Tutorial
This page walks through the interactive explorer and the static phase map. Everything below reads precomputed data shipped with the package — no kinetic model, no ODE solve.
Launching the explorer
using GlycolysisPentosePathwayPhaseMap
explore()explore() opens a native GLMakie window over a cached 3-D ATP × NADPH × R5P demand grid. It blocks until you close the window. To use a different grid CSV, pass a path: explore("path/to/grid.csv").
<!– A screenshot of the explorer will be added here (assets/explorer.png). –>
Reading the cycle-index heatmap
The left panel is a heatmap of the pentose-cycle index over the NADPH × R5P demand plane (see The science for the definition). Under the diverging colormap:
- blue cells = forward pentose cycle (index ≈ 1),
- red cells = reverse PPP (index < 0, non-oxidative R5P production),
- gray cells = non-converged operating points (masked, never silently dropped).
A black contour marks the sign-flip boundary between the cycle and reverse regions.
Clicking cells
Click any cell in the heatmap. The large combined glycolysis + PPP flux network on the right redraws from that operating point's cached fluxes. The footer reports the absolute max |flux| (µM/min) for that cell, its mode, and its cycle index.
The ATP-demand slider
Below the panels is an ATP-demand slider that varies ATP demand across log-spaced levels (roughly 1 %–20 % of maximal ATP supply). Moving it re-slices the cached 3-D grid: the heatmap, its sign-flip contour, and the flux network all update instantly — again, with no ODE re-solve. The explorer opens at the level nearest 10 % of ATP supply.
The flux network
The network is the glycolysis spine plus the oxidative branch (G6PD → PGLS → PGD) and the reversible non-oxidative PPP (RPI, RPE, TKT, TALDO1). Each arrow's color encodes direction (forward vs reverse) and its width is proportional to |flux|, autoscaled per selected cell. Metabolite nodes carry their model symbols (G6P, F16BP, Ru5P, …); arrows carry their enzyme names.
The metabolite panel
Below the network sits a full-width metabolite box-plot panel covering 16 metabolites (Glucose, G6P, F6P, F16BP, DHAP, GAP, ATP, NADP, NADPH, PGLn, PGA, Ru5P, R5P, X5P, S7P, E4P). For the currently selected cell, each metabolite's steady-state pool (µM, log y-axis) is drawn as a purple diamond over a static literature box-and-whisker measured from mammalian cell concentrations. The diamonds redraw on every click and slider move; the boxes are static. Diamonds sitting off their boxes flag known model discrepancies.
The static phase map
For a publication-style figure, render the static Layout-A phase map with CairoMakie:
phasemap() # returns a Figure
phasemap(save="phasemap.png") # returns the Figure and writes a PNGThe figure is a cycle-index heatmap over the NADPH × R5P demand plane (with the sign-flip contour) plus two representative glycolysis + PPP flux schematics — one for a cycle operating point and one for a reverse operating point.