News Archive

We've upated the i5k Workspace@NAL resources for Ephemera danica. 

Ephemera danica resources:

General information:

 

 

Our next i5k Workspace webinar will be April 21st at 1pm MDT.
 
Title:  Manual annotation using the Apollo software
 
The webinar will last an hour and will cover our regular Apollo training:
 
  • Background on the principles of manual annotation;
  • Instructions on using the Apollo software;
  • A live annotation example.  
Click this link to view the event in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+...

Manual annotation is a great way to stay productive and engage undergraduates when you are not able to do research in the lab. The i5k Workspace@NAL has many genomes open for manual annotation, and we can set up our resources for your favorite (public) genome if we don't host it yet. 

Get in touch if you have any questions or suggestions! https://i5k.nal.usda.gov/contact or i5k@ars.usda.gov

A new organism is available at the i5k Workspace: Contarinia nasturtii.

Contarinia nasturtii resources:

General information:

We will have a webinar for the i5k Workspace@NAL today at 3pm EDT. There is no formal agenda or topic. Instead we will use the time to answer any questions you may have about annotation or other tools and resources at the i5k Workspace@NAL.

Call in information:
Topic: i5k Workspace@NAL March Webinar
Time: Mar 17, 2020 03:00 PM Eastern Time (US and Canada)

Join Zoom Meeting
https://zoom.us/j/662808833?pwd=aDgxNjU1T2d4bTlCVDYxdmNmSlcxQT09

Meeting ID: 662 808 833
Password: 088484

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Meeting ID: 662 808 833

Find your local number: https://zoom.us/u/ad3lbayM1j

https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+...

We have updated the Apollo manual annotation software for 8 additional i5k Workspace organisms, following the 21 updates last month. For these organisms, listed below, the i5k Workspace now uses the newer Apollo v2 software. 

This means that the Apollo URL for these organisms has changed. You can find the new Apollo URL for your organism here: https://i5k.nal.usda.gov/available-genome-browsers, or by navigating to the 'Tools -> JBrowse/Apollo -> JBrowse/Apollo Organisms' menu item from our homepage (https://i5k.nal.usda.gov). Your Apollo v1 login credentials should work in Apollo v2, and any existing manual annotations for these organisms were migrated to Apollo v2.

We will update organisms that are still using Apollo v1 in due course.

We hope that you will enjoy the new functionality in Apollo v2! If you have any questions or concerns about Apollo v2, feel free to contact us at i5k@ars.usda.gov.

List of migrated organisms:

  • Aethina tumida
  • Amyelois transitella
  • Locusta migratoria
  • Mayetiola destructor
  • Microplitis demolitor
  • Tigriopus californicus
  • Tribolium castaneum
  • Trichogramma pretiosum

A new organism is available at the i5k Workspace: Galleria mellonella.

Galleria mellonella resources:

General information:

We have updated the Apollo manual annotation software for 21 i5k Workspace organisms. For these organisms, listed below, the i5k Workspace now uses the newer Apollo v2 software. 

This means that the Apollo URL for these organisms has changed. You can find the new Apollo URL for your organism here: https://i5k.nal.usda.gov/available-genome-browsers, or by navigating to the 'Tools -> JBrowse/Apollo -> JBrowse/Apollo Organisms' menu item from our homepage (https://i5k.nal.usda.gov). Your Apollo v1 login credentials should work in Apollo v2, and any existing manual annotations for these organisms were migrated to Apollo v2.

We will update organisms that are still using Apollo v1 in due course.

We hope that you will enjoy the new functionality in Apollo v2! If you have any questions or concerns about Apollo v2, feel free to contact us at i5k@ars.usda.gov.

List of migrated organisms:

  • Bactrocera cucurbitae
  • Bactrocera dorsalis
  • Bemisia tabaci
  • Catajapyx aquilonaris
  • Centruroides sculpturatus
  • Ceratitis capitata
  • Copidosoma floridanum
  • Dufourea novaeangliae
  • Euglossa dilemma
  • Fopius arisanus
  • Habropoda laboriosa
  • Lasioglossum albipes
  • Latrodectus hesperus
  • Limnephilus lunatus
  • Loxosceles reclusa
  • Manduca sexta
  • Megachile rotundata
  • Melipona quadrifasciata
  • Nicrophorus vespilloides
  • Pachypsylla venusta
  • Rhipicephalus microplus
Our next i5k Workspace webinar will be December 17th at 1pm MDT.
 
Title:  Manual annotation using the Apollo software
 
The webinar will last an hour and will cover our regular Apollo training:
 
  • Background on the principles of manual annotation;
  • Instructions on using the Apollo software;
  • A live annotation example.  
 
Click this link to view the event in your time zone:
 
To connect to the webinar: https://zoom.us/j/496804084
 
Meeting ID: 190 427 643
One tap mobile
+19294362866,,190427643# US (New York)
+16699006833,,190427643# US (San Jose)
 
Dial by your location
+1 929 436 2866 US (New York)
+1 669 900 6833 US (San Jose)
Meeting ID: 190 427 643
Find your local number: https://zoom.us/u/ad3lbayM1j
 

 

The i5k Workspace will be at the Entomology 2019 meeting this year. Monica will be at the USDA Booth #223 (https://shows.map-dynamics.com/esa2019?) of the Exhibit Hall on Monday, November 18th, from 10 - 11 am, and 4-5 pm. Feel free to stop by if you want to chat about the i5k Workspace. We are also co-organizing the member symposium "Sequencing the planet - starting with our insect friends" on Sunday at 8 am, room 241 (https://esa.confex.com/esa/2019/meetingapp.cgi/Session/36251). We hope to see you there!