*********** Start of file README ****************** This file is part of the NeuroDNet database. Current Version BN 1.0, January 2011.%% Copyright (c) 2011 Indian institute of Technology Delhi. ********************************************** Last updated November 2011 System requirements: The following hardware and software is required to run Web Page. * An Intel Pentium processor or equivalent, 400 MHz or faster * Windows 98, Windows 2000, Windows XP, Windows Vista or Windows .NET Server 2003 * At least 64 MB of available random-access memory (RAM) (256 MB recommended) * At least 100 MB available disk space * An Internet Explorer 5.0 or higher (IE6.0 or higher recommended) List of files included: -------------------------- 1. Random Network example 2. Real Network example User queries should be directed to webmaster.neurodnet@gmail.com. ***************************************************************************************************************************** 1. Random Network example -------------------------- Input ------- Nodes : 5 Edges : 10 Self-degrading Nodes : 0 Rule : 1 Algorithm : Entire state space Boolean functions : $node[1] = $node[2] + $node[3]; $node[2] = -($node[4]) + $node[5]; $node[3] = -($node[2]) + $node[5]; $node[4] = -($node[1]) + $node[3]; $node[5] = -($node[1]) + $node[4]; Output ------- Steady states : BN_Steady_states.txt Attractor states : Attractor_states.txt Total state space : Total_States.txt Steady states : BN_Steady_states.txt ---------------------------------------- 0 0 0 0 0 Given in File [ Steady_Random10_20.txt ] Trajectory of attractor states : Attractor_states.txt ---------------------------------------- 1-2-3-4-5 00001-->01100 01100-->10010 10010-->00000 00000-->00000 00010-->00001 .........Given in File [ Attractor_Random5_10.txt ] Cyclic attractor states not found. Total state space : Total_States.txt ---------------------------------------- 00000 -> 00000 00001 -> 01100 00010 -> 00001 00011 -> 00101 00100 -> 10010 00101 -> 11110 00110 -> 10011 00111 -> 10111 01000 -> 10000 01001 -> 11000 .........Given in File [ StateSpace_Random5_10.txt ] ***************************************************************************************************************************** 2. Random Network example -------------------------- Input ------- Nodes : 10 Edges : 20 Self-degrading Nodes : 0 Rule : 2 Algorithm : Entire state space Boolean functions : $node[1] = -$node[1]-$node[3]+$node[4]; $node[2] = $node[10]; $node[3] = -$node[8]; $node[4] = $node[6]+$node[9]; $node[5] = $node[5]-$node[7]-$node[8]-$node[9]; $node[6] = $node[7]-$node[2]; $node[7] = $node[2]+$node[3]; $node[8] = $node[10]; $node[9] = $node[4]+$node[6]; $node[10] = $node[5]-$node[1]; Output ------- Steady states : BN_Steady_states.txt Attractor states : Attractor_states.txt Total state space : Total_States.txt Steady states : BN_Steady_states.txt ---------------------------------------- 1-2-3-4-5-6-7-8-9-10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 1 0 1 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 1 0 0 0 1 0 0 0 0 1 1 0 1 0 1 1 0 0 0 1 0 0 0 0 1 1 1 0 0 1 0 1 0 0 1 1 1 0 1 1 0 1 0 1 0 0 1 0 0 0 0 1 0 1 0 0 1 0 0 0 1 1 0 1 0 0 1 0 1 0 0 1 0 1 0 0 1 0 1 0 1 1 0 1 0 0 1 0 1 1 0 1 0 1 0 0 1 0 1 1 1 1 0 1 0 0 1 1 0 0 0 1 0 1 0 0 1 1 1 0 0 1 0 1 1 0 1 0 0 1 0 1 0 1 1 0 1 0 0 1 1 1 0 1 1 0 1 0 1 1 0 1 0 1 1 0 1 0 1 1 1 1 0 Given in File [ Steady_Random10_20.txt ] Trajectory of attractor states : Attractor_states.txt ---------------------------------------- 0000000001-->0100000101 0100000101-->0100001101 0100001101-->0100001101 0000000010-->0001000010 0001000010-->1001000010 1001000010-->1001000010 0000000011-->0101000111 0101000111-->1101001111 1101001111-->1101001110 1101001110-->1101001110 .........Given in File [ Attractor_Random10_20.txt ] Cyclic Attractor states found (1) 0110101001 -> 0100001101 -> 0110101101 |_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _| Total state space : Total_States.txt ---------------------------------------- 0000000000 -> 0000000000 0000000001 -> 0100000101 0000000010 -> 0001000010 0000000011 -> 0101000111 0000000100 -> 0000000100 0000000101 -> 0100000101 0000000110 -> 0001000110 0000000111 -> 0101000111 0000001000 -> 0000011000 0000001001 -> 0100011101 .........Given in File [ StateSpace_Random10_20.txt ] ***************************************************************************************************************************** 1. Real Network example -------------------------- (A) Yeast cell cycle (Li et al. 2003) Input ------- Nodes : 11 Edges : 29 Self-degrading Nodes : 1,4,6,7,11 Rule : 2 Algorithm : Entire state space Boolean functions : $node[1]=0; $node[2]=$node[1]-$node[10]; $node[3]=$node[1]-$node[10]; $node[4]=$node[3]; $node[5]=-$node[4]+$node[7]-$node[8]-$node[10]; $node[6]=$node[7]-$node[10]+$node[11]; $node[7]=$node[10]+$node[11]; $node[8]=$node[2]-$node[7]-$node[9]; $node[9]=-$node[4]+$node[6]+$node[7]-$node[8]-$node[10]; $node[10]=-$node[5]-$node[7]+$node[8]-$node[9]+$node[11]; $node[11]=$node[8]+$node[10]; Output ------- Steady states : BN_Steady_states.txt Attractor states : Attractor_states.txt Total state space : Total_States.txt Steady states : BN_Steady_states.txt ---------------------------------------- 1-2-3-4-5-6-7-8-9-10-11 00000000000 00000000100 00001000000 00001000100 00110000000 01000000100 01001000100 .........Given in File [ Steady_yeast_cell_cycle2003.txt ] Trajectory of attractor states : Attractor_states.txt ---------------------------------------- 00000000001-->00000110010 00000110010-->00000010101 00000010101-->00001110100 00001110100-->00001100100 00001100100-->00001000100 00001000100-->00001000100 00000000010-->00000010011 00000010011-->00000110011 00000110011-->00000110111 00000110111-->00000110101 00000110101-->00001110100 .........Given in File [ Attractor_yeast_cell_cycle2003.txt ] Cyclic attractors not found. Total state space : Total_States.txt ---------------------------------------- Node(t) -> Node(t+1) ------------------------------------------- 00000000000 -> 00000000000 00000000001 -> 00000110010 00000000010 -> 00000010011 00000000011 -> 00000010011 00000000100 -> 00000000100 00000000101 -> 00000110100 00000000110 -> 00000010001 00000000111 -> 00000010011 00000001000 -> 00000001011 00000001001 -> 00000111011 00000001010 -> 00000011011 00000001011 -> 00000011011 00000001100 -> 00000000001 00000001101 -> 00000110011 00000001110 -> 00000010011 00000001111 -> 00000010011 00000010000 -> 00001100100 00000010001 -> 00001110100 00000010010 -> 00000010001 00000010011 -> 00000110011 00000010100 -> 00001100100 .........Given in File [ StateSpace_yeast_cell_cycle2003.txt ] ***************************************************************************************************************************** (B) Mammalian cell cycle Input ------- Nodes : 10 Edges : 49 Self-degrading Nodes : 0 Rule : 1 Algorithm : Entire state space Boolean functions : $node[1]=$node[1]; $node[2]=( !($node[1]) & !($node[4]) & !($node[5]) & !($node[10]) ) | ( $node[6] & !($node[1]) & !($node[10])) ; $node[3]=( !($node[2]) & !($node[5]) & !($node[10]) ) | ( $node[6] & !($node[2]) & !($node[10]) ); $node[4]=( $node[3] & !($node[2]) ); $node[5]=( $node[3] & !($node[2]) & !($node[7]) & !($node[8] & $node[9]) ) | ( $node[5] & !($node[2]) & !($node[7]) & !($node[8] & $node[9]) ); $node[6]=( !($node[1]) & !($node[4]) & !($node[5]) & !($node[10])) |( $node[6] & !($node[4] & $node[5]) & !($node[10]) & !($node[1]) ); $node[7]=$node[10]; $node[8]=( !($node[5]) & !($node[10]) ) |$node[7] |( $node[6] & !($node[10]) ); $node[9]= !($node[8]) |( $node[8] & $node[9] & ($node[7] | $node[5] | $node[10]) ); $node[10]=( !($node[7]) & !($node[8]) ); Output ------- Steady states : BN_Steady_states.txt Attractor states : Attractor_states.txt Total state space : Total_States.txt Steady states : BN_Steady_states.txt ---------------------------------------- 1-2-3-4-5-6-7-8-9-10 0 1 0 0 0 1 0 1 0 0 .........Given in File [ Steady_mammalian_cell_cycle2006.txt ] Trajectory of attractor states : Attractor_states.txt ---------------------------------------- 0000000000-->0110010111 0110010111-->0000001010 0000001010-->0110010110 0110010110-->0100010100 0100010100-->0100010100 0000000001-->0000001011 0000001011-->0000001110 0000001110-->0110010110 0110010110-->0100010100 0100010100-->0100010100 .........Given in File [ Attractor_mammalian_cell_cycle2003.txt ] Cyclic attractor state found. (1) 1000101011 -> 1000001110 -> 1010000110 -> 1011000100 ->1011100100 -> 1001100000 -> 1000100011 |_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _| Total state space : Total_States.txt ---------------------------------------- Node(t) -> Node(t+1) ------------------------------------------- 0000000000 -> 0110010111 0000000001 -> 0000001011 0000000010 -> 0110010111 0000000011 -> 0000001011 0000000100 -> 0110010100 0000000101 -> 0000001000 0000000110 -> 0110010100 0000000111 -> 0000001010 0000001000 -> 0110010110 0000001001 -> 0000001110 .........Given in File [ StateSpace_mammalian_cell_cycle2006.txt ] ***************************************************************************************************************************** END