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Input data formats for the BioCichlid website

available characters

alphabets, numeric character (0,1,2,3,4,5,6,7,8,9) and underscore(_)

format of physical and genetic interaction

node name, node name

...

format of genetic-physical interaction

>genetic node name ('target A gene')

physical node name ( transcription factor regulating 'target A gene')

physical node name ( transcription factor regulating 'target A gene')

...

format of gene expression data

genetic node name, expression value 1, expression value 2, expression value 3, ...

...

Data format in the BioCichlid server

commands

initialize command

#     description    clock  number_of_vertex  number_of_edge  x_size,y_size,z_size   coord_sys
new "SampleGraph" 1 4 3 50 50 50.0004 CS_POSRECT  #
# Tell server to start up
start

set vertex

# setv vtx_num loc0(Float) loc1(Float) loc2(Float) draw_style size color
#        draw_style: VD_CUBE,VD_PYRAMID,VD_SPHERE,VD_NONE
#        color: generally names of color or RGB
setv 0 27 3 20 VD_SPHERE 1.0 white
setv 1 27 3 10.7502 VD_NONE 0.0001 black
setv 2 31 5 20 VD_SPHERE 1.0 255,255,255
setv 3 31 5 10.7502 VD_NONE 0.0001 0,0,0

set edge

# sete edge_num(Integer) vertex0 vertex1 direction draw_style size color
#        direction: ED_BOTH,ED_FORWARD,ED_BACKWARD,ED_NONE
#        draw_style: ER_CYLINDER,ER_LINE
#        color: generally names of color or RGB
sete 0 0 1 ED_NONE ER_CYLINDER 0.5 red
sete 1 2 3 ED_NONE ER_CYLINDER 0.5 red
sete 2 0 2 ED_NONE ER_CYLINDER 1.0 255,0,0

set microarray expression base vertex

# set_spot indicator_vertex(Unsigned Integer)
set_spot 3

set microarray expression data

# set_sample_point indicator_vertex(Unsigned Integer) time_point(Unsigned Integer) expression_level(Float)
#       prepare indicator_vertex in advance
set_sample_point 3 0 30.0
set_sample_point 3 1 10
set_sample_point 3 2 20
set_sample_point 3 3 30

set microarray expression indicator vertex and edge

# set_bar base_vertex indicator_vertex indicator_edge orientation(loc0 loc1 loc2)
#       prepare indicator_vertex in advance
set_bar 2 3 1 0.0 0.0 1.0

set universal information of microarray expression

# set_sample_info number_of_time-points enlargement_ratio_of_indicator duration(Unsigned Float)
#       prepare indicator_vertex and indicator_edge in advance
set_sample_info 4 5.0 5000

server start command

# Tell the server to work with the current data, instead of exiting on EOF
done

example data

new "Test" 1 4 3 50 50 50.0004 CS_POSRECT  # initialize command
start
setv 0 27 3 20 VD_SPHERE 1.0 white
setv 1 27 3 10.7502 VD_NONE 0.0001 black
setv 2 31 5 20 VD_SPHERE 1.0 white
setv 3 31 5 10.7502 VD_NONE 0.0001 black
sete 0 0 1 ED_NONE ER_CYLINDER 0.5 red
sete 1 2 3 ED_NONE ER_CYLINDER 0.5 red
sete 2 0 2 ED_NONE ER_CYLINDER 1.0 red
set_spot 3
set_sample_point 3 0 30.0
set_sample_point 3 1 10
set_sample_point 3 2 20
set_sample_point 3 3 30
set_bar 2 3 1 0.0 0.0 1.0
set_spot 1
set_sample_point 1 0 10
set_sample_point 1 1 20
set_sample_point 1 2 -30
set_sample_point 1 3 10
set_bar 0 1 0 0.0 0.0 1.0
set_sample_info 4 5.0 5000
done

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Dept. of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University