VisANT batch mode

Introduction

The batch-mode of the VisANT makes it possible for VisANT to be run quietly in the background without any user interaction. When VisANT is started in this mode, it will carry out a list of the processes specified in the command file (simply a text file). In addition to the commands detailed later in this document, it can be commented using any line started with "#". Although not required, it is suggested that the first line of a command file to be started with "#!batch commands". The batch mode must be started using command line such as:

java -Xmx512M -Djava.awt.headless=true -jar VisAnt.jar -b res/batch_cmd.txt

more information of command line can be found here.

Starting from version 3.39, all command files can also be directly loaded into VisANT as macros. A macro file is identified by VisANT if the first line of the file starts with #!batch commands. In the near future, this line will also allow user to specify the corresponding menus in VisANT for the macros listed in the file. Be aware that a line starting with #!batch commands can appear anywhere for any times in a command/macro file. However, except the first line, all other lines starting with #!batch commands is treated as general comments, providing user the great flexibility to test their macros using the add button with copy and paste as shown below:

When a command file is processed in VisANT with GUI, it is named as macro file, each command is named as macro. That is to say, a batch/command-file can be processed by VisANT in any running mode, with or without graphical user interface

Try a sample macro file that change the visualization of the nodes Download the sample macro file

Note: You can always stop the macros by press the ESC key.

Batch mode is used to carry out targeted analyses without any user interface. This mode is generally preferred in two cases:

to automate the repeated/multiple tasks. An example using the majority of the commands listed below can be download here and users can easily run it using either run.cmd for Win OS for run.sh for the other OS. The output of the command shall look similar shown in the figure below:

to perform time-consuming tasks, such as layout network with millions of nodes and edges. The performance of VisANT is dramatically improved in the batch mode because network will no long need to be drawn in the screen, which make it be able to handle the network that will otherwise not possible to handle. As a test, we have loaded a network with 15,447 nodes and 1,722,708 edges and laid out using elegant-->spring-embedded relaxing, as shown below (more screenshots can be found in the sample page):

The data of the network is downloaded from http://www.functionalnet.org/mousenet/ and directly loaded into VisANT on a duocore computer with 2G memory and win XP. The command file and data used for this test can be downloaded here. Be aware that we specified the maximum memory size that are available on the test machine in the run.cmd: 1424M, which may not be required by this network and you can therefore reduce it in case necessary. In addition, VisANT can now directly read the zip file therefore the downloaded data is zipped. It takes 5+ hours for the test case to finish.

Note: The batch mode is still in its early release, not all functions are available as batch commands. Please feel free to email us if you need new functions as the batch commands.

Tip: By default, the batch mode will not read the startup VisML file as all other modes do. For this reason, you may want to read an empty startup network (in the format of VisML) to set the initial parameters you prefer.

Available commands

Input/Output Topology Layout Selection Metagraph Expression Database related queries Edge weight Edge Properties Node & Node Properties Loop Miscellaneous

Command	Description	Parameters	Example*
Input/output
read^New	This command reads a file with any format that supported by VisANT. Be aware that VisANT now supports the zip format (the zip file shall contain only one file). this command corresponding to the File/Open menu and Open URL menu	The URL or the the file name and path to be read	read=res/expression.xml read=grouping.txt.zip ^Newread=http://visant.bu.edu/ sample/visml_files/start_up_1.xml
output	The command output is used to specify a file store all the output that will otherwise send to the screen. Some information such as output of shortest paths will also saved to the file. This command however will not trigged to save a network file.	the file name and path to write	output=out/cmd_out.txt
visml	The command save the network in the format of VisML with the specified by the command. It corresponding to the menu File/Save.	same as above	visml =out/expression_loaded.xml
export_all	This command save all the nodes and edges of the current network in the format of Edge-List. It's function is same as the File/Save as Tab-delimited File/All	same as above	export_all=out/export_all.txt
export_nodes	This command save all the nodes of the current network in the format of Edge-List. It's function is same as the File/Save as Tab-delimited File/Nodes only	same as above	export_nodes =out/export_nodes.txt
export_metanodes	This command save all the metanodes of the current network in the format of Edge-List. It's function is same as the File/Save as Tab-delimited File/Metanodes only	same as above	export_metanodes =out/export_metanodes.txt
export_edges	This command save all the edges of the current network in the format of Edge-List. It's function is same as the File/Save as Tab-delimited File/Edge only	same as above	export_edges =out/export_edges.txt
jpg	This command save the network as JPG image. It's function is same as the File/Save as *the Image*	same as above	jpg=out/has_expression.jpg
png^New	This command save the network as PNG image. It's function is same as the File/Save as *the Image*	same as above	*png*=out/has_expression.png
svg ** ^New	this command saves the network in the format of SVG	same as above	svg=out/query_forced.svg
print_statistics	The command prints out the network statistics: current only the number of nodes and edges. The command will print to the file specified by the output command if there is any before it.	N/A	print_statistics
println	Print out a line of string to the screen. If output file is specified, the string will be print out to the specified file	the string to print	println=---------
Node & Node Properties^New
delete_selected_nodes	This command removes all selected nodes. It's function is same as the *Edit/Delete Selected Nodes***	N/A	*delete_selected_nodes*
delete_invisible_nodes	This command removes all invisible nodes if they do not belong to a metanode. It's function is same as the *Edit/Delete Invisible Nodes***		*delete_invisible_nodes*
set_node_property	Customize the property of selected nodes. Format: property_name:value	property name	set_node_property= node_color:blue set_node_property= node_size:15
Edge Properties^New
set_edge_property	customize the property of selected edges. Format: property_name:value	property name	set_node_property= edge_color:255,12,120

Topology
topo_export_degree	Export the degree distribution as tab-delimited text file. The function is same as the menu Topology/Global Statistics/Export Degree Distribution	same as above	topo_export_degree =out/topo_export_degree.txt
topo_export_in_degree	Export the in-degree distribution as tab-delimited text file. The function is same as the menu Topology/Global Statistics/Export In-Degree Distribution	same as above	topo_export_in_degree =out/topo_export_in_degree.txt
topo_export_out_degree	Export the out-degree distribution as tab-delimited text file. The function is same as the menu Topology/Global Statistics/Export Out-Degree Distribution	same as above	topo_export_out_degree =out/topo_out_in_degree.txt
topo_export_cluster_coe	Export the distribution of clustering coefficient as tab-delimited text file. The function is same as the menu Topology/Global Statistics/Export Clustering Coefficient Distribution	same as above	topo_export_cluster_coe =out/topo_cluster_coe.txt
topo_export_average_cluster_coe	Export the distribution of average clustering coefficient as tab-delimited text file. The function is same as the menu Topology/Global Statistics/Export Average Clustering Coefficient Distribution	same as above	topo_average_cluster_coe =out/topo_average_coe.txt
shortest_path	This command detects the shortest paths between selected nodes. The command is ignored if there is no node being selected. The result will be printed to the screen, or the file specified by the output command	N/A	shortest_path
Layout
layout	This command has 5 different types of parameters circle: performs circle layout scramble: performs random layout spoke: performs spoke layout spring_embedded_relaxing:N: performs spring-embedded layout with N iterations elegant_relaxing:N: performs elegant relaxing layout for N iterations relaxing:N: performs relaxing layout for N iterations		layout=circle layout=scramble layout=spoke layout= spring_embedded_relaxing:100 layout=elegant_relaxing:150 layout=relaxing:90
fit_to_page	fit the network to the current size of the network panel	N/A	fit_to_page
Selection^U^pdated
select_node	The command selects the nodes specified by the node names. Nodes do not exist in the current network will be ignored	name of the nodes separated by ","	select_node= YIL111W,YMR042W,YDR522C
select_all_node^U^pdated	selects all the nodes. Optionally, this command allows the selection of nodes based on their properties, such as node_color, node_shape etc. as list in the node properties table. Please also reference the macro set_node_property	property name	select_all_node *select_all_node=node_color:red* *select_all_node= node_shape:circle* *select_all_node=node_size:10* *select_all_node=data_type:3* *select_all_node=position:100, 290*
select_all_metanode	select all visible metanodes	N/A	*select_all_metanode*
select_all_metanode_expanded	select all visible expanded metanodes	N/A	*select_all_metanode_expanded*
select_all_metanode_collapsed	select all visible collapsed metanodes	N/A	*select_all_metanode_collapsed*
reverse_node_selection	reverse the node selection	N/A	*reverse_node_selection*
select_edge	selected edges between specified nodes. If only one node is specified, all the edges connecting the node will be selected	name of the nodes separated by ","	*select_edge=*YDR522C select_edge=YIL111W,YMR042W
select_all_edge	select all visible edges	N/A	*select_all_edge*
reverse_edge_selection	reverse the edge selection	N/A	*reverse_edge_selection*
deselect_all_edge	clear selection of the selected edges	N/A	*deselect_all_edge*
deselect_all_node	clear selection of the selected nodes	N/A	*deselect_all_node*
clear_selection	clear all the selections for both edges and nodes	N/A	clear_selection
Metagraph
group_selected	group selected nodes as a metanode	name of the metanode, optional	group_selected=myGroup group_selected
ungroup_selected	ungroup selected nodes. If the selected node is a metanode, ungroup the metanode; otherwise, ungroup the selected nodes from a metanode	N/A	ungroup_selected
group_subnetwork	group disconnected subnetwork into metanodes	N/A	group_subnetwork
metanode_collapse_all	collapse all metanodes.	N/A	metanode_collapse_all
metanode_expand_all	expand all metanodes	N/A	metanode_expand_all
co_metanode_network	transfer the metanodes as an interaction with fully connected components	N/A	*co_metanode_network*
Expression
clear_expression	remove all expression values attached to the network	N/A	clear_expression
expression_experiement	set the current expression experiment. The command will be ignored If the number exceeds the total number of experiments	the sequence number of the expression	expression_experiement=2
Edge weight ^New
min_edge_weight	set the minimum edge weight, default is 0, may be overwritten by VisML file	numerical value	min_edge_weight=0.2
max_edge_weight	set the maximum edge weight, default is 1.0, may be overwritten by VisML file	numerical value	max_edge_weight=0.9
edge_weight_normalization	Reset all edge weights to the range between 0-1 with max number =1 and min number =0	N/A	edge_weight_normalization
Database related queries ^New
database	change the target database, the default value is Predictome, the available selections so far is: fln The name of the database is case insensitive. The command will not change the drop-down list of the database shown in the toolbar	Predictome fln	*database=fln*
login	login VisANT server	user name and password delimited using ":"	login=zjhu@bu.edu:myPasswd
query_selected_nodes**	query the interaction of the selected nodes if they have not been queried against database	N/A	query_selected_nodes
query_internal**	Query the interactions between selected nodes	N/A	query_internal
name_normalization**	resolve the name of the selected nodes	N/A	name_normalization
forced_query**	query the interaction of the selected nodes regardless whether they have not been queried against database or not.	N/A	forced_query
method_based_query**	load the interactions annotated under specified method	method ID	method_based_query=M0010
loop ^New	VisANT supports simple loop, with the initial requests from the users to monitor the real-time change of the network. The format of the loop is simple, as shown in the following example: Example 1:loop with variables, e.g. k in the following line. k will start with 1, stop at 5, and increase 1 each iteration, there is 1 second delay: loop=k:1:5:1, delay=1000 read=http://visant.bu.edu/other_formats/gml_test#k#.txt loop_end In summary, above example reads 6 files within in about 6 seconds with file name varied with loop variable represented by #k#. Try the loop macros This sample uses a lot of loops Example 2, infinity loop (with no loop variable) that reads the file named out.gml, if you want it to stop, quit VisANT, delay 2.5 second after each read: loop=, delay=2500 read=out.gml loop_end Above macros monitors the change of out.gml, here is the program package that will constantly update the out.gml. To start, unpack the package in the same directory as macro file, and start with the command in a shell/dos window: java Producer
Miscellaneous ^New
species	set the current species of the network	species ID	species=hsa
exit	stop the processing of the commands	N/A	exit
pause	pause for 2 second by default, or at a given milliseconds	none or number for milliseconds	pause pause=700
font_style	global control for the font style of the node labels	bold, plain, italic, bold+italic	*font_style=bold*
set_network_size	set the size of the network canvas	width, height	*set_network_size=1000, 800*
clear_network	remove all nodes and edges	N/A	clear_network

*Each commands must be presented in the same line.

** These commands require internet connection and are required to have a valid user login using the command login to avoid potential abuse of VisANT server. We may reject the query if abuse occurs. If you do not have a VisANT account, registration is free:

http://visant.bu.edu:8080/vserver/register.jsp

List of node/edge properties. Try the sample network Try the sample macro file Download the sample macro file

Note: unless otherwise specified, all properties are applied to the selected nodes only
Name	Comment/Value
List of node properties^U^pdated
node_color	there can be two type of the value: 1.color name, including: black, blue, cyan, darkgray, gray, green, lightgray, magenta, orange, pink, red, yellow 2. RGB value in the format r_value,g_value,b_value, such as node_color:255,0,0 Example: set_node_property=node_color:25,255,105 set_node_property=node_color:red
label_color	similar to above, Example: set_node_property=label_color:25,255,105
fixed	determine whether the position of the node is fixed or not: true or false, e.g. set_node_property=fixed:true
label_on	determine whether the node label is visible or not: true or false, e.g. set_node_property=label_on:true
label_size	the size of node label, integer, range: 6-26, e.g. set_node_property=label_size:16
label_position	the position of the label, value including: center, left, right, above, below, e.g. set_node_property=label_position:center
node_label	the label of the node, e.g. set_node_property=node_label:My new Label
label_style	the value of the style can be plain, bold, italic, bold+italic, e.g., set_node_property=label_style:bold+italic
x	the x position of the node. e.g. *set_node_property=x:200***
y	the y position of the node. e.g. *set_node_property=y:200***
position	the x, y position of the node. e.g. *set_node_property=position:300,200***
node_size	the size of the node, integer, range: 0-30, e.g., set_node_property=node_size:30
node_width	the width of the node for the shape of circle, rectangle, rectangle_3d, round_rectangle, it has the same effect as node_size if the node shape is triangle, diamond, hexagon, octagon, square, and ball. not applicable if the node shape is rectangle_fit, rectangle_3d_fit, or round_rectangle_fit Example: set_node_property=node_width:45
node_height	the width of the node for the shape of circle, rectangle, rectangle_3d, round_rectangle. not applicable if the node shape is triangle, diamond, hexagon, octagon, square, ball, rectangle_fit, rectangle_3d_fit, or round_rectangle_fit Example:*set_node_property=node_height:20*
node_dimension	A combination of node_width and node_height, delimited using ',', e.g., *set_node_property=node_dimension:70,40*
node_shape	By default VisANT determines the shape of node based on its data type (protein, gene, RNA etc.). This command allows user to change the node shape to one of the following: circle, rectangle, rectangle_3d, round_rectangle, triangle, diamond, hexagon, octagon, square, ball, rectangle_fit, rectangle_3d_fit, or round_rectangle_fit.and auto. If auto allows VisANT to determine the node shape based on data type. Example: *set_node_property=node_shape:rectangle_fit*
expanded_node_shape	Only applicable to metanodes. Two options are available: round_rectangle, convex_polygon. Example: *set_node_property=expanded_node_shape:convex_polygon*
desc	set the description of the node, if there are multiple lines, use \n to separate the line. Example: set_node_property=desc:this is first line\nThis is second line
extend_symbol_on	determine whether the +/- of the node is visible or not: true or false
kegg_symbol_on	determine whether the KEGG pathwhay symbol of the node is visible or not: true or false
data_type	determine the type of the node, not complete yet, so far 0 for protein/gene, 1 for compound, and 3 for metanode...

List of edge properties
edge_color	see comments of the node_color. Example: set_edge_property=edge_color:255,0,0
label_on	turn on/off the edge label: true or false
edge_weight	set the weight of the edge: double value between 0-1, e.g., *set_edge_property=edge_weight:0.6*
desc	set the description of the node, if there are multiple lines, use \n to separate the line Example: set_edge_property=desc:this is first line\nThis is second line
opacity	global control, set the transparency of the edges: 0-155, set it to -1 to disable if you no long need it because it will significantly impact the performance.
exclude_metaedge_weight	global control, exclude the metaedge when filter out the edges based their weights: true or false
color_for_weight	global control, turn on/off the option to visualize the edge weight using the edge color: true or false
thickness_for_weight	global control, turn on/off the option to visualize the edge weight using the edge thickness: true or false

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