GlycolysisPentosePathwayPhaseMap.jl

A visualization package for the mammalian glycolysis + pentose-phosphate-pathway (PPP) demand phase map. It shows how perturbing metabolic demand — for NADPH, ribose-5-phosphate (R5P), and ATP — reorganizes the direction and scale of PPP flux, switching the pathway between linear, full pentose-cycle, and reverse (non-oxidative ribose-producing) operation. The package ships precomputed grids of steady-state fluxes and metabolite pools, so its tools work instantly, with no kinetic model and no ODE solve.

The explore() window: click any cell on the pentose-cycle-index heatmap (left) to redraw the glycolysis + PPP flux network (right) and the steady-state metabolite pools (bottom); the slider re-slices the cached 3-D grid by ATP demand.

Installation

using Pkg
Pkg.add(url="https://github.com/DenisTitovLab/GlycolysisPentosePathwayPhaseMap.jl")

Quickstart

using GlycolysisPentosePathwayPhaseMap
explore()                        # interactive GLMakie window (cached grid, no ODE solve)
phasemap(save="phasemap.png")    # static Layout-A phase map figure (PNG)

What you're looking at

Three demand levers drive the integrated glycolysis + PPP model, each set as a fraction φ of that species' sustainable supply ceiling, so all axes mean "percent of what the pathway can make." The ceilings are anchored on ribose-5-phosphate isomerase (RPI), the carbon bottleneck:

Species	Supply ceiling
NADPH	6 · RPI_cap
R5P	1.5 · RPI_cap
ATP	2 · HK1_cap

Each operating point is summarized by the pentose-cycle index (V_ox − V_R5Pase) / V_ox: ≈ 1 is a full forward pentose cycle, ≈ 0 is linear PPP, and < 0 is reverse (non-oxidative R5P production). The explorer's heatmap colors cells by this index (blue = cycle, red = reverse, gray = non-converged) and redraws the glycolysis + PPP flux network for any cell you click; an ATP-demand slider re-slices the cached 3-D grid live.

Recompute

The shipped grids are precomputed. To regenerate them you install the kinetic model (Pkg.add(url="https://github.com/DenisTitovLab/PentosePhosphatePathway.jl")), using PentosePhosphatePathway to activate the recompute extension, then call regenerate_grid(; ...) (solves the ODE model; takes minutes). See the Recompute docs.

Documentation

Full documentation: https://DenisTitovLab.github.io/GlycolysisPentosePathwayPhaseMap.jl/stable/