The Journal Manager sets up the journal, after the system has been installed on a web server, by working through five steps, filling in templates and configuring the management of the journal. The setup does not have to be done all at once: the templates can be filled in and saved; then the Journal Manager can return to Setup to complete the task or make changes at any time.

Setup is available to the Journal Manager on the Journal Management page, and contains its own set of Help texts built into each of the templates. Setting up the journal's web site will require decisions and texts for the following items, among others, which can be prepared in advance in consultation with the Editors or added at a later point.

• Principal contact for the journal
• Technical contact
• Scope and Focus Statement for the journal
• Journal Sections and policies
• Author Guidelines
• Submission requirements for authors
• Indexing elements and appropriate examples
• Peer Review Policy
• Reviewer Guidelines
• Copyright Policy
• Open Access Policy
• Editorial Board/Review Board
• Subscription Policies
• Use of layout editors, copyeditors, and/or proofreaders