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News Archive

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:

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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
 
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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
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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:

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A recording of this webinar can be provided on request.

Website news

Our next i5k Workspace webinar will be November 17th at 1 pm MST.

Title:Facilitating data re-use at the i5k Workspace@NAL

This one-hour webinar will describe some of the activities the i5k Workspace@NAL performs to share data between databases – specifically, manual annotations. It will include the i5k Workspace’s current role in the ‘data ecosystem’; how we submit manual annotations from the Apollo editing tool to NCBI’s GenBank database; and how we generate and share Official Gene Sets. In addition, we will highlight the role gene nomenclature plays in making this process go smoothly, and explain our gene nomenclature guidelines. 

Click this link to view the event time in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+webinar&iso=20201117T13&p1=1947&ah=1

A recording of this webinar can be provided on request.

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Infrastructure update

We are performing maintenance on the Apollo applications today. They will not be available for annotation during 8am and 5pm US Eastern time. We will send an email when the maintenance is complete.

New dataset