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News Archive

Website news

Our next i5k Workspace webinar will be September 19th, 2023 at 1 pm MDT.

The webinar will last one hour and will cover:

  1. A review of the i5k Workspace gene and transcript nomenclature guidelines;
  2. Tips on how to use the i5k Workspace BLAST tool as an entry point to Apollo;
  3. Q&A from webinar attendees.

Click this link to view the event in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+...

Connection details:

https://www.zoomgov.com/j/16121063291?pwd=WmFZd0JHZkVtZHRPSEJneThqSkl3Zz09

Meeting ID: 161 2106 3291

Passcode: 537388

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New Species

Dear all,

We are excited to announce six new Ag100Pest and two new Beenome 100 species at the i5k Workspace@NAL:

  • Ag100Pest: Diorhabda carinulata, Vespa mandarinia, Anthonomus grandis grandis, Pectinophora gossypiella, Anastrepha ludens, Anastrepha obliqua
  • Beenome 100: Hylaeus volcanicus, Hylaeus anthracinus

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.

Finally, please see the below request from VeuPathDB:

Dear colleagues – The VEuPathDB project (including VectorBase) is up for renewal, which is likely to depend on strong support from our user community. Joshua Benoit has drafted a letter on behalf of the VectorBase community, for which we are seeking endorsement by lab heads worldwide (if you are a PI, feel free to bring this note to the attention of your lab head). Responses will be most helpful if received by 1 Aug 2023 ... do it today!

Follow this link to view the support letter and add your name, if desired.  Or copy and paste the following URL into your internet browser: https://upenn.co1.qualtrics.com/jfe/form/SV_9pj0CnJgCziX0EK?Q_DL=KXpM4w9PN12ASAv_9pj0CnJgCziX0EK_CGC_smCVFBhJWpnnQHz&Q_CHL=email

Sincerely -- Omar Harb, Mary Ann McDowell and David Roos... on behalf of the entire VEuPathDB team

New Species

We are excited to announce three new Ag100Pest species at the i5k Workspace@NAL: Plodia interpunctella, Dermatocenter andersonii, and Bombus affinis. The i5k Workspace now hosts 100 species!

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.

Finally, please see the below job announcement for a USDA-ARS postdoctoral research fellow in chromosomal evolution and diversity in pest fruit flies in Hilo, Hawaii.

The Tropical Pest Genetics and Molecular Biology Research Unit is seeking a highly motivated individual to use genomic tools to investigate sex chromosomes and large structural variation in Tephritidae to contribute to foundational and applied research that supports fruit fly pest management programs in the United States.

In this position, the incumbent will investigate genomic structure and characterization of sex chromosome structure and structural variants with applications to species and strain identification and insect diagnostics. The ideal candidate for this position will have a Ph.D. in biology, genetics, bioinformatics or a related field, with a strong background in genomics and molecular biology. Experience working on a command-line interface is required, experience working with insects, particularly tephritid fruit flies, is a plus. Candidates willing to relocate to Hilo, HI are preferred, but remote applicants who are a great fit will also be considered. Starting salary is $71,877 with health benefits and a negotiable relocation allowance. As a postdoctoral fellow at the USDA Agricultural Research Service (ARS), you have access to several high-performance computing clusters, training opportunities, and a large and active network of postdoctoral research fellows as your peers.

About us: The USDA Agricultural Research Service (ARS) represents the research arm of the USDA and has about 100 research centers across the United States. The Pacific Basin Agricultural Research Center is located on the east side of the Big Island (Hawaii Island), in the town of Hilo which has a population of about 50,000. Our in-house multimillion dollar genomics facility has a suite of state-of-the-art instrumentation, with the capacity for high-accuracy short-read sequencing, high-fidelity long-read sequencing, and ultra-long read sequencing, as well as supporting laboratory equipment such as automated liquid handling devices, automated nucleic acid isolation devices, and molecular diagnostics methods.

To apply, please send your CV, cover letter, and most recent peer-reviewed publication to sheina.sim@usda.gov.

Website news

There is a time change to our next i5k Workspace webinar on December 13th. Due to a new scheduling conflict, this webinar will be at 11 am MST. The webinar will last one hour and will cover:

  • Background on the AgBase functional annotation pipeline used by the i5k Workspace;
  • Several use cases that you are likely to come across when using functional annotations during the manual curation process. These range from finding the functional annotations for specific proteins in Jbrowse, to strategies for finding all proteins annotated to a pathway in our resources, and more. We will use examples from the pink bollworm, Pectinophora gossypiella, and the American grasshopper, Schistocerca americana. 

Click this link to view the event in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221213T11&p1=1947&ah=1

Best,

Monica and the i5k Workspace team

Connection details: 

Join ZoomGov Meeting

https://www.zoomgov.com/j/1618648233?pwd=bm9zcGNuRGxkdkJQRmNaU0ltUlZNZz09 

Meeting ID: 161 864 8233
Passcode: 050284
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Find your local number: https://www.zoomgov.com/u/abjAobQ9h3

Website news

Our next i5k Workspace webinar will be December 13th at 1 pm MST. The webinar will last one hour and will cover:

  • Background on the AgBase functional annotation pipeline used by the i5k Workspace;
  • Several use cases that you are likely to come across when using functional annotations during the manual curation process. These range from finding the functional annotations for specific proteins in Jbrowse, to strategies for finding all proteins annotated to a pathway in our resources, and more. We will use examples from the pink bollworm, Pectinophora gossypiella, and the American grasshopper, Schistocerca americana. 

Click this link to view the event in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221213T13&p1=1947&ah=1

Best,

Monica and the i5k Workspace team

Connection details: 

Join ZoomGov Meeting

https://www.zoomgov.com/j/1618648233?pwd=bm9zcGNuRGxkdkJQRmNaU0ltUlZNZz09 

Meeting ID: 161 864 8233
Passcode: 050284
One tap mobile
+16692545252,,1618648233#,,,,*050284# US (San Jose)
+16692161590,,1618648233#,,,,*050284# US (San Jose)

Dial by your location
        +1 669 254 5252 US (San Jose)
        +1 669 216 1590 US (San Jose)
        +1 646 828 7666 US (New York)
        +1 551 285 1373 US
        833 568 8864 US Toll-free

Find your local number: https://www.zoomgov.com/u/abjAobQ9h3

New dataset

We have computed and made available functional annotations for all i5k Workspace organisms! We hope that these new resources are useful for your research. We welcome your feedback on these annotations - feel free to reach out via our contact form, https://i5k.nal.usda.gov/contact, or via email. 

The best way to find functional annotations for your organism is by searching https://i5k.nal.usda.gov/ for "[Genus species] functional annotation"  (e.g. "Amyelois transitella functional annotation").

Learn more about the functional annotation pipeline:

New Species

We are excited to announce three new Ag100Pest species at the i5k Workspace@NAL: the boll weevil, Anthonomus grandis grandis, the pink bollworm, Pectinophora gossypiella, and the Hunt bumblebee, Bombus huntiiBombus huntii is also a Beenome 100 project.

In addition, we have completed set up full resources for four locust genome assemblies, from a collaboration between Ag100Pest (http://i5k.github.io/ag100pest) and the Behavioral Plasticity Research Institute (https://behavioralplasticity.org/). The species are Schistocerca gregaria, Schistocerca cancellata, Schistocerca nitens, and Schistocerca serialis cubense. We previously onboarded two additional species, Schistocerca americana and Schistocerca piceifrons. Unfortunately at this time we are unable to provide BLAST services against the genomes of these locust species due to their size. We hope to offer this capability in the future. In the meantime, NCBI's BLAST services can be used for sequence search against these genomes.

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.

 

New dataset

We have added new mapped RNA-Seq to 32 of our genome browsers! To learn more about our RNA-Seq mapping pipeline:

The following organisms now have new, mapped RNA-Seq on their genome browsers (https://i5k.nal.usda.gov/available-genome-browsers):

Amyelois transitella
Bactrocera dorsalis
Bemisia tabacia
Bombus terrestris
Cephus cinctus
Clitarchus hookeri
Contarinia nasturtii
Diaphorina citri
Drosophila biarmipes
Dufourea novaeangliae
Ephemera danica
Eufriesea mexicana
Euglossa dilemma
Fopius arisanus
Frankliniella occidentalis
Galleria mellonella
Halyomorpha halys
Heliothis virescens
Holacanthella duospinosa
Hyalella azteca
Lasioglossum albipes
Leptinotarsa decemlineata
Medauroidea extradentata
Megachile rotundata
Melipona quadrifasciata
Microplitis demolitor
Nicrophorus vespilloides
Osmia lignaria
Tribolium castaneum
Varroa jacobsoni
Varroa destructor
Bactrocera (Zeugodacus) cucurbitae

Website news

Our next i5k Workspace webinar will be September 20th at 1 pm MST. This webinar is our regular training for anyone who wants to learn more in-depth annotation techniques with Apollo.

The webinar will last one hour and will cover:

  • 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=20220920T13&p1=1947&ah=1

Best,

Monica and the i5k Workspace team

Connection details:

Join ZoomGov Meeting
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Meeting ID: 160 120 0689
Passcode: 267140
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Website news

There are six new locust genome assemblies available, from a collaboration between Ag100Pest (http://i5k.github.io/ag100pest) and the Behavioral Plasticity Research Institute (https://behavioralplasticity.org/). You can learn more about the biology of the locusts, and the process behind generating these high-quality assemblies in spite of their enormous genome size, here:

Full i5k Workspace@NAL resources are available for the American grasshopper, Schistocerca americana, and the Central American locust, Schistocerca piceifrons. Unfortunately at this time we are unable to provide BLAST services against the genomes of these species due to their size. We hope to offer this capability in the future. In the meantime, NCBI's BLAST services can be used for sequence search against these genomes.

  • Schistocerca americana genome assembly iqSchAmer2.1 (GCF_021461395.2), NCBI annotation release 100, and functional annotations of NCBI annotation release 100: https://i5k.nal.usda.gov/bio_data/1394307
  • Schistocerca piceifrons genome assembly iqSchPice1.1 (GCF_021461385.2), NCBI annotation release 100, and functional annotations of NCBI annotation release 100: https://i5k.nal.usda.gov/bio_data/1394321

We will make all i5k Workspace@NAL resources available for the following species, once the genome assemblies have been processed by NCBI's RefSeq resource: