News Archive

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.

 

Our next i5k Workspace webinar will be July 3rd 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

 

We have updated the Colorado Potato Beetle (Leptinotarsa decemlineata) Official Gene Set to OGSv1.2, and have released this OGS at the i5k Workspace and on Apollo. Apollo has now been updated to Apollov2, and has been re-opened for manual annotation. 

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.

#####
 
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.

A new organism, Medauroidea extradentata (the Vietnamese walking stick) is available at the i5k Workspace.

Organism page: https://i5k.nal.usda.gov/medauroidea-extradentata

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

Jbrowse: https://apollo.nal.usda.gov/apollo/Medauroidea%20extradentata/jbrowse/

Apollo (you will need to register in order to get an account): https://apollo.nal.usda.gov/apollo/annotator/index

Thank you to our newest data providers!

On Tuesday, April 24th, at 1pm MDT, we will hold a webinar on using the Apollo manual annotation software.

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.  Please use this 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.

Slides for this webinar are available here: slides (pdf)

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=20180424T13&p1=1947&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.

Two new organisms, Clitarchus hookeri and Holacanthella duospinosa, are now available at the i5k Workspace.
 
Organism pages:
https://i5k.nal.usda.gov/clitarchus-hookeri
https://i5k.nal.usda.gov/holacanthella-duospinosa
 
Blast:
https://i5k.nal.usda.gov/webapp/blast/
 
Jbrowse (note that we are transitioning to a new version of Apollo for new organisms):
Clitarchus hookeri: https://apollo.nal.usda.gov/apollo/1589984/jbrowse/index.html
Holacanthella duospinosa: https://apollo.nal.usda.gov/apollo/1779942/jbrowse/index.html
 
Apollo (you will need to register in order to get an account: https://i5k.nal.usda.gov/web-apollo-registration):
https://apollo.nal.usda.gov/apollo/annotator/index
 
Thank you to our newest data providers!

We will hold a webinar on Tuesday, February 20th, 2018, at 1 pm MST, soliciting your input on our future development.
 
The i5k Workspace@NAL is writing up a new 5-year project plan. We would like to solicit your input on our future development. In this webinar, we’ll start by reviewing the i5k Workspace@NAL accomplishments in the past 5 years. We’ll then transition into suggestions for where our focus should go in the future. Finally, we’ll have an open discussion session in which you can ask questions, give suggestions as well as critiques.
 
Connect to the webinar: https://nal-usda.webex.com/meet/monica.poelchau
 
Link to agenda (comments are welcome): https://i5k.nal.usda.gov/user-feedback-session-next-5-years-i5k-workspacenal
 
Link to see the Webinar time in your local time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+stakeholder+information+session&iso=20180220T13&p1=1947&ah=1
 
We have NEW connection information for the webinar. We are now using WebEx. Even if you have used this software before, you may need to install an additional application for the audio connection - so please give yourself plenty of time to do this.  Alternatively, you may find that a phone connection will provide you the best audio, in which case you can have WebEx call your phone to easily establish that connection.
 
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.