Table of Contents

• Introduction
• Release Notes
• Installation Instructions
• Documentation
• Support
• Acknowledgments
• License

Introduction

Annotare is a tool for annotating biomedical investigations and resulting data. It is a stand-alone desktop application that features 1) a set of intuitive editor forms to create and modify annotations, 2) support for easy incorporation of terms from biomedical ontologies, 3) standard templates for common experiment types, 4) a design wizard to help create a new document, and 5) a validator that checks for syntactic and semantic violation (see figure below). Annotare will help a bench biologist construct a MIAME-compliant annotation file based on the MAGE-TAB format.

Release Notes

• http://code.google.com/p/annotare/wiki/Release_Notes_1_3

Installation Instructions

Annotare installers are available for Windows (XP,Vista, 7) and Mac (OS X) platforms

Requirements

1. Adobe AIR 1.5.2 or above
2. Java 1.5 or above
3. At least 190M disk space for Mac and 70M for Windows

Downloads are subject to our license agreement.

Install On Windows (XP, Vista, 7)

1. Uninstall Annotare before installing a new version.
2. Download the installer for Windows XP/Vista/2000/2003/2008 Installer bundled with JRE and AIR run time
3. The installer bundled with JRE will guide you through the Java installation process via a separate Java setup window. The installer will prompt you for confirmation to upgrade if it detects an older version of JRE.
4. The installer will add Annotare under the Programs menu. Go to Annotare under the Programs menu, and click on startIt to start Annotare.

Install on Mac (OS X)

1. Use the Software Update feature (available from the Apple menu) to check that you have the latest version of Java.
2. Before installing a new version, uninstall Annotare by removing it from /Applications folder.
3. Download the installer for Mac OS Installer bundled with AIR run time.
4. Double click on the zip file to unzip it to pkg file. Then double click on the pkg file to start Annotare installation process.
5. The installer will create Annotare.app under /Applications folder. Double click it to start Annotare.

Uninstall from Windows (XP, Vista, 7)

1. Remove Annotare by using 'Add/Remove programs' from control panel
2. Delete the Annotare folder under the 'Program Files' folder.

Uninstall from Mac (OS X)

Move Annotare.app from /Applications folder to Trash.

Documentation

• User Manual
• Tutorial
• Publication: Annotare - a tool for annotating high-throughput biomedical investigations and resulting data, Bioinformatics. 2010

Support

• Please email annotare-dev@googlegroups.com with questions, feature suggestions or comments.
• Please join the users group to receive announcements on Annotare, and also to post your questions and suggestions.

Acknowledgments

• Annotare development is supported by US National Institutes of Health (the National Human Genome Research Institute, the National Institute of Biomedical Imaging and Bioengineering and the National Cancer Institute) (grant number P41 HG003619), and EMBL.
• Annotare is dependent on the following third-party software:
1. Merapi project
2. Limpopo project

License

Annotare is released under MIT license