<p>I'm trying to connect from my Java application to a development server that has port 8088 closed which is used for RMI. I appreciate any help on how to open that port.</p>

Slicehost have some good documentation on setting up iptables on Ubuntu:
http://articles.slicehost.com/2008/4/25/ubuntu-hardy-setup-page-1
http://articles.slicehost.com/2008/9/2/mail-server-opening-ports-in-the-firewall