Setting up the MEDEA Dot Plot

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

Overview

The MEDEA Dot Plot is part of the MEDEA suite, but can be used independently, and is offered free. It visualizes syntenic alignments between a reference gnome and query genomes. 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 Dot Plot only needs JSON formatted data for the sequences and JSON formatted data for alignments.

Embedding

Following these steps for embedding the MEDEA Dot Plot 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 dotplot.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 JSON formatted data for alignments.
  6. Create the optional JSON formatted data for features.

Example

This example brings all the steps together to visualizes alignments. Feel free to use it as a template in setting up the MEDEA Dot Plot 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: January 26, 2009
Contact: Reinhard Engels, Dennis Jen
medea-support@broad.mit.edu