Comment on page
Metabolic Modeling
Some of the tools in KBase available for metabolic modeling
KBase has a suite of Apps supporting the reconstruction, prediction, and design of metabolic models in microbes and plants. Genome-scale metabolic models can be used to explore an organism’s growth in specific media conditions, determine which biochemical pathways are present, optimize production of an important metabolite, identify high flux pathways, and more.
- MS2 - Build Prokaryotic Metabolic Models – Construct genome-scale metabolic models based on a bacterial genome and media condition
- Red - consumed, green - produced, blue - not consumed
- Compare Flux with Expression – Compare reaction fluxes with gene expression values to identify metabolic pathways where expression and flux data agree or conflict and compare with chemical abundance data
- Escher Pathway Viewer App (in beta) – Display Escher metabolic pathways and combine pathways with flux balance analysis and metabolomics data to view flux or expression.
- When viewing flux is in green and expression is in brown. The oval size and color intensity reflects metabolite abundance.
- Pickaxe is part of the MINE Databases, documentation for which can be found here: https://github.com/tyo-nu/MINE-Database/blob/master/minedatabase/pickaxe.py.
- Fit Model to Exometabolite Data (in beta) – Identify biochemical reactions to add to a draft metabolic model for production and consumption of exometabolites
- Build Metagenome Metabolic Model – Build a metagenome metabolic model from an annotated assembly or bins
Last modified 1mo ago