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i5k Workspace@NAL
U.S. Department of Agriculture

News Archive

Infrastructure update

[08 Apr 2015] Jbrowse/Web Apollo updated to 1.0.4

Jbrowse/Web Apollo updates:

Web Apollo has been updated to version 1.0.4. This includes several feature and stability updates. Please refer to the Web Apollo Git repository for a full list of updates
( https://github.com/GMOD/Apollo/blob/master/ChangeLog.md ).  One major change is the addition of the sequences page as an initial entry point to Web Apollo (e.g. https://apollo.nal.usda.gov/oncfas_training/sequences ).  The sequences page currently exists alongside selectTrack.jsp, and will eventually replace the selectTrack page in future versions of Web Apollo.

New Species

[08 Apr 2015] Three new species in the Workspace@NAL

We would like to welcome three new species to the i5k Workspace@NAL!

More information for each of these organisms is available on their respective organism pages, and they are also available via BLAST and JBrowse. If you are interested in more information about these insects, please contact Scott Geib, community coordinator.

 

Infrastructure update

[08 Apr 2015] BLAST updates

BLAST updates:

The color scheme for reporting HSPs now uses the static system by default. This system is based on the default NCBI system for reporting colors based on bit-score.

Viewing HSPs in Jbrowse/Web Apollo is now in color! Each HSP is colored based on the bitscore value, and uses the same color scale as the static color scale in the BLAST report. Right clicking on a feature to “View Details" now includes additional information at the HSP level based on the BLAST output. The HSPs are still draggable, and may be used as part of a feature annotation strategy. A big thanks to Han Lin for developing this feature!

New Species

[19 Dec 2014] Hyalella azteca is now available

The resources for Hyalella azteca are now online!

New Species

[17 Oct 2014] Blattella germanica, Catajapyx aquilonaris, and Halyomorpha halys genomes now available

We have added three new species from the i5k pilot project to our content:

Blattella germanica: https://i5k.nal.usda.gov/Blattella_germanica

Halyomorpha halys: https://i5k.nal.usda.gov/Halyomorpha_halys

Catajapyx aquilonaris: https://i5k.nal.usda.gov/Catajapyx_aquilonaris

New dataset

[02 Oct 2014] New JBrowse/Web Apollo tracks available for Athalia rosae and Orussus abietinus.

There are several new user-provided tracks available for the Athalia rosae and Orussus abietinus JBrowse/Web Apollo instances.

Note that the tracks 'O. abietinus female cleaned reads, XY-plots' and 'O. abietinus female cleaned reads' replace the tracks 'Orussus abietinus female RNAseq cleaned unassembled reads, XY-Plot' and 'Orussus abietinus female RNAseq cleaned unassembled reads, alignments'. Similarly, the tracks 'O. abietinus male cleaned reads, XY-plots' and 'O. abietinus male cleaned reads' replace the tracks 'Orussus abietinus male RNAseq cleaned unassembled reads, XY-Plot' and 'Orussus abietinus male RNAseq cleaned unassembled reads, alignments'.

For Athalia rosae, the tracks 'AROS_ID05', 'AROS_ID06', 'AROS_ID07', and 'AROS_ID08' have been replaced with 'A. rosae female-1 raw reads', 'A. rosae female-2 raw reads', A. rosae male-2 raw reads', and A. rosae male-1 raw reads', respectively.

New dataset

[01 Oct 2014] Transposon domain track now available for Ceratitis capitata

Dr. Alexie Papanicolaou has provided a set of predicted transposon domains for the Mediteranean fruit fly Ceratitis capitata.

You can view this new data in the C. capitata JBrowse/Web Apollo browser.

Infrastructure update

[26 Sep 2014] Maintenance completed, and website updates

The i5K Workspace @NAL has had some major infrastructural updates, and now runs on Drupal 7 and Tripal 2.0. These changes should improve the speed and reliability of our website. Please let us know if you experience any problems.

New Species

[26 Sep 2014] New species and data available!

We have been working with the group at Agripest to migrate two species into the i5k Workspace@NAL:
 - The Tobacco Hornworm, Manduca sexta (i5k.nal.usda.gov/Manduca_sexta)
 - The Hessian fly, Mayetiola destructor (i5k.nal.usda.gov/Mayetiola_destructor)

Dr. Felipe Barreto has provided a large number of evidence tracks for the Tigriopus californicus JBrowse/Web Apollo instance.

 

Website news

[29 Aug 2014] Feeback survey is now online!

We've been making a lot of changes to our website and resources, and are eager to hear what you think!

We have created a survey to help us better understand how you use our resources.  We are also very interested in learning more about what features are working well for you, and what we can continue to improve.

Please take a few moments to fill out our survey. All feedback is appreciated, and your input will help us better meet our community's needs.

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