BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities. - Eugen Bauer; Johannes Zimmermann; Federico Baldini; Ines Thiele; Christoph Kaleta (PLoS Comput. Biol., 2017)

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. - Federico Baldini; Almut Heinken; Laurent Heirendt; Stefanía Magnúsdóttir; Ronan M. T. Fleming; Ines Thiele (Bioinform., 2019)

pymgpipe: microbiome metabolic modeling in Python. - Yoli Meydan; Federico Baldini; Tal Korem (J. Open Source Softw., 2023)