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.

Flux Balance Analysis

• MS2 - Build Prokaryotic Metabolic Models with OMEGGA – Construct genome-scale metabolic models based on a bacterial genome and media conditions utilizing omics-enabled global gapfilling (OMEGGA)

  • Red - consumed, green - produced, blue - not consumed

• MS2 - Improved Gapfill Metabolic Model with OMEGGA – Fill in missing reactions based on stoichiometry

• Run Flux Balance Analysis – Predict metabolic fluxes based on steady state analyses

• Compare FBA solutions – Determine optimal conditions of flux

• Check Model Mass Balance – Ensure accuracy

• Compare Models – View multiple models side by side

Editing Models

• Edit Metabolic Model – Build unique models suited to specific experiments.

• Create or Edit Media – Create specialized growth conditions

• Bulk Download Modeling Objects – Save modeling data for future analysis

Comparative Genomics

• Propagate Model to New Genome – Translate metabolic models from one organism to another

Expression

• 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
• Simulate Growth on Phenotype Data – Reconcile models with empirical data

Metabolomics

• 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 App (in beta) – Generate novel compounds from an FBA Model and a Chemical Abundance Matrix

  • 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

Microbial Communities

• Merge Metabolic Models into Community Model – Investigate community metabolism
• Build Metagenome Metabolic Model – Build a metagenome metabolic model from an annotated assembly or bins