Microbial Biotechnology and Systems Biology Community

merlin is a simple, graphical and user-oriented solution for the reconstruction of genome-scale metabolic models. It will guide you along the model reconstruction, providing several tools that help to improve and curate the model throughout the whole process. The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes, based on the annotations of the Transporter Classification Database (TCDB). BioISO is aimed at evaluating either the biomass or metabolic network formulation of a given constraint-based metabolic model.

MEWpy is an integrated Metabolic Engineering Workbench for strain design optimization. It offers methods to explore different classes of constraint-based models (GECKO, sMOMENT, ETFL), kinetic models and microbial community models. It also provides Omics integrative methods to enhance phenotypic predictions. SDDB, the Strain Design Database, is a WEB application that gathers designs from in the literature and generated by MEWPy, and allows to simulate genetic modifications and visualize how they impact metabolic pathways.