News Archive

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.

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.

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.

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.

 

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.

We have recently released our new BLAST tool, which is completely reengineered, from the initial query building screen to the results panel.

We realize that the new interface is very different from the previous version, and that it may take time and repeated usage to get used to. Please take some time to read through our newly updated BLAST tutorial to learn more about the new interfaces features and capabilities.

During this time of transition, the original BLAST tool is still available at the Legacy BLAST page.

Our graduate student interns Chien-Yueh Lee, Han Lin, and Jun-Wei Lin from the National Taiwan University have completely re-engineered our BLAST site! You can find the site here: http://i5k.nal.usda.gov/blast And a new BLAST guide here: http://i5k.nal.usda.gov/content/blast-tutorial If you still wish to use the 'legacy' BLAST site, it is available here: http://i5k.nal.usda.gov/blastn Feedback is welcome!

We have added ten new species to the i5k Workspace. They are:

Agrilus planipennis (Baylor i5k pilot)

Centruroides exilicauda (Baylor i5k pilot)

Copidosoma floridanum (Baylor i5k pilot)

Gerris buenoi (Baylor i5k pilot)

Homalodisca vitripennis (Baylor i5k pilot)

Latrodectus hesperus (Baylor i5k pilot)

Limnephilus lunatus (Baylor i5k pilot)

Loxosceles reclusa (Baylor i5k pilot)

Onthophagus taurus (Baylor i5k pilot)

Tigriopus californicus (Burton lab, UCSD)

 

Thanks to these new projects for contributing their content! Organism pages, BLAST, the JBrowse genome browser, Web Apollo, and data downloads are available for each species.

In addition to this, we have been working to improve other aspects of out site. We have updated the each of our species to the latest version of Jbrowse/Web Apollo. We have also implemented a new system for organizing the tracks into categories, though you may need to clear your browser cache to see these. We are actively working to develop these categories, and welcome comments and feedback. We have also made the decision to remove the 'gene pages'. We will re-instate these pages for official gene sets, but we decided to remove them for preliminary gene sets. Please contact us if you have any questions about this. Finally, this has been a major update to multiple aspects of the site, and we have been working hard to make sure everything is working as expected. However, if you notice any unusual behavior, let us know right away.

A new tool is available from the Hamodrakas lab that "allows the accurate detection and classification of putative structural cuticular proteins, from sequence alone, in proteomes". We encourage annotators to read the documentation and try out the tool for the functional annotation of their species.

Our new menu item allows you to navigate and download all of the datasets available for the species hosted at the i5k Workspace@NAL.