Patent ID: 7280921

Claim:
A method for visualizing large-scale protein interaction data on a display by use of a computer, comprising the steps of: producing an initial layout by placing all proteins of protein interaction data as nodes on the surface of a sphere by increasing a horizontal angle (theta) and a vertical angle (phi) of each node in polar coordinates according to the following algorithm: 1: θ increment = 2π/√{square root over (n)} {n: number of nodes} 2: φ increment = 2π/n 3: θ = 0, φ = 0 4: for v ε V do 5: pos[v] = (r, θ, φ) {r: radius of a sphere} 6: θ = θ + θ increment 7: φ = φ + φ increment 8: end for; and yielding a three-dimensional graph by iterating a predetermined number of times a process of moving each node of the initial layout to an equilibrium position and updating node positions based on spring forces between a non-adjacent nodes and the node of the initial layout as well as spring forces between an adjacent nodes and the node of the initial layout, wherein the three-dimensional graph is yielded through the following algorithm: 1: r = 1 2: repeat 3: g =0.01 · r · k 2 {k: natural spring length} 4: for v ε V do 5: D = 0 {D: displacement vector of v} 6: for u ε V, u ≠ v do 7: Δ = pos[u] − pos[v] {pos[u]: position of node u} 8: D = D − g · (Δ/|Δ|) · (|u|/|Δ|) {|u|: distance of u from the origin} 9: if u ε Γ(v) then 10: D = D − Δ/|Δ| · (1 − |Δ|/k)/|Γ(v)| {Γ(v): set of nodes adjacent to v} 11: end if 12: end for 13: pos[v new ] = pos[v old ] + D 14: end for 15: r = 0.98 · r 16: until T times {T: user-determined number or 20 by default}.