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News Archive

Website news

The i5k Workspace@NAL team is streamlining services, in order to gain more time to focus on services that i5k Workspace@NAL users actually want and need. A recent evaluation of user needs demonstrated that the i5k Workspace's gene pages do not provide much value. The data represented in these pages are available elsewhere - NCBI's GenBank or RefSeq databases display information at the gene and protein level; the i5k Workspace@NAL and Ag Data Commons provide information at the dataset level. From a technical perspective, the gene pages are challenging and time-consuming to maintain. Finally, we have not been able to provide gene pages for all gene sets due to personnel shortages.

As a result, we have decided to remove all gene pages from the i5k Workspace. ​

What does this mean for your dataset? This does not mean that the data are lost, or not accessible anymore. You can still find the data at the i5k Workspace@NAL and NCBI (GenBank or RefSeq), and in some cases the Ag Data Commons. Links to these resources are compiled in each dataset page - see the table below for names and links of datasets for which we have removed gene and mRNA pages. In addition, you can still interact with the genes from this dataset in JBrowse and Apollo, including link-outs to gene pages at NCBI (or in a few cases, HymenopteraMine and VEuPathDB) from the individual gene glyphs (https://i5k.nal.usda.gov/available-genome-browsers); and search for them using BLAST (https://i5k.nal.usda.gov/webapp/blast/).

Please let us know if you have any questions or concerns! We hope that the impact on your work will be minimal, but please let us know if this is a major inconvenience for you.

Dataset links table
Dataset name Link to dataset information
Anoplophora glabripennis Official Gene Set v1.2            https://i5k.nal.usda.gov/bio_data/836634
Bombus impatiens annotations bimp_OGSv1.1                  https://i5k.nal.usda.gov/bio_data/836760
Cephus cinctus annotations cepcin_OGSv1.1                  https://i5k.nal.usda.gov/bio_data/836796
Cimex lectularius Official Gene Set v1.2                   https://i5k.nal.usda.gov/bio_data/836754
Ephemera danica annotations ephdan_OGSv1.0                 https://i5k.nal.usda.gov/bio_data/836793
Frankliniella occidentalis annotations fraocc_OGSv1.1      https://i5k.nal.usda.gov/bio_data/836786
Halyomorpha halys annotations halhal_OGSv1.2               https://i5k.nal.usda.gov/bio_data/836785
Hyalella azteca annotations OGSv1.2                        https://i5k.nal.usda.gov/bio_data/836772
Ladona fulva annotations Official Gene Set ladful_OGSv1.1  https://i5k.nal.usda.gov/bio_data/1122356
Laodelphax striatellus Official Gene Set v1.2              https://i5k.nal.usda.gov/bio_data/836763
Microplitis demolitor Official Gene Set micdem_OGSv1.0     https://i5k.nal.usda.gov/bio_data/836813
Nylanderia fulva annotations OGSv1.0                       https://i5k.nal.usda.gov/bio_data/836774
Oncopeltus fasciatus Official Gene Set v1.1                https://i5k.nal.usda.gov/bio_data/836678
NCBI Bradysia coprophila Annotation Release 100            https://i5k.nal.usda.gov/bio_data/836830
NCBI Chelonus insularis Annotation Release 100             https://i5k.nal.usda.gov/bio_data/836804
NCBI Contarinia nasturtii Annotation Release 100           https://i5k.nal.usda.gov/bio_data/836790
NCBI Diachasma alloeum Annotation Release 101              https://i5k.nal.usda.gov/bio_data/836802
NCBI Drosophila bipectinata Annotation Release 102         https://i5k.nal.usda.gov/bio_data/1245536
NCBI Drosophila elegans Annotation Release 102             https://i5k.nal.usda.gov/bio_data/931160
NCBI Drosophila eugracilis Annotation Release 102          https://i5k.nal.usda.gov/bio_data/931162
NCBI Drosophila ficusphila Annotation Release 102          https://i5k.nal.usda.gov/bio_data/1245537
NCBI Drosophila kikkawai Annotation Release 102            https://i5k.nal.usda.gov/bio_data/931164
NCBI Drosophila rhopaloa Annotation Release 102            https://i5k.nal.usda.gov/bio_data/1319624
NCBI Drosophila takahashii Annotation Release 102          https://i5k.nal.usda.gov/bio_data/1319626
NCBI Galleria mellonella Annotation Release 101            https://i5k.nal.usda.gov/bio_data/836788
NCBI Lucilia sericata Annotation Release 100               https://i5k.nal.usda.gov/bio_data/836900
NCBI Manduca sexta Annotation Release 102                  https://i5k.nal.usda.gov/bio_data/836825
NCBI Odontomachus brunneus Annotation Release 100          https://i5k.nal.usda.gov/bio_data/836798
NCBI Osmia lignaria Annotation Release 100                 https://i5k.nal.usda.gov/bio_data/836799
NCBI Photinus pyralis Annotation Release 100               https://i5k.nal.usda.gov/bio_data/836812
NCBI Rhipicephalus microplus Annotation Release 100        https://i5k.nal.usda.gov/bio_data/1141200
NCBI Tribolium madens Annotation Release 100               https://i5k.nal.usda.gov/bio_data/1212157
NCBI Varroa jacobsoni Annotation Release 100               https://i5k.nal.usda.gov/bio_data/836770
NCBI Venturia canescens Annotation Release 100             https://i5k.nal.usda.gov/bio_data/905595

New Species

A new organism from the Ag100Pest project (http://i5k.github.io/ag100pest) is available at the i5k Workspace.

New organism:

  • Helicoverpa zea genome assembly ilHelZeax1.1 (GCF_022581195.2) and NCBI annotation release 100

New organism and dataset pages (https://i5k.nal.usda.gov/organisms); 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!

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

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

One tap mobile

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Dial by your location

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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
One tap mobile +16692545252,,1619965511#,,,,*387775# US (San Jose) +16468287666,,1619965511#,,,,*387775# US (New York)
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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
One tap mobile
+16692545252,,1600415142#,,,,*483658# US (San Jose)
+15512851373,,1600415142#,,,,*483658# US
Dial by your location
        +1 669 254 5252 US (San Jose)
        +1 551 285 1373 US
        +1 646 828 7666 US (New York)
        +1 669 216 1590 US (San Jose)
        833 568 8864 US Toll-free
Meeting ID: 160 041 5142
Passcode: 483658
Find your local number: https://www.zoomgov.com/u/awJSL0mCg