News Archive

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.

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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.

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.
     

At long last, we've put together guidelines for naming genes and proteins at the i5k Workspace: https://i5k.nal.usda.gov/i5k-workspace-gene-and-protein-naming-guidelines. We invite all of our users, new and seasoned, to review these guidelines. If you have comments, suggestions, critiques, please let us know - we've opened up a comments form at the bottom of the document, or you are welcome to email us with feedback.

Dear users,

We have updated our dataset submission forms to include only one form, instead of the previous 3. We hope this change minimizes confusion when submitting your datasets!

You can find the new form here (login required):

https://i5k.nal.usda.gov/datasets/submit-a-dataset
 

Best,

Monica and the i5k Workspace team

The assembly GCA_002176555.1 of the Southern cattle tick Rhipicephalus microplus is now available at the i5k Workspace.

Organism page: https://i5k.nal.usda.gov/rhipicephalus-microplus  
Jbrowse/Apollo: https://apollo.nal.usda.gov/rhimic/jbrowse/

This assembly is open for community curation - however, note that no annotations are currently available.

Thank you to our newest data providers!

Dear all,

We will hold a webinar on Tuesday, December 19th, 2017, at 1 pm MST, on 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 the AT&T Connect software.  Please use the link below to join the conference.  If you have not used AT&T Connect before, please download the application and try to connect a few minutes before the start time.

Use this link to see the Webinar time in your local time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+webinar%3A+using+the+Apollo+manual+annotation+software&iso=20171219T13&p1=1947&ah=1

To join AT&T Connect Conference:
--------------------------------------------
Option 1. To connect using the AT&T Connect application, click here:
https://connect16.uc.att.com/usda/meet/?ExEventID=88586822
The link will provide a prompt to download the application and will launch the application once installed.
(Please note, if you use the Firefox browser, I have found this link does not always properly launch the application.  If you are having problems connecting, please try the link in another web browser.)
 
Option 2. Connect through your WEB BROWSER without downloading the AT&T Connect application (usually requires accessing audio via phone connection)
https://www.connectmeeting.att.com
Meeting Number: 8888449904       Meeting Code: 8586822

Audio connection if not possible via computer:
1. USA Access: USA Toll-Free: 888-844-9904, then enter Code: 8586822# or USA Caller Paid: 816-423-4261, then enter Code: 8586822#
2. International Access Numbers. A number in your country or in a country close to you (may not be toll free).
3. When prompted, enter the Meeting Access Code: 8586822#
 
Best,
Monica and the i5k Workspace@NAL Team