INCA (Isotopomer Network Compartmental Analysis)¶
Resource Location
/labs/SysMedBio/Q/Resources/MFA/INCA
/Volumes/lab/SysMedBio/Resources/MFA/INCA
Q:\SysMedBio\Resources\MFA\INCA
INCA is a MATLAB-based computational platform designed for Metabolic Flux Analysis (MFA) and Isotopically Non-Stationary Metabolic Flux Analysis (INST-MFA).
Scientific Context¶
Intracellular metabolic fluxes (the rates at which molecules are converted through biochemical pathways) cannot be measured directly. Metabolic Flux Analysis (MFA) solves this by introducing stable isotope-labeled tracers (e.g., \(^{13}\text{C}\)-glucose or \(^{15}\text{N}\)-glutamine) into metabolic networks. The resulting enrichment patterns (isotopomer distributions) in cellular metabolites are measured using Mass Spectrometry (MS) or Nuclear Magnetic Resonance (NMR) and regressed to calculate intracellular fluxes.
Key Capabilities of INCA¶
- Elementary Metabolite Units (EMU): INCA uses the EMU framework to model isotope labeling. The EMU algorithm dramatically reduces the computational complexity of simulating isotope tracer experiments compared to traditional isotopomer-based methods, allowing complex metabolic networks to be modeled efficiently.
- Isotopically Non-Stationary MFA (INST-MFA): Conventional MFA requires the system to reach isotopic steady-state, which can take hours or days and is often unfeasible for cells with slow metabolism or large metabolite pools (e.g., mammalian cell cultures). INST-MFA models transient, time-dependent isotope enrichment, drastically shortening experiment duration (often to minutes) and expanding the feasibility of flux analysis to previously unmodelable systems.
- Applications: Crucial for metabolic engineering (e.g., maximizing biochemical yield in microbes), cancer biology (understanding altered cancer metabolism), and systems biology (phenotypic profiling).
Main Publication¶
- Title: INCA: a computational platform for isotopically non-stationary metabolic flux analysis
- Author: Jamey D. Young
- Journal: Bioinformatics (2014, Volume 30, Issue 9, Pages 1333–1335)
- DOI: 10.1093/bioinformatics/btu015
Available Files¶
The INCA directory contains the INCA MATLAB package:
inca2.4_0.zip: Compressed archive of the INCA software distribution.inca2.4/: Main directory containing the INCA package, which includes:inca.p: Main executable script for launching the INCA environment.