bio-systems-biology-context-specific-models

What problem does it solve?

Constrain generic genome-scale metabolic models (GEMs) with transcriptomics or proteomics to produce tissue-, cell-type-, or condition-specific metabolic networks that reflect active metabolism and enable context-aware flux predictions.

Core Features & Use Cases

• Expression integration: Map gene or protein abundance to reactions using GPR rules and aggregate using max/min/mean logic.
• Context model algorithms: Apply GIMME, iMAT, or INIT-style approaches to penalize low-expression reactions and enforce minimum biological objectives.
• Validation & comparison: Preserve growth or objective activity, quantify constrained reactions, and compare flux distributions between original and context models.
• Use Case: Create a liver-specific Recon3D model from GTEx TPMs to study altered pathway activity in metabolic disease or build cancer cell models from tumor RNA-seq.

Quick Start

Create a liver-specific metabolic model from Recon3D using GTEx TPMs and apply GIMME to constrain reactions based on expression.