Changes to the GEP Web Framework - Spring 2016

Change log for the Genomics Education Partnership Web Framework
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wleung
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Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Changes to the GEP Web Framework - Spring 2016

Post by wleung » Sat Jan 16, 2016 2:01 am

Hello Everyone,

We have reset the GEP Web Framework for the 2016 Spring semester. The list of key changes are summarized below:

1. Annotation projects for Spring 2016
  • 46 D. elegans and one D. biarmipes Muller D element projects from Fall 2015
  • 55 new annotation projects from the D. ficusphila Muller F element
2. Transcription Start Sites (TSS) projects for Spring 2016
  • 69 D. biarmipes Muller F element TSS projects from Fall 2015
3. Sequence improvement projects for Spring 2016
  • 15 D. biarmipes and 37 D. elegans projects from Fall 2015
  • 19 new sequence improvement projects from the D. ficusphila Muller F element
4. Updates to the GEP web framework
  • New GEP web site optimized for mobile devices
    • New web addresses for GEP wiki and forum
  • Upgraded GEP UCSC Genome Browser to version 324
  • Added graphical view of D. melanogaster gene structure to Gene Record Finder
5. Synchronize GEP annotation resources to FlyBase release 6.08
  • Updated GEP web framework tools (e.g., Gene Model Checker, Gene Record Finder)
  • Updated D. melanogaster Genome Browser to the latest GenBank assembly
6. Updated curriculum materials
  • Revised curriculum based on changes to the default NCBI BLAST parameters
  • Revisions based on FlyBase release 6.08 and NCBI BLAST+ 2.3.0
Below is a more detailed description of the changes that we have made for Spring 2016:

1. Annotation projects for Spring 2016
There are 46 D. elegans Muller D element projects and one D. biarmipes Muller D element project remaining from Fall 2015. All of these projects have been claimed at least twice in the Project Management System but 26 of the D. elegans Muller D element projects have no submissions. The D. elegans projects with no submissions have the highest priority in Spring 2016. If your students have previously completed annotation projects during Fall 2015, please submit these projects at your earliest convenience.

Based on the requests from GEP faculty, I have also created a new set of 55 annotation projects from the D. ficusphila Muller F element [Jan. 2016 (GEP/Dot)] assembly. These projects were derived from eight F element scaffolds in version 2.0 of the D. ficusphila assembly.

Our preliminary analyses have identified putative consensus errors within six coding exons of F element genes. We have fixed these consensus errors prior to the creation of the D. ficusphila annotation projects. However, there might be additional errors in the consensus sequences of the D. ficusphila projects that could interfere with the annotation of the coding regions. Please see the "Sequence Updater User Guide" (available under "Help" -> "Documentations" -> "Web Framework") for additional details on how to identify and document these consensus errors.

As a reminder, the TSS section of the GEP Annotation Report is optional so you can submit a project without TSS annotations. However, if time permits, we would like to encourage your students to annotate the TSS after they have completed the annotation of the coding regions.


2. TSS projects for Spring 2016
Most (69/70) of the TSS projects from the D. biarmipes Muller F element [Aug. 2013 (GEP/Dot) assembly] are still available to be claimed. While the TSS projects are more challenging than the annotation of the coding regions, we would like to encourage you and your students to contribute to this aspect of the project as the TSS annotations are essential to the subsequent phylogenetic footprinting analyses.

We have previously held a webinar in Fall 2015 that provides an overview of the current TSS annotation protocol. The webinar recording and the presentation are available through the "GEP Webinar on the Annotation of Transcription Start Sites" link on the GEP Private Wiki home page. You can also view one of the recordings directly at https://wustl.adobeconnect.com/p5oxtaknz55/

[Note that the GEP Private Wiki page contains the links to two different webinar recordings (one for the 11:00am session and the other for the 3:00pm session). The contents of both recordings are the same.]


3. Sequence improvement projects for Spring 2016
We have created 19 D. ficusphila sequence improvement projects in order to assess the quality of the F element scaffolds prior to creating the annotation projects. However, there are 52 sequence improvement projects from D. biarmipes and D. elegans that have either zero or one submissions. These projects have higher priority than the D. ficusphila projects.

Because the GEP no longer runs a central pipeline for generating new sequencing data for problematic regions, your students will need to run additional PCR and sequencing reactions locally in order to resolve low quality regions and gaps in the assembly during the semester. Alternatively, please add a "dataNeeded" tag to the regions that require additional sequencing data and design the corresponding sets of PCR primers prior to project submission so that we can more quickly generate the needed sequencing data during the summer.


4. Updates to the GEP web framework
As we have announced previously, the new GEP site is now online and it is optimized for mobile devices and different screen sizes. We have also upgraded the software for the GEP wiki and forum so that they provide better support for mobile devices. As a reminder, the GEP wiki and forum are now hosted on a different server and the new web addresses are as follows:
We have also setup redirects so that the previous web addresses (e.g., http://gep.wustl.edu/wiki/) should still continue to work.

We have updated all the GEP curriculum and documentations so that the screenshots are in concordance with the new GEP web site. However, if you have already developed curriculum for the Spring semester that are based on the old GEP website, an archive of the previous version of the GEP web site is available at http://community.gep.wustl.edu/oldgepsite/.

We have also migrated the tools in the GEP web framework (e.g., GEP UCSC Genome Browser, Gene Model Checker) to a new server. As part of this migration, we have upgraded the GEP UCSC Genome Browser to release 324. In addition to bug fixes and improved compatibility with newer web browsers (e.g., Internet Explorer 11, Microsoft Edge), the new version of the Genome Browser also includes additional navigation features. For example, you can use keyboard shortcuts to control the Genome Browser (press the "?" key on the Genome Browser page to see a list of available shortcut keys). One important change to the Genome Browser layout is that the "DNA" link used to retrieve the contig sequence is now listed under the "View" menu on the main toolbar.

We have updated all the screenshots in the GEP curriculum materials to the new version of the Genome Browser. However, if you have already developed curriculum materials for the Spring semester based on the old version of the GEP UCSC Genome Browser, an archive of the previous version of the Genome Browser (version 270) is available at http://oldgander.wustl.edu.

We have also added a new feature to the Gene Record Finder based on feature requests from GEP faculty. The "mRNA Details" section of the Gene Record Finder now includes a Genome Browser image of the D. melanogaster gene structure (where the thin boxes denote the untranslated regions, the thick boxes denote the coding exons, and the lines denote the introns). Clicking on this image will open a new web browser window with the Genome Browser for D. melanogaster. The "FlyBase Exons" and the "FlyBase CDS" tracks in the D. melanogaster genome browser demarcate the placement of each transcribed exon and coding exon in the D. melanogaster assembly, respectively.

For sequence improvement, we have updated the VirtualBox Virtual Appliance so that it is compatible with VirtualBox 5.0.12 in order to facilitate the use of Consed on MS Windows.

5. Synchronize GEP annotation resources to FlyBase release 6.08
The databases for the Gene Record Finder, the Gene Model Checker, the Annotation Files Merger, and the blastx reports in the annotation packages have been updated to FlyBase release 6.08. We have also updated the protein alignments and gene prediction tracks (i.e. blastx protein alignments, SPALN transcript alignments, and genBlastG gene predictions) on the GEP UCSC Genome Browser for the D. biarmipes and D. elegans projects. Similarly, the "D. mel Proteins" and "CDS Mapping" tracks for the whole genome (BCM-HGSC) assemblies of nine other Drosophila species have been updated to release 6.08.

We have also updated the D. melanogaster Genome Browser to the most recent GenBank assembly (GCA_000001215.4) and changed the naming conventions for the unplaced scaffolds so that they conform to the dm6 assembly on the official UCSC Genome Browser.


6. Updated curriculum materials
NCBI has recently increased the default word size parameter for blastp, blastx, and tblastn database searches from 3 to 6 (see the announcement at NCBI for details). However, NCBI BLAST will continue to use a word size of 3 when comparing two sequences (e.g., mapping coding exons against the contig sequence with blastx). We have updated the GEP curriculum materials to account for this change in the default BLAST parameters for database searches.

Curriculum materials with major revisions:

The following curriculum materials have undergone major revisions because of changes in the annotation protocol, GEP web site, web databases, or web tools:
  • Annotation of Drosophila Primer
  • BLAST Output Viewer Generator
  • Detecting and Interpreting Genetic Homology
  • GEP Live CD User Guide
  • Gene Record Finder User Guide
Curriculum materials with minor revisions

These curriculum materials have undergone minor revisions to maintain compatibility with the most recent version of the GEP UCSC Genome Browser, Gene Record Finder, database records at FlyBase, NCBI, and UniProt. Most of the changes can be attributed to changes in the FlyBase gene names and exon identifiers. Some of the revisions are caused by the change in the default word size for the new version of NCBI BLAST+ (version 2.3.0).
  • Understanding Eukaryotic Genes (Modules 1-6)
  • An Introduction to NCBI BLAST
  • Annotation Files Merger User Guide
  • Annotation Strategy Guide
  • Annotation of Conserved Motifs in Drosophila
  • Annotation of D. virilis
  • Annotation of Drosophila (workshop presentation)
  • Annotation of Transcription Start Sites in Drosophila
  • Annotation of a Drosophila Gene
  • Chimp BAC Analysis
  • GEP Annotation Report
  • GEP TSS Report
  • Gene Model Checker User Guide
  • Introduction to ab initio and Evidence-based Gene Finding
  • Introduction to web databases
  • Motif discovery in Drosophila
  • Searching for Transcription Start Sites in Drosophila
  • Sequence Updater User Guide
  • Simple Annotation Problem
  • Small Exon Finder User Guide
  • Using mRNA and EST Evidence in Annotation

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