News Archive

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.

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

 

The assembly GCA_002382865.1 of the tobacco budworm Heliothis virescens and associated annotations are now available at the i5k Workspace.

 

Organism page: https://i5k.nal.usda.gov/heliothis-virescens  
Jbrowse/Apollo: https://apollo.nal.usda.gov/helvir/jbrowse/

 

Thank you to our newest data providers!

The assembly GCF_001854935.1 of the whitefly Bemisia tabaci and associated annotations are now available at the i5k Workspace.

Organism page: https://i5k.nal.usda.gov/bemisia-tabaci
Jbrowse/Apollo: https://apollo.nal.usda.gov/bemtab/jbrowse

Thank you to our newest data providers!

We will hold a webinar on October 31st, 2017, at 1 pm MDT, with an open Q&A session on manual annotation using the Apollo software at the i5k Workspace@NAL.

The webinar will last an hour, and will be a great opportunity for anyone who has questions about the annotation process, or questions about annotating a specific model.

If you have a specific problem that you’d like for us to work on together, you can send the URL and any other information that you think is relevant to our email address: i5k@ars.usda.gov. Alternatively, make sure that you have this information available during the webinar.

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%40NAL+Workspace+webinar+-+manual+annotation+Q%26A&iso=20171031T13&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#