News Archive

Our next i5k Workspace webinar will be June 4th 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:

 

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

Dear all,

Our next i5k Workspace webinar will be April 16th at 1pm MST.

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+4%2F16%2F2019&iso=20190416T15&p1=1928&ah=1

To connect to the webinarhttps://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

We are gauging the interest in an Apollo curation clinic prior to this year's Arthropod Genomics Symposium, to be led by Rob Waterhouse.

If you would like to attend, please take a minute to fill out the short form!

https://docs.google.com/forms/d/e/1FAIpQLSeVJs58aKfhf1Si-b4n5u4A89b4EGja...

Registration is now open for the 12th Annual Arthropod Genomics Symposium, June 12, 2019 to June 14, 2019, K-State Alumni Center, Kansas State University, Manhattan, Kansas 66506.

ABSTRACT DEADLINES IN 2019:

  • Monday, March 11 – Abstracts due for Oral Presentation consideration
  • Monday, May 20 - Abstracts due for Poster Presentations

More information is available here: https://www.k-state.edu/agc/ags/

Dear all,

Our next i5k Workspace webinar will be February 19th at 1pm MST.

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+Apollo+training&iso=20190219T13&p1=1947&ah=1

To connect to the webinarhttps://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

Dear all,

Our next i5k Workspace webinar will be November 20th 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 webinarhttps://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

We have 2 important topics to announce. We encourage you to read through this entire email to minimize disruption for your work at the i5k Workspace.

Transition to new genome assemblies

Most of the i5k pilot species now have updated genome assemblies (https://www.ncbi.nlm.nih.gov/assembly/?term=i5k).The i5k Workspace wants to migrate its resources to the next assembly version, but also needs your feedback on when to do the migration. This migration may significantly disrupt ongoing annotation efforts. Therefore, we are surveying the community for your annotation plans, in order to minimize the disruption for your work. The survey below gauges annotation activity for a subset of the i5k pilot organisms. Please complete the survey by October 23rd, 2018.

https://docs.google.com/forms/d/1bmBMy_70WWd1OiGP8ZD8FIGfARjXgyMb0xHq2HAXwHw/

Transition to the Apollo2 software

We are transitioning many of our genome browsers from the Apollo1 to the Apollo2 software.

Apollo2 has many more functions and features than Apollo1. You can find training and documentation on Apollo2 here:

We have updated the software version and browser URLs for Apollo for the following 10 organisms. You can also find all up-to-date browser URLs here: https://i5k.nal.usda.gov/available-genome-browsers

We will transition the remaining Apollo1 browsers in due course. Genomes with active annotation efforts will be transitioned once the annotation effort is complete.

 

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

 

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

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

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

Eufriesea mexicanahttps://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.

Please note: this event has been rescheduled for one week later: Tuesday, September 4th, at 3pm EDT.

 

We will hold a webinar on manual annotation via the Apollo software. The date for this webinar has been updated to Tuesday, September 4th, at 3pm EDT,

The webinar will last an hour and will cover:

  • Background on the principles of manual annotation;
  • A live annotation example.

This webinar will be hosted using Webex software. Slides may be made available on request.  This webinar will not be recorded.

 

Please use the link below to join the conference. If you have not used Webex before, please download the application and try to connect a few minutes before the start time.

To convert the time to your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k%40NAL+Workspace+webinar+-+manual+annotation+with+Apollo&iso=20180904T15&p1=263&ah=1

Connect using this URL: https://nal-usda.webex.com/meet/monica.poelchau

Options for WebEx connection: Connect to the Web Conference using the WebEx application. Using the link above, enter your name and email then select “Join Meeting” to download the application, which will launch once installed.

Connect through your WEB BROWSER without downloading the WebEx application: Using the link above, enter your name and email then select “Join by browser”.

The options described can only be selected after entering a name and valid email.