Request for help regarding constrain based metabolic model

[Tanaya Bhowmick]

Hello everyone, how are you?

I have a few questions and would be very grateful if somebody can help me out. 

I have done metabolic modelling for a biofilm consortium by downloading whole genome sequences from NCBI and then using gapseq for reconstruction and gap filling. Then I inserted gene expression data using CobraPy. After that, I got an excel file which contains the flux value for activated reactions and metabolites. It also contains biomass reactions (for some bacteria the output name is bio1 and for some bacteria the output name is pseudo_biomass, however some bacteria are named both bio1 and  pseudo_biomass). I have biomass and flux value for each bacteria.

My questions are: 
1. What is the unit of the flux values
2. What is the unit of biomass reaction
3. Which procedure should I follow for normalization of the flux values (i don't have triplicates)
4. Which biomass reaction should I take? (bio1 or pseudo_biomass)
5. Also how to choose the top 10 reactions and metabolites which are activated
6. Lastly, I am unable to do the community simulation and I have biomass and flux value for each bacteria. How can I simulate it as a community (using which algorithm or tool). Can anyone please suggest which code to use.

Tanaya Bhowmick

CSIR- Senior Research Fellow

School of Environmental Studies

Jadavpur University

Kolkata-700032, INDIA