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Required Properties

Following properties are required Integrated Genome Browser contains a Bookmarks REST endpoint external programs can use to control IGB.

This endpoint was originally developed for users to record genome locations and data sets that they might want to come back to. It was also developed to enable Web sites to embed links to IGB. 

IGB bookmarks endpoint is: 

http://localhost:7085/IGBControl

Required parameters - one per bookmark

version: Genome version. e.g. version=H_sapiens_Mar_2006

...

end: End position on the sequence. e.g. end=52983241

(Start and end position are used to zoom on the coordinates)

Following properties are required

loadresidues: Indicates whether sequence bases should also be loaded, e.g. loadresidues=false

To load a dataset, use the "feature" parameters. Each "feature" corresponds to a data set track within IGB. 

Required Properties - one per feature

server_url :- List of servers to be enabled before looking for the features. e.g. http%3A%2F%2Fbioviz.org%2Fdas2%2FgenomeIGB attempts to access the data files indicated in the bookmark (see below).

query_url :- URLs of features to be loaded.  e.g. http%3A%2F%2Fbioviz.org%2Fdas2%2Fgenome%2FA_thaliana_Jun_2009%2FEST%2B%2528multiple%2Bmap%2529 

Optional properties (per track)

feature_url_0 :- Url of feature to which the track belongs to. e.g. feature_url_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz

sym_method_0 :- Method name of track. (Usually it would be url of feature but it could be different too). e.g. sym_method_0=http%3A%2F%2Figbquickload.org%2Fquickload%2FA_thaliana_Jun_2009%2FTAIR10_mRNA.bed.gz

sym_yheight_0 :- Height of each glyph in a track.

sym_col_0 :- Foreground color of track in hexadecimal. e.g. sym_col_0=0x00FFFF

sym_bybg_0 :- Background color of track in hexadecimal. e.g. sym_bg_0=0x000000

sym_name_0 :- Preferred user-friend display name for the track. e.g sym_name_0=TAIR10+mRNA

(For multiple optional properties corresponding names would be sym_method_1, sym_yheight_1, sym_method_2, sym_yheight_2 etc.)

Optional properties - graphs only

graph_float_0 :-

view_mode_0 :

loadresidues=falseBoolean value to indicate if graph should be floating. e.g. graph_float_0=false

graph_show_label_0 :- Boolean value to indicate if graph label should be shown or not. e.g. graph_show_label_0=true

graph_show_axis_0 :- Boolean value to indicate if axis should be visible or not. e.g. graph_show_axis_0=false

graph_minvis_0 :- Float value for minimum graph value. e.g graph_minvis_0=0.0

graph_maxvis_0 :- Float value of maximum graph value. e.g. graph_maxvis_0=372.0

graph_score_thresh_0 :- Graph threshold value. e.g. graph_score_thresh_0=186.0

graph_maxgap_thresh_0 :- e.g. graph_maxgap_thresh_0=100

graph_minrun_thresh_0 :- e.g. graph_minrun_thresh_0=30

graph_show_thresh_0 :- Boolean value to indicate if threshold should be visible or not. e.g. graph_show_thresh_0=false

graph_style_0 :- Graph style. e.g. graph_style_0=Stairstep

graph_thresh_direction_0 :- Threshold direction. e.g. graph_thresh_direction_0=1