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We have been working on some major updates to our infrastructure. HMMER and Clustal (beta release) are now available to users of the i5k Workspace.
For more information about the tools, and how they are set up at the i5k Workspace, please see our user guides. Similar to BLAST, saved searches will be available for one week after they are run.
HMMER user guide
Clustal user guide
*Note: The i5k Workspace implementation of Clustal includes both ClustalW and Clustal-Omega.
We have some exciting new features at the i5k Workspace!
New data submission forms.
Many of you have generously made your datasets available to the i5k community - whether you've set up a new i5k Workspace project with your genome assembly and gene predictions, or you've shared transcriptome assemblies, RNA-Seq data, or new gene predictions to better curate a genome that we host.
We've now developed new submission forms to make it easier for you to share your data with us and the i5k community. For an overview of how to submit your datasets to the i5k Workspace, follow this link:
https://i5k.nal.usda.gov/data-submission-overview
In order to submit your datasets, we'll ask you to create an account with the i5k Workspace (which will be different from your Web Apollo account, if you have one). You'll then be able to view and complete our dataset submission forms. You can find these new forms under our "Data" menu bar, or click on the "Submit Data" button on our homepage.
We'd love to hear feedback about these forms, if you have any - feel free to contact us!
Updated home page.
We've made a few changes to our home page menu and layout. We hope you like the changes! We always welcome feedback; feel free to contact us.
Updated tutorials.
We've updated our tutorials on how to share files with us, and how to upload files via CyVerse (formerly the iPlant Collaborative). Expect more updates to our tutorials in our next release.
There are three new genomes available at the i5k Workspace: the navel orangeworm, Amyelois transitella, the parasitoid wasp Microplitis demolitor, and the red flour beetle, Tribolium castaneum.
All genomes are open for manual curation. As always, you can register to be put in contact with the genome project’s community contact.
Thank you to our newest data providers!
There are two new genomes available at the i5k Workspace: the Southeastern blueberry bee, Habropoda laboriosa, and the redheaded pine sawfly, Neodiprion lecontei.
Both genomes are open for manual curation. As always, you can register to be put in contact with the genome project’s community contact.
Thank you to our newest data providers!
We are pleased to release the i5k Workspace, version 2.0! This newest release features a fully updated user-interface that we designed for easier navigation for new and recurrent users. If you have bookmarked your favorite links within the i5k Workspace - all of our tools and pages are still available under the same URLs. We hope that you enjoy the new interface, and as always welcome your feedback and suggestions!
We have several new datasets available for viewing on our genome browsers:
Diaphorina citri: Several new RNA-Seq datasets are available. There are also new mapped results from proteomics data generated by John Ramsey, Surya Saha and Michelle Cilia.
Hyallela azteca: Helen Poynton's group has mapped results from some recent RNA-Seq experiments to the genome.
Blatella germanica: Kim Walden has aligned published RNA-Seq data to the genome; you can view the tracks here. Additionally, new RNA-Seq data from NCSU are also available for viewing.
Frankliniella occidentalis: Dorith Rotenburg's group has generated a new transcriptome assembly with cufflinks.
We have a number1 of new datasets visualized on several genome browsers:
- Two new transcriptomes mapped to the Frankliniella occidentalis genome
- New RNA-Seq data for Bactrocera dorsalis
- new OGS uploaded for Anoplophora glabripennis
- Transposable element predictions and miRNA predictions in Leptinotarsa decemlineata
- RNA-Seq and transcriptome data from the 1Kite project contributed to Catajapyx aquilonaris
We have re-structured our data downloads section (https://i5k.nal.usda.gov/data; or, for a nicer graphical user interface, https://i5k.nal.usda.gov/content/data-downloads). We hope that the new structure is easier to navigate. Please note that if you have bookmarked certain datasets before, that thse links are likely now broken.
Six new transcriptome datasets have been added to the Bactrocera dorsalis JBrowse. These data were contributed by Scott Geib, USDA-ARS, and include egg, pupae, larvae, male adult, unmated female adult and mated female adult. The original data are available through SRA: http://www.ncbi.nlm.nih.gov/bioproject/167923, and are published in BMC Genomics (doi:10.1186/1471-2164-15-942).
