OCIAL NETWORK APP USER GUIDE
TABLE OF CONTENTS PART 1: INTRODUCTION / REQUIREMENTS PART 2: INSTALLATION PART 3: LAUNCHING THE APP PART 4: SOCIAL NETWORK APP BASICS PART 5: FEI (FREQUENTLY ENCOUNTERED ISSUES)
PART 1: REQUIREMENTS / AUDIENCE This user guide is for absolute beginners (users who are not already familiar with Cytoscape 3.0).
PART 2: INSTALLATION The Social Network App only runs on the latest version of Cytoscape (Cytoscape 3.0). Instructions for downloading and installing Cytoscape 3.0 can be found HERE. The Social Network App itself is currently available in the Cytoscape App Store. You can access it through this link HERE. Alternatively, you may go to the Cytoscape App Store HERE and search for 'Social Network App' (without quotes)
PART 3: LAUNCHING THE APP: * Click on 'Apps' * Scroll over to 'Social Network' * Click on 'View Panel' A new panel entitled 'Social Network' will pop up on the left side of Cytoscape.
PART 4: SOCIAL NETWORK APP PANEL BASICS The Social Network App User-Panel is divided into four main sections: (1) Category: this section allows you to select a Social Network 'category'. The four main categories are 'Academia', 'Twitter', 'LinkedIn' and 'Youtube'. To select a category, simply move the cursor over to the category panel and click on '--SELECT CATEGORY--'. (2) Search: the search section contains three important features: the search-box, the search button and the search filter. * Search Box: enter the key-word or query you want to build a network out of here. * 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 an author, search for a MeSH term). To select specify a filter click on '--SEARCH FILTER--' (3) Info-Panel: the info-panel section displays extra information specific to each category. There are four types of info-panels (Academia, Twitter, LinkedIn, Youtube). In-depth descriptions of the features contained inside these panels are provided below: * Academia: the Academia Info-Panel consists of only one section: Incites.
- - Incites: The Incites section allows you to build co-publication networks using Incites derived text files. To load an Incites data file, click on the button marked (...). To specify the name of the network you are building fill the 'Specify Network Name' form field. Finally, to create the network, click on 'Create Network'.
* Twitter: [RESERVED] * LinkedIn: [RESERVED] * Youtube: [RESERVED] (4) Network Panel: Clicking on a social network in this panel results in a custom set of visual styles being displayed to you. Each specific network has its own set of visual styles. To select a visual style click on '--SELECT VISUAL STYLE--' 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 3.0's VizMapper CLICK HERE.
PART 5: FEI (Frequently Encountered Issues) I clicked on 'View Panel' but the Social Network panel failed to show up:
- - You might be using the wrong version of Cytoscape. Refer back to PART 2: INSTALLATION. Make sure that you are running the latest version of Cytoscape.
I tried searching for a network but encountered a 'Network could not be loaded' error message.
- - This means that Cytoscape was not able to build a network because the query you used was too terse, too broad or too niche. Try to be more specific with your query. Use seach filters.
Cytoscape was unable to build a network out of my Incites data:
- - This issue usually arises because:
(1) The file you're trying to load is invalid. Verify that the file you are trying to load is in fact a valid Incites data file. A valid Incites data file should contain 6 columns and the columns should be separated by spaces. (2) The path to the file is broken. It may be that you loaded the file correctly but in the process the file's path got corrupted. In order to fix this issue simply re-load the file again. (3) The network name has not been specified. Make sure that the 'Specify network name' form field has been filled. (4) The network already exists. If you supply a network name that's already been taken, Cytoscape will refuse to build the network. In order to fix this, simply switch the network's name to a more unique alternative. (5)The buttons are non-responsive.
- - This isn't an issue associated with the app itself. It's a Cytoscape 3.0 issue. This usually happens when Cytoscape is starving for memory. If your machine has the capacity, it might be a good idea to increase Cytoscape's memory usage. For more on this (as well as other general Cytoscape 3.0 issues) CLICK HERE
TIP FOR PROOFREADING * 3 edits, staggered over a significant length of time are enough. More than 3 edits is overkill and will net you diminishing returns.