Changes to the GEP Web Framework - Fall 2018

Change log for the Genomics Education Partnership Web Framework
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Changes to the GEP Web Framework - Fall 2018

Post by wleung » Fri Aug 31, 2018 3:45 pm

The GEP curriculum materials and the web framework have been updated for Fall 2018. The list of key changes are summarized below:

1. Curriculum Updates
  • Four new Transcription Start Sites (TSS) Modules are available on the "Introducing Genes" page of the GEP web site
    • Contact Meg Laakso ( if you would like to help collect student feedback and contribute to a CourseSource paper
    • Contact Anya Goodman ( if you would like to help pilot the TSS quiz questions
  • Curriculum materials have been revised so that they are compatible with the new GEP UCSC Genome Browser, FlyBase release 6.22, and NCBI BLAST 2.8.0+
  • FlyBase released an update (6.23) on August 23, 2018. Please let us know if you encounter any major discrepancies between the new FlyBase release and the curriculum materials.
    • The changes to the FlyBase interface (e.g., new Pathway and Gene Group reports) did not affect the GEP curriculum
    • The new FlyBase release changed the names of 101 genes, added 52 transcript records, and removed 50 transcript records. These changes should only have minor impact on the GEP annotation projects.

2. Professional Development and Mentoring Committee Updates
  • Request videos of student presentations
    • Please contact Catherine Reinke ( if you have videos of student presentations of their annotation work. She would like to include these videos as part of the online QUBES training for new GEP members
  • Please sign up for the GEP Committee communication tools if you have not already done so

3. Projects for Fall 2018
  • Annotation projects
    • 16 projects remaining from the D. takahashii F element
    • 55 new annotation projects from the D. takahashii D element
  • TSS-only projects
    • 42 projects remaining from the D. elegans F element
  • Sequence improvement projects
    • 77 projects remaining from D. biarmipes, D. elegans, D. ficusphila, and D. eugracilis
      • Attempted multiple times to resolve the gaps in these projects
      • Please focus on resolving errors within mononucleotide runs
    • 32 projects remaining from the D. takahashii F element
    • 21 new projects from the D. takahashii D element

4. Update to the GEP UCSC Genome Browser
  • Updated UCSC Genome Browser software to release 369
  • New evidence tracks for the whole genome assemblies of 27 Drosophila species besides D. melanogaster
    • BLAT alignments of RefSeq transcripts from 26 Drosophila species ("Drosophila Gnomon Transcripts" evidence track)
    • Added search indices for Gnomon gene predictions and RefSeq transcript alignments
    • Chain and Net alignments against the D. melanogaster assembly
    • RNA-Seq read coverage, splice junctions, TransDecoder transcripts
      • RNA-Seq evidence tracks available for 26 out of 27 Drosophila species (all species except for D. navojoa)
    • RAMPAGE evidence tracks from more than 20 embryonic stages
      • Available for D. ananassae, D. erecta, and D. pseudoobscura
  • New evidence tracks for D. melanogaster
    • New "Variations" section
      • SNPs and structural variations identified by UniProt, dbSNP, dbVar, DGRP v2, and the FlyVar EMS screen
    • modENCODE ChIP-chip data for Kc167, BG3, and S2 cells
      • Data from 31 histone modifications and 47 chromosomal proteins
    • modERN optimal peaks for 356 transcription factors
    • Chromatin accessibility data from FAIRE-Seq and ATAC-Seq
    • ChIP-nexus of basal transcription factors in Kc167 cells
    • ChIP-seq and ChIP-exo data for architectural proteins

We hope that you find these resources useful. Please let us know if you encounter any issues accessing these resources, or if you have any questions or concerns. Thanks.


Meg Laakso (On behalf of the Curriculum Committee)
Wilson Leung (On behalf of the Science/IT Committee)
Joyce Stamm (On behalf of the Professional Development and Mentoring Committee)

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