|
Size: 5478
Comment: Logo
|
Size: 5326
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| {{attachment:UserguideSocialNetworkApp/socialNetwork_logo.png|Social Network Logo|align="right"}} <<BR>> <<BR>> <<BR>> <<BR>> == Social Network App Download Page == |
{{attachment:UserguideSocialNetworkApp/socialNetwork_logo.png|Social Network Logo|align="right"}} <<BR>> <<BR>> <<BR>> = Social Network App Download Page = |
| Line 9: | Line 9: |
| The Social Network Cytoscape app creates a visual summary of how individuals are connected. Biological networks can be visualized and analyzed using Cytoscape. Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and institutions. Who tends to publish together? What institutions are most collaborative? Are there inter-disciplinary connections in my institution? The app addresses these questions by building co-publication networks where the nodes represent authors and edges represent the publications that different authors share. | The Social Network Cytoscape app creates a visual summary of how individuals are connected. Biological networks can be visualized and analyzed using Cytoscape. Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and institutions. Who tends to publish together? What institutions are most collaborative? Are there inter-disciplinary connections in my institution? The app addresses these questions by building co-publication networks where the nodes represent authors, edges represent co-authorship and edge thickness represents how frequently co-authors collaborate. |
| Line 38: | Line 38: |
| {{attachment:social_network_panel.png|Social Network App User Panel|align="right"}} | === PubMed Search === {{attachment:pubmed_search.png|Social Network App User Panel (PubMed Search)|align="right"}} |
| Line 42: | Line 44: |
| 1. '''Search''': The Pubmed search section contains three important features: | 1. '''PubMed Search''': Enter the key-word or query you want to build a network out of here (i.e. an author's last name and first initial). |
| Line 44: | Line 46: |
| * '''Search Box''': Enter the key-word or query you want to build a network out of here (i.e. an author's last name and first initial). | 1. '''Max authors per pub''': Specify the maximum number of authors you require in a publication here. Limit is set to 500 by default. This means that publications containing more than 500 authors will not be visualized by the app. Setting the limit to a high value increases the computational demands of the app and is therefore not recommended. |
| Line 46: | Line 48: |
| * '''Search Button''': Click this button to commit a search. The app will search for and automatically build a network from the query you entered in the search box. * '''Search Filter''': Filter your searches here. If a broad search doesn't get you want you want, then try filtering it (i.e. instead of searching for ''authors'', search for ''MeSH'' terms). |
1. '''Time Interval''': Specify the time interval here. By default the maximum date is set to the current year and the minimum date is set to five years before the current year. |
| Line 50: | Line 50: |
| 1. '''Information Panel''': Information panels display extra information specific to each category. The Social Network App currently supports only one information panel ('''Academia'''). | 1. '''Create Network''': Once you've provided all the required information (i.e. '''''Load File''''' and '''''Specify Network Name'''''), click here to create your network. If the information you provided is found to be lacking, the app will notify you of this, and offer tips on how to remedy the situation. |
| Line 52: | Line 52: |
| * '''Academia''': The Academia information panel enables you to build networks out of data files. It currently only supports data files from two sources: ('''Incites''' and '''Scopus''') | 1. '''Network Summary Section''': In this section, a summary of the network's attributes is provided: * # of nodes and edges in the network * Type of the network (InCites, Scopus or PubMed) * Various other attributes (i.e. a list of any unidentified faculty). |
| Line 54: | Line 57: |
| 1. '''Select Database''': Select a database here. There are only two databases available. As stated above, the Social Network App only supports reports generated by '''Incites''' and '''Scopus''' at the moment. | <<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>> |
| Line 56: | Line 59: |
| 1. '''Load File''': Provide a path to your data file here. To load a data file, click on the button marked '''(...)'''. | === File Input === {{attachment:file_input.png|Social Network App User Panel (File Input)|align="right"}} 1. '''Select Database''': Select a database here. There are only three databases available. As stated above, the Social Network App only supports reports generated by '''Incites''', '''PubMed''' and '''Scopus''' at the moment. 1. '''Load File''': Provide a path to your data file here. To load a data file, click on the button marked '''(...)'''. Here are some example files: [[attachment:incites_example.zip|InCites]], [[attachment:pubmed_example.xml|PubMed]], [[attachment:scopus_example.csv|Scopus]], |
| Line 60: | Line 69: |
| 1. '''Create Network''': Once you've provided all the required information (i.e. '''''Load File''''' and '''''Specify Network Name'''''), click here to create your network. If the information you provided is found to be lacking, the app will notify you of this, and offer tips on how to remedy the situation. 1. '''Network Panel''': The network panel consists of two sections: * '''Network Summary Section''': In this section, a summary of the network's attributes is provided: * # of nodes and edges in the network * Type of the network (InCites, Scopus or Pubmed) * Various other attributes (i.e. a list of any unidentified faculty). * '''Visual Style Filter''': Each specific network has its own set of visual styles. To select a visual style click on the arrows. It is also possible to create your very own visual styles. To create visual styles from scratch, click on the VizMapper tab in the Control Panel. For a tutorial on how to use Cytoscape 3.x's VizMapper click [[http://wiki.cytoscape.org/Cytoscape_3/UserManual#Visual_Styles|HERE]]. |
<<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>><<BR>> |
| Line 71: | Line 73: |
== Development == [[http://baderlab.org/Software/SocialNetworkApp/Development|Setting up Eclipse (or other IDE) for development of the app]] |
|
| Line 81: | Line 86: |
== Development == [[http://baderlab.org/Software/SocialNetworkApp/Development|Setting up Eclipse (or other IDE) for development of the app]] |
Social Network App Download Page
Contents
Brief Description
The Social Network Cytoscape app creates a visual summary of how individuals are connected. Biological networks can be visualized and analyzed using Cytoscape. Often researchers want to go beyond the network of proteins or genes and also look at the inter-connectedness between colleagues and institutions. Who tends to publish together? What institutions are most collaborative? Are there inter-disciplinary connections in my institution? The app addresses these questions by building co-publication networks where the nodes represent authors, edges represent co-authorship and edge thickness represents how frequently co-authors collaborate.
Installation
The Social Network App only runs on the latest version of Cytoscape (Cytoscape 3.x). Instructions for downloading and installing Cytoscape 3.x can be found HERE.
Once Cytoscape 3.x is installed and running:
Download this jar & store it in a local folder: social-network-app-1.0.jar
Go to the menu bar and click on Apps.
Go to App Manager. The App Manager enables you to install the app in one of two ways:
Search: Here you can install the app through the Cytoscape app store. To do this simply search for Social Network App or use a similar descriptive query. A list of relevant apps will be presented to you. Once you've located the app, select it and click Install.
Install from file : Here you can install the app locally. Since the Cytoscape App Store currently doesn't hold the Social Network App this is the option that we will venture to use in this tutorial.
Click Install from File
Locate the locally stored app file (i.e. social-network-app.jar) and select it.
Voila! The app should now be installed.
Launching The App
In Cytoscape 3.x:
Click on Apps
Scroll over to Social Network
Click on View Panel
A new panel called Social Network will pop up on the left side of Cytoscape.
Getting Started
PubMed Search
The Social Network App is divided into three main sections (Search, Information, Network):
PubMed Search: Enter the key-word or query you want to build a network out of here (i.e. an author's last name and first initial).
Max authors per pub: Specify the maximum number of authors you require in a publication here. Limit is set to 500 by default. This means that publications containing more than 500 authors will not be visualized by the app. Setting the limit to a high value increases the computational demands of the app and is therefore not recommended.
Time Interval: Specify the time interval here. By default the maximum date is set to the current year and the minimum date is set to five years before the current year.
Create Network: Once you've provided all the required information (i.e. Load File and Specify Network Name), click here to create your network. If the information you provided is found to be lacking, the app will notify you of this, and offer tips on how to remedy the situation.
Network Summary Section: In this section, a summary of the network's attributes is provided:
File Input
Select Database: Select a database here. There are only three databases available. As stated above, the Social Network App only supports reports generated by Incites, PubMed and Scopus at the moment.
Load File: Provide a path to your data file here. To load a data file, click on the button marked (...). Here are some example files: InCites, PubMed, Scopus,
Specify Network Name: Specify the name of your network here.
User Guide
Development
Setting up Eclipse (or other IDE) for development of the app
Examples
