News Archive

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:

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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.

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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

There are several new organisms available at the i5k Workspace:

The burying beetle, Nicrophorus vespilloides.
Organism page: https://i5k.nal.usda.gov/nicrophorus-vespilloides
Jbrowse/Apollo: https://apollo.nal.usda.gov/nicves/jbrowse

The small hive beetle, Aethina tumida:
Organism page: https://i5k.nal.usda.gov/aethina-tumida
Jbrowse/Apollo: https://apollo.nal.usda.gov/aettum/jbrowse

Thank you to our newest data providers!
 

The i5k Workspace will participate in the 10th Arthropod Genomics Symposium and Arthropod Bioinformatics Workshop. This will be a great opportunity for new or potential i5k Workspace users to become familiar with the services that we offer. The Symposium and workshop will be held from June 7 - June 11, 2017, at the University of Notre Dame.

For more information, please visit the Symposium website and workshop website.

We will be at the International Congress of Entomology XXV (ICE 2016) next week, to help promote the i5k Workspace@NAL, the upcoming i5k webinar series and and the larger i5k initiative. You can also learn more at http://i5k.github.io/. The i5k Workspace@NAL is presenting poster #D3385, and representatives from the i5k initiative will be at booth 320.

We have been working on some major updates to our infrastructure. HMMER and Clustal (beta release) are now available to users of the i5k Workspace.

For more information about the tools, and how they are set up at the i5k Workspace, please see our user guides. Similar to BLAST, saved searches will be available for one week after they are run.

HMMER user guide

Clustal user guide

*Note: The i5k Workspace implementation of Clustal includes both ClustalW and Clustal-Omega.

 

We have some exciting new features at the i5k Workspace!

New data submission forms.

Many of you have generously made your datasets available to the i5k community - whether you've set up a new i5k Workspace project with your genome assembly and gene predictions, or you've shared transcriptome assemblies, RNA-Seq data, or new gene predictions to better curate a genome that we host.

We've now developed new submission forms to make it easier for you to share your data with us and the i5k community. For an overview of how to submit your datasets to the i5k Workspace, follow this link:
https://i5k.nal.usda.gov/data-submission-overview

In order to submit your datasets, we'll ask you to create an account with the i5k Workspace (which will be different from your Web Apollo account, if you have one). You'll then be able to view and complete our dataset submission forms. You can find these new forms under our "Data" menu bar, or click on the "Submit Data" button on our homepage.

We'd love to hear feedback about these forms, if you have any - feel free to contact us!

Updated home page.

We've made a few changes to our home page menu and layout. We hope you like the changes! We always welcome feedback; feel free to contact us.

Updated tutorials.

We've updated our tutorials on how to share files with us, and how to upload files via CyVerse (formerly the iPlant Collaborative). Expect more updates to our tutorials in our next release.

There are three new genomes available at the i5k Workspace: the navel orangeworm, Amyelois transitella, the parasitoid wasp Microplitis demolitor, and the red flour beetle, Tribolium castaneum.
All genomes are open for manual curation. As always, you can register to be put in contact with the genome project’s community contact.
Thank you to our newest data providers!