Columbia Medical School and Annotation Factory

Just got back from a really fun trip to New York City. I visited my colleagues in the Maniatis Lab at Columbia medical school. I got a chance to work with Sean O’Keeffe who is running ExpressionPlot there. He has set up gbrowse for some of the data over there. It it a fantastic user interface. I wonder how hard it would be to install it along with ExpressionPlot and have an option to link seqview to it instead.

Sean also encouraged me to automate the part of EP that generates annotation files. I hadn’t bothered when I made the original version, seeing as how it was already quite complicated, but I realize now that people will want to be able to make more annotations without consulting me. So that is now in the works. I’ve got a few steps mapped out and described in the User’s Guide, and once it is done I will release version 0.7, which will include the bunch of scripts necessary to make a new annotation.

If you make a new annotation, be sure to post what you did to the expressionplot google group so we can upload your files to the repository and make them available to others.

One Response to “Columbia Medical School and Annotation Factory”

  1. Brad Says:

    I finished incorporating the annotation generating system into ExpressionPlot. It is available since version 0.8 (although you should always get the latest version!!!).

    The system is described in detail in the User’s guide http://www.expressionplot.com/wiki/index.php?title=Generating_new_annotations

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A web-based framework for analysis of RNA-Seq and microarray gene expression data