Setting up the MEDEA ChromoMap

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

Overview

The MEDEA ChromoMap is part of the MEDEA suite, but can be used independently, and is offered free. It visualizes feature densities and syntenic alignments with respect to reference chromosomes. 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 ChromoMap only needs JSON formatted data for the assemblies. If you want to display syntenic alignments, you'll need to provide JSON formatted data for alignments. If you want to display densities, you'll need provide JSON formatted data for the feature tracks (for example, Blast) and JSON formatted data for individual features.

Embedding

Following these steps for embedding the MEDEA ChromoMap 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 chromomap.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 assemblies.
  6. Create the optional JSON formatted data for tracks, features, and alignments.

Example

This example brings all the steps together to visualizes densities and alignments. Feel free to use it as a template in setting up the MEDEA ChromoMap on your site.

Contact

If you need help, please contact medea-support@broadinstitute.org.

If you'd like to be alerted to updates to the software, please email medea-support@broadinstitute.org 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 23, 2009
Contact: Reinhard Engels, Dennis Jen
medea-support@broadinstitute.org