News Archive

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#
 

We will be giving a general webinar about the i5k Workspace for the i5k consortium webinar series on October 4th, 2017.

See http://i5k.github.io/webinar#details for webinar and connection details.

Please join us!

 

 

For those who missed it, or would like to review - the slides from our Apollo webinar on August 29th are available on our presentations page, or here: Slides (pdf)

We've been working to improve our data submission process, and now support the SHA512 checksum for ensuring data integrity. We have also added the ability to directly upload your files at the time of submission. See our dataset submission overview for a summary of the dataset submission process.

The assembly NIJG01 of the orchid bee Euglossa dilemma and associated annotations are now available at the i5k Workspace.

Organism page: https://i5k.nal.usda.gov/euglossa-dilemma
Jbrowse/Apollo: https://apollo.nal.usda.gov/eugdil/jbrowse/

Thank you to our newest data providers!
 

Dear all,

We will hold a webinar on August 29th, 2017, at 1 pm MDT, 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 on the organism Eurytemora affinis.  

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=20170829T13&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

 

We will be holding a webinar on Friday July 14 at 1pm Eastern to introduce users to the resources available at the i5k Workspace@NAL.  The webinar will last an hour and will cover:

  • An introduction to the i5k Workspace project and website
  • Methods to search for data and tutorials on our website
  • How to join an annotation project
  • A primer on our tools: BLAST, Clustal, HMMER, JBrowse and Apollo
  • Pulling it all together with example workflows

 

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:

 

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

https://www.connectmeeting.att.com

Meeting Number: 8888449904       Meeting Code: 8586822

 

 

URL for the time zone tool if you are unable to use the link above:

https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace%40NAL+Webinar+-+Introduction+to+our+resources&iso=20170714T13&p1=263&ah=1

 

Assembly Lm_v2.2 of the migratory locust, Locusta migratoria, is now available at the i5k Workspace:

Organism page: https://i5k.nal.usda.gov/locusta-migratoria
Jbrowse/Apollo: https://apollo.nal.usda.gov/locmig/jbrowse

Thank you to our newest data providers!
 

Our colleagues Ricky Punzalan, Morgan Daniels, Katie Gucer, and Adam Kriesberg at University of Maryland have developed a survey on data practices of agricultural researchers. If you consider yourself an agricultural researcher, please consider participating in this survey! See details below.

#####

Greetings on behalf of the Agricultural Data Curation project at the University of Maryland College of Information Studies. We are studying the data practices of agricultural researchers in multiple settings. As part of our project, we are conducting a survey of these communities.

We will ask you about your research practice, data management, reuse, and data sharing practices, in addition to some questions about the current state of research data management. This survey is voluntary and will take approximately 15 minutes to complete.

The survey is located at http://ter.ps/db6.

Thank you in advance for your time and consideration. The data we collect from you and others will be reported in aggregate to provide valuable insight into data curation practice among agricultural researchers.

If you have questions, please do not hesitate to contact us via email (arclab@umd.edu).

 

Sincerely,

Ricky Punzalan, Assistant Professor

Morgan Daniels, Postdoctoral Fellow

Kathryn Gucer, Postdoctoral Fellow

Adam Kriesberg, Postdoctoral Fellow

University of Maryland College of Information Studies