Hi Ann,

It is a real pleasure to have the possibility to talk to you. I have no problems coding in Java (computer engineering is actually my major), but a plugin doesn't look like the best possible solution. Actually I haven't had the possibility to examine this solution deeply. However, I will try to evaluate the three options you posted and see if I can obtain what I need. I will let you know. If there is a way to communicate directly through email, it would be really helpful for my research.

Thanks again,
Piero

Hi Ann,

I add this here as well so that if someone else is interested can see the developing of the discussion.

I examined the options you wrote me about and I came to the following conclusions:

• OSGi services: I think this solution is not feasible for my problem. What I am trying to do is not to add a service on top of the IGB Genome Browser. My idea is to use some of the functionalities of IGB inside another application. Probably the other two solutions are the best options.
• Option Two: Use IGB links - port 7085: I have tried this solution and it works fine. But it has a limitation I haven't found a way to overcome: once you have load a track you cannot delete it or at least hide it through the script language. Am I correct? In my idea I want to provide the user with the ability of changing the visualized tracks without starting a new instance of the genome browser. Summarizing, I would need a "unload" or "delete" command that so far is not available.
• Option Three: Use IGB commands - port 7084: this can be the perfect solution. To send commands to IGB inside my application. It won't be a R application, but that shouldn't change the attuability of this solution. Am I correct? I am looking forward for the release of version 8.2.

Please correct me, if I made some mistakes in my analysis. I am really glad for your help and, if you are interested, I am more than available to explain what we are working on.

Thanks,
Piero