News Archive

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
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Meeting ID: 190 427 643
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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! 

We've updated the Hyalella azteca i5k Workspace resources to the newest genome assembly, Hazt_2.0.1 (https://www.ncbi.nlm.nih.gov/assembly/GCA_000764305.3), and Official Gene Set, OGSv1.2 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/764/305/GCA_000764305.3_Hazt_2.0.1https://data.nal.usda.gov/dataset/hyalella-azteca-official-gene-set-v12). Now Apollo and BLAST are based on these new data resources. New gene pages for OGSv1.2 are also available. 

Our next i5k Workspace webinar will be October 29th at 1pm MDT (rescheduled from October 22nd).

Title:  Manual annotation using the Apollo software

The webinar will last an hour and will cover:

  • 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/190427643

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

 

There will be an 'Insects' breakout session during the G10K-VGP EBP 2019 Meeting (https://www.eventbrite.com/e/the-g10k-vgpebp-meeting-tickets-59112745814). This year's meeting is a joint effort between the Vertebrate Genomes Project (VGP) and the Earth BioGenome Project (EBP). The discussion-based insects breakout session is scheduled for 9am -12 pm Eastern, Wednesday, August 28th.

The session agenda is available here: https://i5k.nal.usda.gov/sites/default/files/Earth%20BioGenome%20meeting%202019%20-%20insect%20session%20agenda.pdf

For the full meeting agenda, see https://vertebrategenomesproject.org/s/At-a-Glance-Agenda-12-Aug_update-website-4kh9.pdf.

If you are not coming to the meeting, but are interested in shaping the discussion about insects or arthropods in the Earth BioGenome Project, we encourage you to attend the session remotely. We will have a zoom connection open during the meeting, and will do our best to make the audio acceptable. If you are interested, please register for the discussion in advance: https://zoom.us/meeting/register/6036afd9af5a0a9a7510d14dfea9e911

After registering, you will receive a confirmation email with information about joining the meeting.

Our next i5k Workspace webinar will be August 20th at 1pm MDT.

Title:  Manual annotation using the Apollo software

The webinar will last an hour and will cover:

  • 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/928754037

One tap mobile
+19294362866,,928754037# US (New York)
+16699006833,,928754037# US (San Jose)
 
Dial by your location
        +1 929 436 2866 US (New York)
        +1 669 900 6833 US (San Jose)
Meeting ID: 928 754 037
Find your local number: https://zoom.us/u/ad3lbayM1j