MaCSBio PhD student Chaitra Sarathy publishes first paper
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge.
In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes.
The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1260) and large (human, Recon 2.2) genome-scale metabolic models.
EFMviz is open-source and integrated into COBRA Toolbox. The analysis workflows used for the two use cases are detailed in the two tutorials provided with EFMviz along with the data used in this study.
Also read
-
More than another ‘to-do’: how the UTQ helped me rethink my teaching
At Maastricht University, the University Teaching Qualification (UTQ) is a professional development programme designed to strengthen teaching and learning. It supports teachers in developing core teaching competencies through a combination of workshops, peer learning, on-the-job experience, and...
-
Brightlands Circular Space focuses on integrated approach to entire plastic value chain
Construction has officially started today in Limburg of Brightlands Circular Space, a demonstration facility that accelerates the transition to circular plastics.
-
MaaSec – The Netherlands' Only Active ACM Student Chapter captures the flag
In January, a group of Computer Science students at Maastricht University launched MaaSec, currently the only active ACM student chapter in the Netherlands. And in just a few months, they've already made a name for themselves; especially in the world of Capture the Flag (CTF) competitions.