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i5k Workspace@NAL
U.S. Department of Agriculture

News Archive

Infrastructure update

[29 Aug 2014] Legacy BLAST interface

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.

Infrastructure update

[21 Aug 2014] A new BLAST interface is available!

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!

New Species

[15 Aug 2014] Ten new species have been added to the i5k Workspace, and other updates

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.

Website news

[16 Jun 2014] A new cuticular protein family prediction tool to aid functional annotation has been published.

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.

Infrastructure update

[11 Jun 2014] We have implemented a new menu for bulk data downloads.

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

New Species

[11 Jun 2014] Eight species from the Drosophila modENCODE project and the Baylor College of Medicine have been added to the Workspace.

Website news

[04 Jun 2014] Join the Insect Genetic Technologies Research Coordination Network!

From the website (http://igtrcn.org):

The goal of the NSF-funded Insect Genetic Technologies RCN is to connect insect scientists for the purpose of disseminating advanced technologies for genome modification of insects through symposia, technical workshops, and training fellowships. The network is open to all: students, postdocs, researchers, technicians and faculty.

Infrastructure update

[06 May 2014] BLAST resources have been updated

The BLAST tools have been enhanced in the following ways.

Users may now search across multiple databases in one search. You may select any combination of nucleotide databases, or any combination of peptide databases, but you cannot run one search against a mix of nucleotide and protein databases. Please note, the more genomes you select for your search, the longer the search will take.

BLAST results now contain link outs to our gene pages and JBrowse instances as appropriate. If you are an annotator, you can log in using the button at the top right to go into edit mode and still see your BLAST results.

Website news

[29 Apr 2014] The Annotation Rules tutorial has been updated.

Website news

[10 Apr 2014] The I5K Workspace@NAL is live again!

The I5K Workspace@NAL is live again!

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