News Archive

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.

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!

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!

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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