Tonight I started watching the KBase “Microbial Community Modeling Workshop.” Jose Faria from Argonne National Laboratory began with a session titled “Background on ModelSEED and OMEGGA Apps.” GSP 2024 is the public narrative they described. There is also a preprint with all the details. The ModelSEED2 app is the first significant update in fifteen years, said Faria. They redid the entire pipeline. The pipeline begins with RAST. A machine learning phenotype predictor leads to a core model of the organism before expanding to the genome level. Faria noted that RAST is consistent in annotation. The Build Prokaryotic Models with OMEGGA helps build a draft model. A new addition is the addition of a model summary with details on gap filling. ATP production is tested against fifty media. The draft model can then be built for glucose minimal media next. Gapfilling analysis includes information about the genes/functions needed. Faria explained that the narrative is annotated with explanations for each app and analysis. Flux balance analysis comes next and there are updated maps to view pathways. Flux solutions and expression data can be pointed onto the maps. You can switch between complete media to auxotrophic media. Users now have the ability to select reactions to “ban” and evaluate different pathways. While there are some known issues with the set of apps, improvements are continuously being released. I am curious how we can use ModelSEED2 with Biolog GEN3 data!
