This announcement came out while I was at a conference last week–but I wanted to pass it along. This appears to be a big change in the way Phytozome works. And there will be down-time before it rolls out, starting May 1. I like to post major announcements from mailing lists because I know everyone isn’t signed up on every mailing list in bioinformatics as I am…. I can’t figure out how to link to their mailing list archive, so I’m posting the whole thing here.
Via the mailing list, from David Goodstein:
Subject: May 1st retirement of Phytozome v9
The last full day of support for v9 of Phytozome will be Friday, May 1st. Over the subsequent weekend, v9 will be brought down and forwarding services will be put in place to ensure as many URLs as possible find the correct, or at least related, pages in Phytozome v10.
1. Why does v9 of Phytozome need to be retired?
The Phytozome v9 website, at http://www.phytozome.net, is based on an older technology stack that is no longer supported by any developers on the Phytozome team. Newer genome releases, and newer data sets (diversity and expression data) are also not hosted on v9. In the interests of focussing our limited developer resources in the most effective way possible, and having a single location for access to Phytozome genomic data and analysis, we will have a single website going forward: Phytozome v10, located at http://phytozome.jgi.doe.gov .
2. What happens to the genomic data contained in Phytozome v9?
The vast majority of v9 genomes and annotations are available at the Phytozome v10 website, often in updated form (one genome, B. Rapa chiifu, is not being carried forward). Users can still find bulk data files containing all the genomes and annotations from Phytozome v9 at the JGI Genome Portal: http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9
3. I have bookmarks to various resources/genes/families at v9; what happens to those URLs?
-Links to the main site, help pages, release notes, and organism info pages will be automatically forwarded to the corresponding pages in v10.
-Gene pages: forwarding scripts will attempt to determine the corresponding gene page in v10
-GBrowse pages: GBrowse in v9 is replaced by JBrowse in v10. We will attempt to forward URLs to the corresponding location in JBrowse if it exists; if not, the URL will be forwarded to the default location in the corresponding organism’s JBrowse.
-The following v9 URLs/pages will NOT forward to new locations in v10:
—Gene family pages
—Sequence Query results (BLAST results) and BioMart query results. Note that these expire after 3 days and are therefore not archivable at the present time.
—Keyword Search Results pages
4. I have no idea how to use the new Phytozome v10 interface. Help!
There’s a Phytozome Quick Start Guide available at http://phytozome.jgi.doe.gov/pz/QuickStart.html . Release notes for Phytozome v10 are at http://phytozome.jgi.doe.gov/pz/portal.html#!releaseNotes.
5. I have further questions. What should I do?
Email the Phytozome development team at email@example.com
Thanks for using Phytozome.
Goodstein D.M., S. Shu, R. Howson, R. Neupane, R. D. Hayes, J. Fazo, T. Mitros, W. Dirks, U. Hellsten, N. Putnam & D. S. Rokhsar & (2011). Phytozome: a comparative platform for green plant genomics, Nucleic Acids Research, 40 (D1) D1178-D1186. DOI: http://dx.doi.org/10.1093/nar/gkr944
UPDATE: From the Phytozome team–v10 has been available already.
— Phytozome (@phytozome) April 27, 2015