Hello, I am working on community smetana of emp datasets using gems reconstructed by carveme. And I want to ask you some questions.
Firstly, I recurrent your experiment from reference: (2010) Establishment and metabolic analysis of a model microbialcommunity for understanding trophic and electron accepting interactions of sub-surface anaerobic envs. However, the smetana score using default parameters is not consistent with the experiment result from the reference. So, I want to know what extra things need to be done before computing the smetana score? For example, modify GEMs or manipulate the medium?

Secondly, I want to know which medium you have used to do the analysis of emp data in your recent paper? Did the medium need to be modified according to the specific community you are computing or just set a default fixed medium?

Thank you very much for replying!

Hello,

When I tried to reproduce your work, I met a problem. I noticed that in paper fig1, you said that 'Green and orange dots mark competitive and cooperative co-occurring communities, respectively'. And I found the green and orange dots correspond to the "bin_rnd_001" and "bin_rnd_01" files, respectively, I want to know how did you seperate the "bin_rnd_001" and "bin_rnd_01" files? Or based on what principle to divide competitive and cooperative co-occurring communities?

Thanks.