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News Archive

New Species

Four new organisms from the Ag100Pest project (http://i5k.github.io/ag100pest) are available at the i5k Workspace.

New organisms:

  • Diprion similis: genome assembly iyDipSimi1.1 (GCF_021155765.1) and NCBI annotation release 100
  • Neodiprion fabricii genome assembly iyNeoFabr1.1 (GCF_021155785.1) and NCBI annotation release 100
  • Neodiprion pinetum: genome assembly  iyNeoPine1.1 (GCF_021155775.1) and NCBI annotation release 100
  • Neodiprion virginiana: genome assembly iyNeoVirg1.1 (GCF_021901495.1) and NCBI annotation release 100

New organism and dataset pages (https://i5k.nal.usda.gov/); browsers with mapped RNA-Seq (https://i5k.nal.usda.gov/available-genome-browsers); file downloads, including functional annotations (https://i5k.nal.usda.gov/content/data-downloads); and BLAST databases (https://i5k.nal.usda.gov/webapp/blast) are available. Apollo registration for all organisms can be accessed at https://i5k.nal.usda.gov/web-apollo-registration

Please let us know if you notice any issues!

Website news

Dear all,

Save the date. Our next webinar is scheduled for March 29, 2022 at 3:00PM Eastern.

Topics include a brief introduction to the services at the i5k workspace, and then discuss the new features and interfaces in the recently updated Apollo2 software. There will also be time for questions and discussion.

Connection details:

Topic: What's new at the i5k workspace: Apollo2 updates

Time: Mar 29, 2022 03:00 PM Eastern Time (US and Canada)

https://www.zoomgov.com/j/1619610450?pwd=TFJPRnRYeGRCSU9rK285WU5DZnhoQT09

Meeting ID: 161 961 0450

Passcode: 189689

Website news

Registration for both the Arthropod Genomics Symposium 2022 (June 9 - 11) and the pre-symposium VectorBase hands-on Workshop 2022 (June 5-9) are both online! https://web.cvent.com/event/c19bd7ed-9ebc-47f4-9876-a524061871ed/summary

The VectorBase hands-on Workshop will also feature training on the Apollo manual curation tool. Please see the description below from VectorBase for more information, as well as the website: https://web.cvent.com/event/c19bd7ed-9ebc-47f4-9876-a524061871ed/summary

Registration is now open for the VectorBase hands-on Workshop 2022
6:00 pm on Sunday, 5th June to 12:00 pm (noon) on Thursday, 9th June 2022
University of Notre Dame, Notre Dame, Indiana
In-person (sessions will not be virtual or recorded)

This workshop is scheduled as an Arthropod Genomics Symposium (AGS) pre-meeting event, and even if you are not attending AGS, you are more than welcome to attend the workshop.

This is a 5-day intensive workshop that will provide you with hands-on training on how to effectively use VectorBase to mine the available data and to analyze your own data. Since VectorBase is part of the VEuPathDB Bioinformatics Resource Center (BRC), all learned knowledge can be applied to its other components such as those supporting vector-transmitted pathogens Plasmodium (PlasmoDB), Leishmania, Trypanosoma (TriTrypDB), Babesia, and Theileria (PiroplasmaDB).

Find out more: https://vectorbase.org/vectorbase/app/static-content/ags2022.html
Travel grant: https://web.cvent.com/event/c19bd7ed-9ebc-47f4-9876-a524061871ed/websitePage:60a0e006-4530-4e09-836e-25832e14a7ce
Register here: https://web.cvent.com/qvLA93

Please forward to colleagues working in arthropods of medical importance!

 

New Species

Dear all,

  1. The Biology Department at Washington Jefferson College invites applications for a visiting assistant professor position in computational biology starting in Fall 2022. Please follow this link to the position advertisement for more information: https://www.washjeff.edu/applicantpro/job/Pennsylvania/Washington/Visiting-Assistant-Professor-of-Biology/2028795/. If there are any questions about the position, the application process, or about the college, potential applicants can contact Tom Contreras at tcontreras@washjeff.edu.
  2. A new organism, Tribolium madens, is available at the i5k Workspace.
    1. Find more information from this organism: https://i5k.nal.usda.gov/tripal_elasticsearch/search_website/?search_box=tribolium+madens
    2. Genome browser:https://apollo.nal.usda.gov/apollo/Tribolium_madens/jbrowse/
    3. Apollo registration:https://i5k.nal.usda.gov/web-apollo-registration

Best,

Monica and the i5k Workspace team

Website news

Dear all,

Our next i5k Workspace webinar will be November 23rd at 1 pm MST.

The webinar will last one hour and will cover:

  • Background on the principles of manual annotation;
  • Instructions on using the Apollo software, including changes in Apollo v2.6;
  • 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%40NAL+webinar&iso=20211123T13&p1=1947&ah=1

Best,

Monica and the i5k Workspace team

Connection details:

Join ZoomGov Meeting

https://www.zoomgov.com/j/1600617095?pwd=QmgzZzBiTzNSMFdJQnMrQkxCaXhjUT09

Meeting ID: 160 061 7095

Passcode: 906496

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Meeting ID: 160 061 7095

Passcode: 906496

Find your local number: https://www.zoomgov.com/u/abdOQ7RO71

New Species

Three new organisms are available at the i5k Workspace, and five additional organisms have been updated to the latest genome assembly.

New organisms:

  • Bradysia coprophila (genome assembly GCF_014529535.1 and NCBI Annotation Release 100)
  • Lucilia sericata (genome assembly GCF_015586225.1 and NCBI Annotation Release 100)
  • Venturia canescens (genome assembly GCF_019457755.1 and NCBI Annotation Release 100)

Updated organisms:

  • Drosophila elegans (update from GCF_000224195.1 to GCF_018152505.1)
  • Drosophila eugracilis (update from GCF_000236325.1 to GCF_018153835.1)
  • Drosophila kikkawai (update from GCF_000224215.1 to GCF_018152505.1)
  • Ladona fulva (update from Baylor College of Medicine assembly Lful_2.0)
  • Rhipicephalus microplus (update from Rmi_v2.0 to ASM1333972v1)

New and updated organism, dataset, and gene pages (https://i5k.nal.usda.gov/); browsers with mapped RNA-Seq (https://i5k.nal.usda.gov/available-genome-browsers); file downloads, including functional annotations (https://i5k.nal.usda.gov/content/data-downloads); and BLAST databases (https://i5k.nal.usda.gov/webapp/blast) are available. Apollo registration for all organisms can be accessed at https://i5k.nal.usda.gov/web-apollo-registration

For updated genomes, file downloads and dataset pages of the older assemblies and annotations are still available, and are archived at the Ag Data Commons (https://data.nal.usda.gov) and NCBI GenBank where appropriate.

Please let us know if you notice any issues!

Website news

On Tuesday, August 24th, at 1pm MDT, the i5k Workspace@NAL will answer any questions that you have about i5k Workspace@NAL data and tools, including annotating using the Apollo manual curation tool. You are welcome to bring annotation problems, ask questions about the datasets that we host, or provide comments or constructive criticism.
Please submit your questions in advance to monica.poelchau@usda.gov by August 23rd. If there is time, there will also be the opportunity to ask questions that were not submitted previously. 
 
Click this link to find the event time in your timezone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=I5k+Workspace+webinar&iso=20210824T13&p1=1947&ah=1
 
Connection details:
https://www.zoomgov.com/j/1619965511?pwd=RXVEaVBmbUxLNjFFdFErRjdaS0lYZz09
Meeting ID: 161 996 5511
Passcode: 387775
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US Toll-free Meeting ID: 161 996 5511
Passcode: 387775
Find your local number: https://www.zoomgov.com/u/aejkx7pvZU

Website news

Our next i5k Workspace webinar will be May 25th at 1 pm MST.

Title: New and upcoming features and datasets at the i5k Workspace@NAL

The webinar will last 1 hour, and will cover new features and datasets that are in place or coming soon:

  • RNA-Seq tracks in Apollo - how to interpret and use them;
  • Functional annotations of proteins - how we generate them, and upcoming search strategies;
  • New datasets from the Ag100Pest project that are coming soon;
  • Upcoming Apollo software updates and new features;
  • Upcoming i5k Workspace software updates and new features.

Click this link to view the event in your time zone:https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+webinar&iso=20210525T13&p1=1947&ah=1

Connection details:

Join ZoomGov Meeting
https://www.zoomgov.com/j/1600415142?pwd=UC9Ld2lNZmRURnc1U0gwNGc0Tk9NQT09

Meeting ID: 160 041 5142
Passcode: 483658
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        833 568 8864 US Toll-free
Meeting ID: 160 041 5142
Passcode: 483658
Find your local number: https://www.zoomgov.com/u/awJSL0mCg

Website news

Our next i5k Workspace webinar will be February 16th at 1 pm MST.

Title: Manual annotation using the Apollo software

The webinar will last 1 hour, and will cover Apollo functionality for editing annotation structure:

  • Adding and removing exons;
  • Merging and splitting gene models;
  • Adjusting UTRs;
  • Adding isoforms based on RNA-Seq evidence;
  • Changing the sequence start, stop, and open reading frame;
  • Working with splice sites;
  • Genome sequence alterations;
  • Adding non-coding features.

Click this link to view the event in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=I5k+Workspace+webinar&iso=20210216T13&p1=1947&ah=1

Connection details:

Join ZoomGov Meeting
https://www.zoomgov.com/j/1614399223?pwd=M2lhZklEMzgvaDhRZWxjd096ZXZTUT09

Meeting ID: 161 439 9223
Passcode: 898436

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Dial by your location
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        +1 646 828 7666 US (New York)
        +1 669 216 1590 US (San Jose)
        +1 551 285 1373 US
        833 568 8864 US Toll-free

Meeting ID: 161 439 9223
Passcode: 898436

Find your local number: https://www.zoomgov.com/u/adSmW5XIFM

A recording of this webinar can be provided on request.