Phenote User Guide

System requirements

Phenote runs on most modern platforms, but requires Java 1.5 (aka Java 5) or later. An appropriate Java is pre-installed with Mac OS X 10.4 or newer (Phenote cannot run on Mac OS X 10.3). For Windows, you can download the latest Java from http://www.java.com/. If you're running Linux, please consult your system documentation for how to get Java.

Installation

Phenote can be downloaded from the OBO Sourceforge project site. There are separate downloads available for Mac and Windows, as well as a download of the application source code. Download the appropriate zip file for your platform.

• Mac: Double-click the downloaded file to unzip it. You should see the application, "Phenote.app". Drag it anywhere you like to install. Double-click the application to launch Phenote.
• Windows: Double-click the downloaded file. Click on "Extract all files" in the resulting window. Use the Extraction Wizard to put the Phenote folder wherever you want. Launch Phenote by double-clicking "Phenote.bat" inside the Phenote folder. It will take several seconds for the Phenote window to appear. Do not attempt to run Phenote from "inside" the zip file - it will not work properly without first extracting the files to another folder.
• Linux/Unix: forthcoming

The first time you launch Phenote you will be presented with a window from which you can choose a configuration. Select "phenoscape" and press OK. This window can be accessed any time via the Settings > Set Configuration... menu item. Choose the Phenoscape interface layout via the View > Layouts > Phenoscape menu item.

Using the docking interface

Phenote's interface consists of "docking" components which can be arranged into any layout the user prefers. A default layout for Phenoscape can be accessed via the menu item View > Layouts > Phenoscape. Each component can be minimized or closed using the window-like controls in its title tab. Pressing the arrow in a title tab will pop out a component into its own floating window. Pressing the arrow in the floating component's title tab will return it to the main window. Components can be grouped together in tab groups, where only one of the tabbed components is shown at a time. Click on a title tab to bring a component to the front. If there is not enough space, all tabs in a tab group may not be visible. In this case, left and right arrows will appear in the control tab for that group, which can be used to cycle through the components. Alternatively the downward pointing arrow can be used to display a selectable menu of the tabbed components.

Components that are not currently displayed can be accessed through the View > Show menu. Components are grouped into functional collection submenus. Some components can be opened repeatedly to display multiple instances (e.g. Complete Ontology Tree View), while others will only display a single instance (e.g. Annotation Editor).