GRN Trajectory Simulation

Simulation Controls

Cells: 100

Speed: 0.1x

Noise: 0.10

Show Reference (ghost cells)

Faded cells show default behavior for comparison

Time

0.0 hours

Population

100 cells

Color By

Lineage Time Gene Expression

Lineage Distribution

Cell State Space

PC1 (Lineage Axis)

PC2 (Differentiation)

Scroll to zoom, drag to pan

Dynamics

Scroll to zoom, drag to pan

Selected Cell Expression

No cell selected

Track Genes

Select a cell to choose genes

Applies all parameter changes and restarts simulation

Simulation Time

Duration: 24h

▼ Cell Steering

Direct GRN manipulation - force cells into unusual states

Lineage Forcing (direct TF activation)

Add external signal to lineage TFs: -1=inhibit, 0=none, +1=activate

Lin 1 0.0

Lin 2 0.0

Lin 3 0.0

Lin 4 0.0

Lin 5 0.0

Lin 6 0.0

Position Bias (visual)

X (L↔R) 0.0

Y (D↔U) 0.0

Click Attractors (visual)

Strength 0.30

Click on plot to place visual attractors

▼ Knockouts

Progenitor TFs

Lineage TFs

Ligands

Receptors

▼ Gene Modifiers

Adjust activity: 0=inhibited, 1=normal, 2=activated

Progenitor TFs

Lineage TFs

Ligands

Receptors

▼ Morphogens

Enable/Disable

Strength

M11.0

M21.0

M31.0

M41.0

M51.0

M61.0

Uniform application

Apply to all cells equally (no spatial gradient)

▼ Network Edges

Purple=enabled, Red=disabled

▼ Advanced Parameters

Initial Expression

Prog TFs 1.50

Lin TFs 0.00

Ligands 0.20

Regulatory

Prog Bias 0.08

Lin Bias 0.00

Prog Decay 0.25

Lin Decay 0.15

Inhibition 2.50

Morphogen

Activation 4h

Strength 0.80

Hill Function

Coefficient n 4

Threshold k 1.00

Selected Cell

Hover over a cell to see details

Legend

GRN Dynamics

Progenitor State: TF_PROG genes maintain pluripotency through mutual activation.

Lineage Commitment: Lineage TFs inhibit each other, creating bistable switches.

Differentiation: Committed cells activate lineage-specific targets and ligands.