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.
d3flux
by Peter St. John
Tags: visualization
This package implements a d3.js based visualization tool for cobrapy models.
escher
by Zachary A. King
Tags: visualization
Escher is a web-based tool for building, viewing, and sharing visualizations of biological pathways. These ‘pathway maps’ are a great way to contextualize data about metabolism.
SAMMI
by Andre Schultz
Tags: visualization
SAMMI is an interactive tool for the visualization of constraint-based models. While automated features allow for easy network partitioning, navigation, and node positioning, SAMMI also offers a wide array of manual map editing features. This combination allows for fast, context-specific visualization of metabolic networks as well as the development of standardized, large-scale, visually appealing maps.
StrainDesign
by Philipp Schneider, Pavlos Stephanos Bekiaris, Axel von Kamp, Steffen Klamt
Tags: strain-design , visualization , cell-factories , minimal cut sets
StrainDesign, a comprehensive Python package that integrates the most popular deterministic metabolic design algorithms, including nested strain optimization methods such as RobustKnock, OptCouple and OptKnock, as well as the more general minimal cut sets approach. The optimization approaches are embedded in individual modules, which can also be combined for setting up more elaborate strain design problems. Advanced features, such as the efficient integration of GPR-rules, the consideration of gene and reaction additions and of regulatory interventions are available for all modules.