I am trying to install and run Genome Browse from a single instance on a server/cluster with virtualized nodes running 64 bit Linux (CentOS 6.6) for multi-user access. It is a headless server and most of the researchers will be using Windows 7. Some others will be using OS X. I have tried X11 forwarding from a node with ImageJ until the server admin installs the libraries necessary for running Genome Browse. I have found that ImageJ is rather laggy using xming and a little better using mobaxterm. I assume for now that it would be even slower with Genome Browse because of semantic zoom etc.
Is there an ideal X server for windows? Should I use xrdp and use Microsoft Remote Desktop Connection? Essentially there might be some lag/latency issues, but I do not want it to be extremely laggy. It will all be over LAN as well.
Certain kind of GUIs are very hard on remote X connections. In X sessions, any interaction with the GUI (including many mouse movements) will trigger a number of mandatory back-and-forths over the network between the X client and server, and some GUI frameworks in particular multiply this, which (as you've seen) can make things unusably laggy. (Java/Swing is one of those which seem to interact poorly with remote X, so your problems with ImageJ don't surprise me.)
If your remote system allows it and you can use something like a VNC rather than a remote X session, that can often greatly improve performance for these sorts of applications. I'm not familiar with xrdp, but it seems to be VNC-based and so could help.
I'll be testing vnc, xrdp, etc. as soon as the server admin installs them. I will also hopefully be testing them with Genome Browse.
Obviously this is a single instance test until we can get it working to run for all users.
I have a feeling this is so deep into infrastructure it might actually belong more on Stack Overflow.
I run GenomeBrowse with X11 forwarding to a Linux client, which works reasonable well. You don't get quite the same responsiveness as if installed locally, but it's a workable solution. For Windows clients it might look different and I also remember xming to be quite slow.
Have you tried installing GenomeBrowse locally and access BAM files over the network? I was actually quite surprised how well this works given the large size of the BAM files.