Metabolic Modeling in KBase

Metabolic modeling

KBase has a suite of Apps and data that support the reconstruction, prediction, and design of metabolic models in microbes and plants. Genome-scale metabolic models are primarily reconstructed from protein functional annotations. These 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.

Metabolic models can be used to evaluate an organism’s metabolic capability by simulating growth under different conditions to answer important biological questions such as:

  • What biochemical pathways are present?
  • What are the high flux pathways under a certain growth condition?
  • Could the organism grow anaerobically?
  • Would it grow under certain minimal media conditions?
  • Could the organism be optimized to produce a particular drug molecule or industrially important biofuel?

KBase Metabolic Modeling Capabilities

Generate Genome-scale Metabolic Models

  • Construct genome-scale metabolic models from a genome and media condition with Build Metabolic Model
  • Fill in missing reactions based on stoichiometry with Gapfill Metabolic Model
  • Build unique models suited to specific experiments with Edit Metabolic Model
  • View multiple models side by side with Compare Models

Analyze Flux Balance

  • Predict metabolic fluxes with Run Flux Balance Analysis
  • Create specialized growth conditions with Edit Media
  • Determine optimal conditions of flux with Compare FBA Solutions
  • Ensure accuracy with Check Model Mass Balance

Extrapolate Models

  • Reconcile models with empirical data with Simulate Growth on Phenotype Data
  • Translate metabolic models from one organism to another with Propagate Model to New Genome
  • Investigate community metabolism with Merge Metabolic Models into Community Models
  • Save modeling data for future analysis with Bulk Download Modeling Objects

Flowchart of apps used in Metabolic Modeling.



  Learn more

The flowchart above shows KBase’s metabolic modeling tools (green) as well as some other analysis tools. Check the App Catalog for the latest set of metabolic modeling analysis tools (Apps).

The video tutorial at right presents an introduction to building metabolic models in KBase. The “Microbial Metabolic Model Reconstruction and Analysis” Narrative tutorial lets you see and try out for yourself some examples of KBase’s metabolic modeling functionality in action. Common questions and answers about KBase’s metabolic modeling tools can be found in the Metabolic Modeling FAQ.


Metabolic Modeling Resources in KBase


Narrative Tutorial and FAQ

Build and Gapfill Metabolic Model

Flux Balance Analysis

Evaluate, Compare and Edit Models

Phenotype and Expression

Community Modeling

Publications about Metabolic Modeling in KBase