Application Preferences

The application's preferences can be accessed from the drop-down menu by selecting File-->Preferences-->Application Preferences.

All options require that any modification to a preference be retained only if you click on the Save button at the bottom of the relevant tab. You can click on the "Restore Defaults" button to revert to the original settings. 

You must restart IPA before any changes go into effect.


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APPLICATION tab of Application Preferences:

Molecule and Stacked Bar Chart Coloring
Allows you to customize the colors that signify up-and-down-regulation for the Expression Value types. Clicking on a colored square will open the color selector, from which you can select the color of your choosing. 


Comparison Analysis Bar Chart Coloring
You can change the colors of the bars in Canonical Pathways, Diseases & Functions Analysis, My Pathways Analysis, and List Analysis. For the observation you would like to change, click on the colored square, then choose a color for the color palate. 


System Memory Allocated to IPA

The amount of system memory (i.e., the amount of RAM) allocated for the IPA application can be set using the pull-down menu. IPA needs at least 750 Mb of system memory to be available to it. Ideally, if you have at least 4 GB of installed RAM on your computer, you would set the setting to at least 1000 or 1200 mb. If you have a computer with 6 GB or more, set IPA to 2000 or more. If you create large Comparison Analyses, want to use more advanced features (such as Causal Network Analysis, IsoProfiler, Analysis Match, etc.), set IPA to >4000 Mb if you have enough installed RAM on your computer. However, note that IPA won't start up if you allocate it more memory than is available in your system memory. If this happens, please go to this URL and start IPA with this URL: https://analysis.ingenuity.com/pa/launch.jsp?maxMemory=750. This will allow you to go back to the IPA preferences and set it back to the original memory setting that had worked on your computer.
 

Projects

Displaying the pre-loaded Example Analyses can be disabled under Projects. Un-checking the box for Display Sample Project will hide the sample project link in the Projects pane.

 

Notifications

A default notice is sent to your email address each time the application has completed running an analysis. This feature can be disabled by un-checking the box for Send Analysis Status E-mail. You can also prevent IPA from showing the pop-up bar at the bottom of the IPA screen that appears when your analysis is complete.

 

Work Flow Instructions

Keeping this box checked will allow you to see the respective workflow instructions when you choose to either run an analysis or perform a search or create a pathway from the quick start screen. If you do not want to see the workflow instructions simply uncheck the box and save the settings.

 

Quick Start Screen

You can choose to either show or hide the quick start screen when your IPA workspace has loaded. Note that hiding the screen will prevent you from viewing updates, such as downtime notifications and other news about IPA.

Auto hide status bar
This prevents you from viewing the status of your analyses.

Set the maximum number of Pathways, Networks, or Lists that can be opened in a window 
This setting allows you to open and work with up to 10 pathways, networks, or lists simultaneously. 


Set the maximum number of analyses that can be opened in a window 
This setting allows you to keep up to 5 IPA analyses open simultaneously.


GRAPH APPEARANCE tab of Application Preferences:

Checking the Measurement Values checkbox displays the corresponding values in IPA Pathways and Networks. 

The Node label position relative to node allows you to move the node label in the middle of a node or below the node.

You can include or exclude Overlay Tag Lines. By default, the Molecule Activity Predictor (MAP) is turned on by default, but you can turn it off in this section.

Node fill outline color refers to what color is used for the outline of a node when it is selected in a pathway or network. 

Changing the font size for Molecule Name, Expression Value, Relationship Labels, and the Tag name are also available in this window.


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BUILD FILTERS tab of Application Preferences:

These options allow you to select the default filters you will use when using BUILD tools in My Pathways.


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ANALYSIS FILTERS tab of Application Preferences:

Allows you to set the analysis parameters to allow IPA to run all your analyses with pre-defined filter settings without having to specify them individually for each analysis.


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CACHE tab of Application Preferences:

The cache stores encrypted data locally for subsequent quick retrieval. The minimum disk space to use for caching is 200 mb. If you have ample free disk space, it is recommended that you increase it to at least 500 MB. This is a good option to try when you are experiencing any errors messages that appear when viewing your analyses.



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