CNApy
by Sven Thiele, Philipp Schneider, Axel von Kamp, Pavlos Stephanos Bekiaris, Steffen Klamt
Tags: strain-design , visualization , general-modeling , cobra , metabolic-model , minimal-cut-sets , models
CNApy is a graphical integrated environment for metabolic network analysis. With CNApy, it is possible to load, edit and create metabolic models together with interactive network maps. Many standard and advanced COBRA techniques (including, e.g., Flux Balance Analysis, Flux Variability Analysis and Minimal Cut Sets) are supported and all main results of these techniques can be directly visualized in the network maps. Furthermore, CNApy also provides a GUI for all major functions of the StrainDesign package.
mackinac
by Mike Mundy
Tags: ModelSEED , models , gapfilling , reconstruction
Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Mackinac is a Python package that combines ModelSEED’s ability to automatically reconstruct metabolic models with COBRApy’s advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms.