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Models/Acidaminococcus_intestini_R圜_MR95.xmlĥ rows × 26 columns Saving and loading communities #Ĭontructing large community models can be slow which is due to performance limitations of the solvers. Models/Acidaminococcus_fermentans_DSM_20731.xmlĪcidaminococcus intestini R圜-MR95 (568816.4) Models/Achromobacter_xylosoxidans_NBRC_15126.xmlĪcidaminococcus fermentans DSM 20731 (591001.3) Models/Abiotrophia_defectiva_ATCC_49176.xmlĪchromobacter xylosoxidans NBRC 15126 = ATCC 2. Saccharolytic, fermentative or respiratory Here the “file” column only contains the base names for the files but you can easily prepend any path as demonstrated in the following:Ībiotrophia defectiva ATCC 49176 (592010.4) For microbial communities micom includes a larger taxonomy for 773 microbial species from the AGORA paper. The presented community here is pretty simplistic. Since we did not specify this in the original taxonomy micom assumes that all individuals are present in the same quantity. This column quantifies the relative quantity of each individual in the community. In order to convert the specification in a community model we will use the Community class from micom which derives from the cobrapy Model class.Īs you can notice we have gained a new column called abundance. One special example is “abundance” which we will get to know soon :) The logic behind requiring the community information in this table format is that this table can be appended as supplement to your project or publication as is and describes your community composition without any doubt. In fact the specification may contain any number of additional information which will be saved along with the community model. home/cdiener/code/micom/micom/data/e_coli_cor.Īs we see this specification contains the required fields and some more information.
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