Cytoscape-Teaching - Revision history

Shtsai at 00:30, 5 April 2026

2026-04-05T00:30:36Z

← Older revision		Revision as of 20:30, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Teaching		Teaching

	=== Version ===		== Version ==

	3.9.1		3.9.1

	=== Author / Distributor ===		== Author / Distributor ==

	Please see https://cytoscape.org/		Please see https://cytoscape.org/

	=== Description ===		== Description ==

	"Cytoscape is an open source software tool for integrating, visualizing, and analyzing data in the context of networks."		"Cytoscape is an open source software tool for integrating, visualizing, and analyzing data in the context of networks."
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	more details at [http://www.cytoscape.org/documentation_users.html CytoScape]		more details at [http://www.cytoscape.org/documentation_users.html CytoScape]

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==
	<pre class="gcommand">		<pre class="gcommand">
	ml Cytoscape/3.9.1-Java-11		ml Cytoscape/3.9.1-Java-11
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]
	=== Installation ===		== Installation ==

	Code downloaded from https://cytoscape.org/download-platforms.html		Code downloaded from https://cytoscape.org/download-platforms.html

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai: /* Running Program */

2023-09-06T18:19:05Z

Running Program

← Older revision		Revision as of 14:19, 6 September 2023
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	To use version 3.9.1, please first load the module with		To use version 3.9.1, please first load the module with
	<pre class="gcommand">		<pre class="gcommand">
	ml Cytoscape/3.9.1		ml Cytoscape/3.9.1-Java-11
	</pre>		</pre>

Shtsai at 18:18, 6 September 2023

2023-09-06T18:18:37Z

← Older revision		Revision as of 14:18, 6 September 2023
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	=== Version ===		=== Version ===

	3.7.2		3.9.1

	=== Author / Distributor ===		=== Author / Distributor ===
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	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]

	*Version 3.7.2 is installed in /apps/eb/Cytoscape/3.7.2		*Version 3.9.1 is installed in /apps/eb/Cytoscape/3.9.1-Java-11

	To use version 3.7.2, please first load the module with		To use version 3.9.1, please first load the module with
	<pre class="gcommand">		<pre class="gcommand">
	~~module load~~ Cytoscape/3.7.2		ml Cytoscape/3.9.1
	</pre>		</pre>

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	To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then		To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then
	<pre class="gcommand">		<pre class="gcommand">
	~~xqlogin~~		interact -x11
	~~module load~~ Cytoscape/3.7.2		ml Cytoscape/3.9.1-Java-11
	Cytoscape [options]		Cytoscape [options]
	exit		exit
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	~~module load~~ Cytoscape/3.7.2		ml Cytoscape/3.9.1-Java-11

	cytoscape.sh [options]		cytoscape.sh [options]
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	=== Documentation ===		=== Documentation ===
	<pre class="gcommand">		<pre class="gcommand">
	~~module load~~ Cytoscape/3.7.2		ml Cytoscape/3.9.1-Java-11
	cytoscape.sh -h		cytoscape.sh -h

Shtsai: /* Running Program */

2020-08-28T02:21:24Z

Running Program

← Older revision		Revision as of 22:21, 27 August 2020
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	=== Running Program ===		=== Running Program ===

	Also refer to [[Running Jobs on the ~~Teaching Cluster~~]]		Also refer to [[Running Jobs on the teaching cluster]]

	*Version 3.7.2 is installed in /apps/eb/Cytoscape/3.7.2		*Version 3.7.2 is installed in /apps/eb/Cytoscape/3.7.2

Shtsai at 02:20, 28 August 2020

2020-08-28T02:20:53Z

← Older revision		Revision as of 22:20, 27 August 2020
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	=== Running Program ===		=== Running Program ===

	Also refer to [[Running Jobs on ~~Sapelo2~~]]		Also refer to [[Running Jobs on the Teaching Cluster]]

	*Version 3.7.2 is installed in ~~/usr/local~~/apps/eb/Cytoscape/3.7.2		*Version 3.7.2 is installed in /apps/eb/Cytoscape/3.7.2

	To use version 3.7.2, please first load the module with		To use version 3.7.2, please first load the module with

Moses: /* Running Program */

2020-08-12T14:22:02Z

Running Program

← Older revision		Revision as of 10:22, 12 August 2020
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	</pre>		</pre>

	This program has a graphical interface. Please refer to [[Running_Jobs_on_the teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] and [[~~Running_Jobs_on_Teaching~~#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]].		This program has a graphical interface. Please refer to [[Running_Jobs_on_the teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] and [[Running_Jobs_on_the teaching_cluster#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]].

	To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then		To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then

Moses at 14:21, 12 August 2020

2020-08-12T14:21:39Z

← Older revision		Revision as of 10:21, 12 August 2020
Line 33:		Line 33:
	</pre>		</pre>

	This program has a graphical interface. Please refer to [[~~Running_Jobs_on_Teaching~~#How_to_open_an_interactive_session \| Run interactive Jobs]] and [[Running_Jobs_on_Teaching#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]].		This program has a graphical interface. Please refer to [[Running_Jobs_on_the teaching_cluster#How_to_open_an_interactive_session \| Run interactive Jobs]] and [[Running_Jobs_on_Teaching#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]].

	To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then		To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then

Moses at 14:20, 12 August 2020

2020-08-12T14:20:33Z

← Older revision		Revision as of 10:20, 12 August 2020
Line 33:		Line 33:
	</pre>		</pre>

	This program has a graphical interface. Please refer to [[~~Running_Jobs_on_Sapelo2~~#How_to_open_an_interactive_session \| Run interactive Jobs]] and [[~~Running_Jobs_on_Sapelo2~~#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]].		This program has a graphical interface. Please refer to [[Running_Jobs_on_Teaching#How_to_open_an_interactive_session \| Run interactive Jobs]] and [[Running_Jobs_on_Teaching#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]].

	To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then		To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then

Moses at 14:19, 12 August 2020

2020-08-12T14:19:10Z

← Older revision		Revision as of 10:19, 12 August 2020
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	module load Cytoscape/3.7.2		module load Cytoscape/3.7.2
	</pre>		</pre>


	This program has a graphical interface. Please refer to [[Running_Jobs_on_Sapelo2#How_to_open_an_interactive_session \| Run interactive Jobs]] and [[Running_Jobs_on_Sapelo2#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]].		This program has a graphical interface. Please refer to [[Running_Jobs_on_Sapelo2#How_to_open_an_interactive_session \| Run interactive Jobs]] and [[Running_Jobs_on_Sapelo2#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities \| Run X window Jobs]].


	To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then		To run this program in an interactive session using the graphical front end: Start an X terminal (Mac), X window (Windows) at the local computer first, then
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	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash
	#SBATCH --job-name=~~amberjob~~		#SBATCH --job-name=jobname
	#SBATCH --partition=batch		#SBATCH --partition=batch
	#SBATCH --mail-type=ALL		#SBATCH --mail-type=ALL
	#SBATCH --mail-user=username@uga.edu		#SBATCH --mail-user=username@uga.edu
	#SBATCH --ntasks=4		#SBATCH --ntasks=1
	#SBATCH --mem=~~10gb~~		#SBATCH --mem=4gb
	#SBATCH --time=08:00:00		#SBATCH --time=04:00:00
	#SBATCH --output=~~Amberjob.~~%j.out		#SBATCH --output=%j.out
	#SBATCH --error=~~Amberjob.~~%j.err		#SBATCH --error=%j.err

	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
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	cytoscape.sh [options]		cytoscape.sh [options]
	</pre>		</pre>

	where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, and the job name need to be modified appropriately as well.		where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, and the job name need to be modified appropriately as well.

	Example of submission to the queue:		Example of submission to the queue:
	<pre class="gcommand">		<pre class="gcommand">
	~~qsub~~ ./sub.sh		sbatch ./sub.sh
	</pre>		</pre>

	=== Documentation ===		=== Documentation ===
	<pre class="gcommand">		<pre class="gcommand">

	module load Cytoscape/3.7.2		module load Cytoscape/3.7.2
	cytoscape.sh -h		cytoscape.sh -h
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	format).		format).
	-S,--script <file> Execute commands from script file.		-S,--script <file> Execute commands from script file.
	-R,--rest <port> Start a rest service.		-R,--rest <port> Start a rest service.

	</pre>		</pre>

Moses at 14:16, 12 August 2020

2020-08-12T14:16:45Z

← Older revision		Revision as of 10:16, 12 August 2020
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	Example of a job submission script sub.sh to run a batch job (note: this is not the cytoscape execution command script):		Example of a job submission script sub.sh to run a batch job (note: this is not the cytoscape execution command script):
	<pre class="gscript">		<pre class="gscript">
	#~~PBS -S~~ /bin/bash		#!/bin/bash
	#~~PBS~~ -q batch		#SBATCH --job-name=amberjob
	#~~PBS~~ -~~N jobname~~		#SBATCH --partition=batch
	#~~PBS~~ -~~l nodes~~=~~1:ppn~~=1		#SBATCH --mail-type=ALL
	#~~PBS~~ -~~l walltime~~=48:00:00		#SBATCH --mail-user=username@uga.edu
	#~~PBS~~ -~~l mem~~=~~16gb~~		#SBATCH --ntasks=4
			#SBATCH --mem=10gb
			#SBATCH --time=08:00:00
			#SBATCH --output=Amberjob.%j.out
			#SBATCH --error=Amberjob.%j.err

	cd $~~PBS_O_WORKDIR~~		cd $SLURM_SUBMIT_DIR

			module load Cytoscape/3.7.2

	~~module load Cytoscape/3.8.0-Java-11~~
	cytoscape.sh [options]		cytoscape.sh [options]
	</pre>		</pre>
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	=== Documentation ===		=== Documentation ===
	<pre class="gcommand">		<pre class="gcommand">
	~~module load Cytoscape/3.8.0-Java-11~~

			module load Cytoscape/3.7.2
	cytoscape.sh -h		cytoscape.sh -h