,'eq',{'r_0657'},0); model30D=setParam(model30D,'eq',{'r_1127'},0); model30D=setParam(model30D,'eq',{'r_0559'},0); model30D=setParam(model30D,'eq',{'r_0606'},0); model30D=setParam(model30D,'eq',{'r_0846'},0); model30D=setParam(model30D,'eq',{'r_0848'},0); model30D=setParam(model30D,'eq',{'r_0853'},0); model30D=setParam(model30D,'eq',{'r_0019'},0); model30D=setParam(model30D,'eq',{'r_0410'},0); model30D=setParam(model30D,'eq',{'r_0411'},0); model30D=setParam(model30D,'eq',{'r_0768'},0); model30D=setParam(model30D,'eq',{'r_1160'},0); model30D=setParam(model30D,'eq',{'r_1161'},0); model30D=setParam(model30D,'eq',{'r_1174'},0); sol30D=solveLP(model30D,1); printFluxes(model, sol30D.x, true, 10^-7); # to print the fluxes of exchange reactions
The result shows: mistake in dispEM (line 50) The number of fluxes and the number of reactions must be the same wrong in printFluxes (line 69) dispEM(EM)

Could you tell me what's wrong in the simluation operation, and how about the correct way for simulation in the 30D condition?

simas232 commented 4 years ago

@wenjuanmo, you need to set the contraints for in silico YPD medium first. See #6 for the more information.

wenjuanmo commented 4 years ago

Thanks a lot!

-----原始邮件----- 发件人:"Simonas Marcišauskas" notifications@github.com 发送时间:2020-02-19 02:01:39 (星期三) 收件人: SysBioChalmers/Kluyveromyces_marxianus-GEM Kluyveromyces_marxianus-GEM@noreply.github.com 抄送: wenjuanmo wenjuanmo@fudan.edu.cn, Mention mention@noreply.github.com 主题: Re: [SysBioChalmers/Kluyveromyces_marxianus-GEM] Help: For intergrating the TSS seq of 30D, 30DS, and 45D into the K. marxianus model (#7)

@wenjuanmo, you need to set the contraints for in silico YPD medium first. See #6 for the more information.

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