IM Browser - Frequently Asked Questions, Problems, and Solutions
1. Will IM Browser work with any internet browser?
It depends on the version of Java installed on your machine. WIth Java version 6, IM Browser works well with Safari, Firefox, and Chrome, and with Internet Explorer in Windows. Chrome is not compatible with Java version 7 and therefore cannot run Java applets like IM Browser.
2. Is Java necessary to run IM Browser?
Yes, IM Browser requires Java to be installed and enabled on your machine. To download and install Java go here.
3. How do I configure security settings to enable IM Browser?
With Java versions 1.5 through 6, you enable Java in your web browser settings/preferences.
To use IM Browser with Java version 7 the Java security settings must be set to allow applications to be launched from http://www.droidb.org. On a Mac go to System Preferences and Java. Under the Security tab edit the Exceptions List by adding http://www.droidb.org.
4. When I click on "Start IM Browser", a page opens but nothing happpens.
If you are using one of the recommended browsers (see 1 above), you may not have Java installed or enabled. Go here for instructions.You will also find instructions for how to download and enable Java.
Click here to see the typical Java message.
When you see this, click on Trust so that you will be able to use IM Browser to save interaction maps, tables of data, and queries to your computer. Since this will allow the applet to write to your computer hard drive (but only as you specify), Java believes you should be concerned about whether the applet is originating from a trusted source. To authenticate that we are in fact Wayne State University, we employ a Java Code Signing Certificate issued by the company Thawte. Details can be seen by clicking on Show Certificate. Note that if you click on Don't Trust, most features of IM Browser will still work, but you will not be able to save your work to your computer. Note also, if you click on Don't Trust, you may need to click on it several times before IM Browser continues.
5. What should I see when IM Browser successfully starts?
After Java loads and asks whether you trust Wayne State University, you should see the IM Browser window and a brief message, "Welcome to IM Browser". If yo d not see this message or you see a Java security message see FAQ 3 above. To start a search for genes go to the" Add" menu and select "Add Genes/Proteins". A query form will open that looks like this. Notice that there are two steps to finding interactions. Step 1 is to find the gene, either by searching a lookup table (top button), searching Flybase (middle button), or by loading a list from your computer (bottom button). If you know the FBgn of your gene(s), you can enter it manually in space provided. Step 2 is to select the interaction data table(s) you wish to search. After completing those two steps, click on OK. If DroID has data for your query, it will draw an interaction map.
6. What can I do with the interaction map that IM Browser draws?
A lot. Here are a few examples. Grab and move individual or groups of genes/proteins around. You can change the layout (Settings/Default Layout) and zoom in our out (View). If you right-click on a gene/protein you can get more informaiton about it, connect to its Flybase page, change its shape or color, delete it, or find its interactors (Expand). Right-click on an edge to get experimental details about the interaction. You can also add to the map by conducting additional searches (Add). You can filter (Filter) or color (Color) based on a variety of gene/protein or interaction attributes. And much more. For a tutorial click here.
7. Can I access DroID with Cytoscape instead of IM Browser?
Yes. Cytoscape is a powerful network visualization and analysis program. To access DroID from within the Cytoscape environment use the DroID plugin.
8. IM Browser is still not working for me. Where can I get more help?
You can e-mail us at Droid(at)wayne.edu.