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News Archive

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: 

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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)
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        +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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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:

 

Website news

Our next i5k Workspace webinar will be July 19th at 1 pm MDT. Please join us! 

The webinar will last about 30 minutes, and will cover our recent gene page removal:

  • We'll explain why we removed the pages;
  • The data are still accessible - we'll show you the best ways to find what you need;
  • We'll have a Q&A to address any questions or concerns you may have.

Click this link to view the event in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace+webinar+7%2F19+-+changes+to+gene+and+protein+data+access+&iso=20220719T13&p1=1947&am=30

 

Connection details:

Join ZoomGov Meeting

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Meeting ID: 160 026 7760

Passcode: 373884

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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!