An Anno-J 'instance' is a website that you can visit to use the application. For example, the Salk Epigenome site is an 'instance'. Using an instance of Anno-J is simple; just visit the website using a W3C compliant web browser such as Safari or Firefox.
Creating an instance is a little more involved and requires website administration skills plus access to a web server (Mac OS X users: you already have access to the Apache web server). If you don't feel confident at this stage, then contact your local website administrator for advice.
Hosting an instance of Anno-J requires access to a web server of your choice (although Apache is recommended), and the creation of a single HTML page. If you want to connect to remote data sources, then you will also need to know how to properly configure a reverse proxy. If you are not familiar with using web-servers, then you should contact your local web-admin and ask him or her for assistance as web-server documentation is beyond the scope of this document.
When just starting out, you may want to host an instance of Anno-J on your personal machine via http://localhost. A special note to Mac OS X users: you already have the Apache web server locked and loaded, just turn it on through System Preferences -> Sharing -> Personal Web Sharing. Your personal website is then accessible via http://localhost/~your_user