Difference between revisions of "Cytoscape"

Latest revision as of 14:23, 15 August 2022

Description

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.

Environment Modules

Run module spider cytoscape to find out what environment modules are available for this application.

System Variables

HPC_CYTOSCAPE_DIR - installation directory

Additional Information

This is a GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs

Basic usage:

module load gui cytoscape
launch_gui_session -e Cytoscape

Connect with xpra locally using the xpra command

xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Phylogenetics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|cytoscape}}
@@ Line 21: / Line 21: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-<!--
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-* {{#var:app}}
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 45: / Line 35: @@
 Basic usage:
-  module load gui orange3
+  module load gui cytoscape
-  launch_gui_session -e orange-canvas
+  launch_gui_session -e Cytoscape
 Connect with xpra locally using the xpra command