Changes to the GEP Web Framework - Spring 2013

Change log for the Genomics Education Partnership Web Framework
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Location: Washington University in St. Louis

Changes to the GEP Web Framework - Spring 2013

Post by wleung » Mon Jan 07, 2013 4:40 am

The GEP web framework has been reset for the Spring 2013 semester.

Summary of key changes
1. New D. ananassae annotation projects from the 3L reference region available
2. Updated GEP Web Framework and annotation materials (Note: new NCBI BLAST output format)
3. D. ananassae sequence improvement projects available for claiming
4. New curriculum materials dealing with misassemblies
5. Recordings of GEP webinars available online

Detailed descriptions of key changes
1. New D. ananassae annotation projects
For annotation, the primary focus this semester will be the remaining projects from the D. biarmipes dot chromosome. Because most of the projects from D. biarmipes dot have been claimed more than twice, we have also created a new set of 45 annotation projects from the D. ananassae Muller D element (3L euchromatic reference region).

You can access the new D. ananassae annotation projects through the Project Management System or the GEP Data Repository. These projects have the project prefix "dananassae_3Lcontrol_Jan2013". You can view the projects using the GEP UCSC Genome Browser Mirror by selecting "D. ananassae" under the "genome" field and "Jan. 2013 (GEP/3L Reference)" under the "assembly" field on the Genome Gateway page.

2. Updates to GEP web framework
Below is a summary of the major changes we have made to the GEP web framework:

A. Synchronized GEP annotation resources to FlyBase Release 5.48

The BLASTX report in the annotation packages, databases for the Gene Record Finder and Gene Model Checker, Annotation Files Merger and the BLASTX protein alignment track on the Genome Browser have all been updated to D. melanogaster release 5.48.

Note that because some faculty members are using projects from the sandbox Project Management System for training, all the annotation packages and genome browsers have been updated to release 5.48 irrespective of whether they are available for claiming in the production Project Management System.

As a reminder, if you have already claimed projects during the fall semester, you can download the new packages using the GEP Data Repository without claiming the projects again.

B. Updates to curriculum materials; changes in BLAST!

NCBI has changed some of the default BLAST parameters and made substantial changes to the BLAST output format. Note in particular that you will want to be conscious of how you set the algorithm parameters, as the default parameters have changed. In general, you should turn off compositional adjustments (i.e. change the "Compositional adjustment" field to "No adjustment") when mapping individual exons using bl2seq with either BLASTX or TBLASTN.

We have revised all the exercises and walkthroughs so that they use the new BLAST output format. To get a quick overview of the major changes, we would recommend reviewing the revised "Simple Introduction to NCBI BLAST" exercise. NCBI has also posted a video on its YouTube channel that covers the key new features of the NCBI BLAST output.

We have also updated the curriculum materials to maintain compatibility with the most recent records in the various public databases (e.g. NCBI, FlyBase, and UniProt). Note that all exon identifiers for FlyBase (e.g. used by the Gene Record Finder) have changed in release 5.48 when compared to release 5.46.

The following documents have been revised for Spring 2013:
  • Annotation Strategy Guide
  • Basics of BLAST
  • Chimp BAC analysis
  • Common Bioinformatics Programs
  • Detecting and Interpreting Genetic Homology
  • Introduction to ab initio and evidence-based gene finding
  • Simple Annotation Problem
  • Simple Introduction to NCBI BLAST
We have also created a new lecture for the Jan. 2013 Faculty/TA workshop:

3. D. ananassae sequence improvement projects
For sequence improvement, we have reset all the D. ananassae sequence improvement projects and incorporated the reads that were called last year into the project packages. Most of the projects available to be claimed are green (easy) projects but there are a few projects with major misassemblies. Note that we have removed the assembly pieces from all the projects because they often introduce new misassemblies.

For faculty members involved in sequence improvement, we have tentatively scheduled collection of the first round of the finishing reaction orders on Wednesday, January 30th, 2013. Reaction orders will be collected by Wednesday midnight CST and the reaction results should be ready by the following Wednesday. Please let us know if you would like to order reactions before this date.

4. New curriculum materials dealing with misassemblies
As we have mentioned in a previous message, we have developed additional curriculum materials and tools for dealing misassemblies. If your students are working on red or difficult yellow clones from D. ananassae, they will likely benefit from these materials. You can find the new walkthroughs and reference materials through the Resolving Misassemblies page on the GEP web site (under "Curriculum" -> "Course Materials" -> "Washington University" -> "Finishing and Sequence Improvement")

New curriculum materials for sequence improvement:
  • Identifying and Sorting Tandem Duplications and an Inverted Repeat
  • GEP Misassembly Tools User Guide
  • Common Misassembly Protocols
  • Workflow to Resolve Misassembly

5. GEP Webinar
As many of you know, we have hosted two webinars during Fall 2012 on new or improved web site materials. We have recorded both webinars and you can view these recordings online at the web addresses below. Both webinars are approximately 1 hour long:
  1. GEP 2012 web framework update
  2. GEP sequence improvement webinar

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