Possible questions are answered below:

Cytoscape web uses flash, so check your flash settings and enable it.
You can use the "Search Box" while "Gene/Protein Name" button is selected (which is default). A list of suggestions will come up as you start typing.
It will be highlighted (red) on the network and the information regarding the gene/protein you searched for will be listed in the "Notes" area below the network.
The network we provide here right now includes only data from eye development as a starting point and an example to hopefully convince you of its usefulness and to make you contribute data from your field of interest, so that development of the various organs can be compared.
Use the "Comments/Remarks" section to as precisely as possible describe it. Try to use the most frequent and accurate expressions. You might find them in the dropdowns the next time you "Filter" the network.
In the first row of dropdowns select “at least one inner PR” in the "Cell type 2" dropdown. Add another row of dropdowns (using the "+") and select the boolean "NOT" between the two rows. For the "Cell type 2" in the second row, select “at least one outer PR” (combination with NOT means "in not even one" or simply "none").
Yes, we actually encourage you to do that. You can first apply a filter and then highlight a subnetwork by using the select button or the search box.