Changes to the GEP Web Framework - Spring 2012

Change log for the Genomics Education Partnership Web Framework
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Changes to the GEP Web Framework - Spring 2012

Post by wleung » Sat Jan 14, 2012 10:38 pm

Hello Everyone,

The GEP web framework has been reset for the Spring semester.

For annotation, the primary focus this semester will be the remaining projects from the D. mojavensis euchromatic reference (control) region. These projects have the prefix dmojavensis_3Lcontrol_Apr2011 in the Project Management System.

However, because D. erecta projects are substantially easier to annotate than D. mojavensis, we also have a set of D. erecta projects from the 3L extended and the 2nd 3L control regions available for claiming.

For sequence improvement, we will focus our efforts on scaffolds from the D. ananassae Muller F and Muller D elements. Because of the high repeat density of the D. ananassae Muller F element, fosmids derived from this region are more likely to contain misassemblies. In addition, we have used assembly pieces (reads with "asmpiece" in their read name) to help guide the assembly of some of the more repetitious clones. Any projects that contain assembly pieces are labeled as “red” clones in the Project Management System irrespective of whether there are obvious assembly problems according to Assembly View.

Because we have the support of professional finishers at the Genome Institute, Bio 4342 have already claimed many of these red clones. (As a reminder, the number of times a project has been claimed is listed under the “# Claimed” column). Please avoid claiming these projects if possible.

For faculty members involved in sequence improvement, please note that the first round of the finishing reactions order will be processed on Wednesday, February 1st, 2012. Reaction orders will be collected by Wednesday midnight CST and the reaction results should be ready by the following Wednesday.

Below is a list of key changes we have made to the GEP web framework for the Spring semester:

1. Update to the Project Management System Interface
In order to improve support for more modern web browsers (and maintain support for older web browsers), we have updated the Project Management System interface. While there are changes to the page layout, the mechanics of claiming and submitting projects remained the same.

The documentations for the Project Management System have been updated to reflect changes to the web interface. Documentations for the updated Project Management System are available under “Help” -> “Documentations” -> “Web Framework” (or directly at

2. Synchronized GEP annotation resources to FlyBase Release 5.42

The BLASTX report in the annotation packages, databases for the Gene Record Finder and Gene Model Checker and the BLASTX protein alignment track on the Genome Browser have all been updated to D. melanogaster release 5.42.

Note that because some faculty members are using projects from the Demo claim system for training purpose, all the annotation packages and genome browsers have been updated to release 5.42 regardless of whether they are available for claiming in the Project Management System.

As a reminder, if you have already claimed projects, you can download the updated packages through the GEP Data Repository (at without claiming the projects again.

3. Updates to curriculum materials
We have updated the following curriculum materials to maintain compatibility with current versions (as of 01/10/2011) of NCBI, FlyBase, ExPASy, and the Gene Record Finder.

- Simple Introduction to NCBI BLAST
- Simple Annotation Problem
- Exercise #1: Detecting and Interpreting Genetic Homology

We have also updated the following lectures for the Jan. 2012 Faculty/TA workshop

- Introduction to ab initio and Evidence-based Gene Finding
- Web Databases for Drosophila

Please let me know if you have any questions or encounter any problems with the updated Project Management System, the updated project packages or revised curriculum materials. Thanks.

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