Half-day workshop on bioinformatics tools for Plant Genomics (Nov. 29, Noon-5PM)

Prior to the start of the CSHL Plant Genomes Meeting, a half-day workshop will be sponsored by the Gramene (NSF #1127112) and CyVerse (NSF # 1265383) projects and will cover public bioinformatics tools and resources in support of reference genome assemblies, automated prediction and community curation of gene annotations, and data submission of RNA-seq and other omics data to public repositories such as Track Hub. Lunch and coffee will be included. See more information and registration info at http://www.cyverse.org/content/half-day-workshop-cshl-plant-genomes-and-biotechnology-meeting-nov-29th-2017.



  1. Plant genome and pan-genome browsers. Gramene, the plant comparative database for genomes and pathways. Data submission and data visualization in Gramene.

  2. Best practices and new technologies in genome sequencing and assembly. Genome annotation tutorial with the MAKER pipeline

  3. MAKER annotation with SciApps & CyVerse

  4. Visualization and editing of sequence annotations with Apollo



Hands on tutorials and short lectures will get users started using these tools, resources, and databases right away. While some familiarity with command line is beneficial, the majority of exercises will make use of easy-to-use web-based interfaces, including the CyVerse Discovery Environment, Gramene Databases, and SciApps.





Please obtain a free CyVerse account and register for the workshop. The workshop is free and in-person attendees (limited to 30) will also receive complimentary lunch and coffee. Please bring a Wi-Fi enabled laptop to the session.



Register for the livestream – you and interested colleagues can register to watch - see link above. Recording will be available shortly after the program.

CyVerse and Gramene are funded by the National Science Foundation (#DBI-1265383 and #IOS-1127112, respectively).  Gramene is also partially by the USDA-ARS (1907-21000-030-00D).  Our resources are driven by and freely available to the community.



1 Bungtown Rd, Cold Spring Harbor, NY


Primary Contacts:

Marcela Karey Tello-Ruiz - Gramene

Liya Wang & Jason Williams - CyVerse

Cristina Fernandez-Marco - MaizeCode



Wednesday, November 29, 2017 Noon - 5 PM