News Archive

Dear all,

Our next i5k Workspace webinar will be November 20^th at 1pm MDT.

Title:  Manual annotation using the Apollo software

The webinar will last an hour and will cover:

• Background on the principles of manual annotation;
• Instructions on using the Apollo software;
• A live annotation example.  

Click this link to view the event in your time zone:

https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+webinar+-+November+2018&iso=20181120T13&p1=1947&ah=1

To connect to the webinar: https://nal-usda.webex.com/meet/monica.poelchau

To join by phone: 

Call-in toll-free number (ATT Audio Conference):1-888-8449904

Call-in number (ATT Audio Conference):1-816-4234261

Access Code: 7620882

There are 5 new organisms available at the i5k Worskpace@NAL:

Apis mellifera: https://i5k.nal.usda.gov/apis-mellifera

Bombus impatiens: https://i5k.nal.usda.gov/bombus-impatiens

Bombus terrestris: https://i5k.nal.usda.gov/bombus-terrestris

Eufriesea mexicana: https://i5k.nal.usda.gov/eufriesea-mexicana

Varroa destructor: https://i5k.nal.usda.gov/varroa-destructor

Apollo/Jbrowse URLs for each organism: https://i5k.nal.usda.gov/available-genome-browsers

BLAST: https://i5k.nal.usda.gov/webapp/blast/

Only Varroa destructor and Eufriesea mexicana are available for manual annotation via Apollo at this time. The bee datasets are available in collaboration with BeeBase – if manual annotation of these organisms is desired, please contact hymenopterabase@gmail.com. We provide links in each of the organism pages to the original BeeBase datasets. Note that all BeeBase datasets were updated for display on the RefSeq genome assemblies, so there are minor changes in the gene sets. Details can be found in the readme files associated with each dataset.

Our next i5k Workspace webinar will be July 3^rd at 1pm MDT.

Title: The i5k workspace's recommendations for managing genome project data

This webinar will cover our recommendations for managing your genome project data. We will describe recommended repositories for typical data types generated as part of a genome project, and submission timing. We will describe how to use the i5k Workspace’s tools and resources during the course of your genome project.

Click this link to view the event in your time zone:

https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+webinar+-+July+2018&iso=20180703T13&p1=1947&ah=1

To connect to the webinar: https://nal-usda.webex.com/meet/monica.poelchau

To join by phone:

Call-in toll-free number (ATT Audio Conference):1-888-8449904

Call-in number (ATT Audio Conference):1-816-4234261

Access Code: 7620882

Cross-posting from the i5k pilot mailing list. This symposium is likely of interest to most of our users. The i5k Workspace will participate in the Bioinformatics workshop taking place one day prior to AGS.

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Early registration for the 11th Arthropod Genomics Symposium ends this Friday, 4/27/18.  After Friday, registration prices will increase.  Please note, we have extended the deadline for submission of abstracts for consideration as contributed talks to 4/27/18 as well.  
 
This year the symposium will be held at the University of Illinois at Urbana-Champaign on Thursday-Saturday June 7-9, 2018. This annual meeting originated with Susan Brown and colleagues at Kansas State University and now rotates between them, Notre Dame, and us. It is a relatively informal meeting allowing for lots of interactions and discussion of the progress in arthropod genomics in the past year and prospects for the future.
 
We have retained the format of years before, with a plenary talk by Michael Lynch from Arizona State University on Thursday evening, then six talk sessions on Friday and Saturday each with two invited speakers (see agenda below) and two contributed talks, covering topics such as the i5k, microbiomes, vector biology, social insects, and comparative and population genomics. Each afternoon will have a poster session that does not overlap with the talks.
 
This is a relatively inexpensive meeting and we provide student residence hall accommodation to help minimize costs, so while we hope that faculty colleagues will attend, we particularly encourage students and postdocs to attend. If you know of labs or colleagues new to arthropod genomics, please forward this announcement to them as they may not be on one of the list servers we have access to.
 
For those new to genomics, on the Thursday afternoon before the meeting starts we will have a hands-on Bioinformatics workshop covering genome databases (exemplified by i5k Workspace@NAL), the Apollo tool for manual gene modeling, the OrthoDB orthology database, and the BUSCO tool for evaluation of genome assembly and gene set completeness.
 
On Friday evening we will have an optional dinner with May Berenbaum as speaker, preceded by free tours of the campus with themes of Genomics, Entomology, and Art.
 
Registration, the meeting agenda, poster abstract submission (including for consideration for a contributed talk if desired), lodging, and travel information can be obtained here.