Diff for "Cytoscape_3/UserManual/ProgrammaticAccess"

Differences between revisions 6 and 7

Programmatic Access to Cytoscape Features

In this chapter, you will learn how to use Cytoscape from command line and scripts.

Topics

Commands
RESTful API
- Command REST API
- cyREST

Background

Cytoscape has intuitive graphical user interface for interactive network data integration, analysis, and visualization. It is a great way for exploratory data analysis, but what happens if you have hundreds of data files or need to ask someone to execute your data analysis workflows? It is virtually impossible to apply same operations to hundreds of networks manually with GUI, and more importantly, although you can save your results as session files, you cannot save your workflows if your analysis is based on point-and-click GUI operation. Recording workflows is the key feature for reproducible data analysis, but it was a missing feature in past versions for Cytoscape. The latest version of Cytoscape has several options to script and automate your workflows.

Options for Programmatic Access

There are two ways to access Cytoscape programmatically: Commands and RESTful API.

Commands

Commands is the built-in Cytoscape feature to automate your workflow as a simple script. You can learn more about this feature in this section:

Command Tool

Sample Scripts

(TBD)

RESTful API

In some cases, you may need to use fully featured programming languages, such as Python, R, Ruby, or JavaScript,

Commands REST API

In addition to running scripts, Commands have REST API to access the

By default, this feature is disables. To run REST server for Commands, please follow these steps:

Open a terminal session:
- PowerShell (For windows)
- Terminal or [[|iTerm]] (For Mac)
- Terminal (For Linux)
Start Cytoscape from command-line:
- For Mac/Linux
```
./cytoscape.sh
```
  For Windows
```
./cytoscape.bat
```

(TBD)

cyREST

https://raw.githubusercontent.com/idekerlab/cyREST/master/docs/images/logo300.png

cyREST is available from

Debugging your workflows

(TBD)

Cytoscape_3/UserManual/ProgrammaticAccess (last edited 2016-04-26 22:22:57 by server2)

-  ← Revision 6 as of 2015-06-22 19:14:47 →
  Size: 2164
  Editor: KeiichiroOno
  Comment:
+  ← Revision 7 as of 2015-06-22 19:25:56 →
  Size: 2327
  Editor: KeiichiroOno
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-In this section, you will learn how to use programmatic access features for advanced Cytoscape users.
+In this chapter, you will learn how to use Cytoscape from command line and scripts.
-Line 13:
+Line 14:
-=== Background ===

Cytoscape has intuitive graphical user interface for interactive network data integration, analysis, and visualization.  It is a great way to exploratory analyze your data sets, but what happens if you have hundreds of data files?  It is virtually impossible to apply same operations to hundreds of networks manually with GUI.



More importantly, although you can save your ''results'' as session files, you cannot save your '''''workflows''''' if your analysis is based on point-and-click GUI operation.  Recording workflows is the key feature for reproducible data analysis, but it was a missing feature in past versions for Cytoscape.  Latest version of Cytoscape has several options to script and automate your workflows.
+== Background ==

Cytoscape has intuitive graphical user interface for interactive network data integration, analysis, and visualization.  It is a great way for exploratory data analysis, but what happens if you have hundreds of data files or need to ask someone to execute your data analysis workflows?  It is virtually impossible to apply same operations to hundreds of networks manually with GUI, and more importantly, although you can save your ''results'' as session files, you cannot save your '''''workflows''''' if your analysis is based on point-and-click GUI operation.  Recording workflows is the key feature for reproducible data analysis, but it was a missing feature in past versions for Cytoscape.  The latest version of Cytoscape has several options to script and automate your workflows.
-Line 19:
+Line 18:
-=== Options ===
+=== Options for Programmatic Access ===
-Line 24:
+Line 23:
-[[attachment:CommandTool.png]]
+ {{attachment:CommandTool.png}}
-Line 72:
+Line 71:
+[[cyREST|https://raw.githubusercontent.com/idekerlab/cyREST/master/docs/images/logo300.png]]