Setting up the MEDEA Stack Map

  1. Overview
  2. Embedding
  3. Example
  4. Contact

Overview

The MEDEA Stack Map is part of the MEDEA suite, but can be used independently, and is offered free. It provides a linear view of one or more sequences along with syntenic alignments and dynamic levels of zoom of features. This flash application makes calls to javascript configuration methods to request data and pass along user requests. The javascript configuration documentation provides more details about these required and optional methods used by the application.

At its minimum, the MEDEA Stack Map only needs JSON formatted data for the sequences, feature tracks, and features. If you want to display syntenic alignments, you'll need to provide JSON formatted data for alignments. If you want to display the sequence at the nucleotide level, you'll need to provide a text document listing the sequence as A, T, G, or C.

Embedding

Following these steps for embedding the MEDEA Stack Map on your web page and visualizing your data:

  1. Download all files.
  2. Create a web page with required and optional javascript configuration methods.
  3. Include the javascript for loading the flash application.
  4. Add the path of stackmap.swf for "src" variable in the javascript configuration methods in the previous step. Don't include the .swf extension to the path.
  5. Create the required JSON formatted data for sequences, feature tracks, and features.
  6. Create the optional JSON formatted data for alignments.

Example

This example brings all the steps together to visualizes sequences, features, and alignments. Feel free to use it as a template in setting up the MEDEA Stack Map on your site.

Contact

If you need help, please contact medea-support@broad.mit.edu.

If you'd like to be alerted to updates to the software, please email medea-support@broad.mit.edu to be added to the medea-announce mailing list. If you're internal to the Broad Insitute, you can add yourself to the medea-announce mailing list. This list is appropriate for those embedding MEDEA in their web sites--not for end users.

Last Updated: February 10, 2009
Contact: Reinhard Engels, Dennis Jen
medea-support@broad.mit.edu