Back in November 2012 we announced that the Xfam team in the UK was moving from the Wellcome Trust Sanger Institute to the European Bioinformatics Institute (EMBL-EBI), just next door on the Wellcome Trust Genome Campus. On Tuesday we completed that move by switching off the Pfam and Rfam websites inside Sanger and redirecting all traffic to our shiny new home at xfam.org. You can now find the Pfam and Rfam websites at pfam.xfam.org and rfam.xfam.org respectively.
A new site for Xfam
You’ll notice that although we’ve moved to EMBL-EBI, we’re not moving the website to the .ebi.ac.uk domain, but to a new xfam.org domain. The website at xfam.org is a showcase for the now fairly large number of resources that are run by the Xfam consortium, from AntiFam to Dfam, iPfam to TreeFam.
The Pfam and Rfam websites in EMBL-EBI are running on the same underlying datasets as they were in Sanger (Pfam 27.0 and Rfam 11.0) and there have not been any major changes during the move, besides the appearance of the EMBL-EBI logo and the new address. However, there are a few things that we still need to update, so please bear with us as we finish off the move and fix some known issues. As always, if you have any problems you can submit a trouble-ticket via the email addresses at the bottoms of the pages, and we’ll do our best to help.
We’ve previously run mirror sites for Pfam and Rfam in the US and Sweden, but the mirror sites have also turned off their local servers and started directing traffic to their equivalents on xfam.org. Maintaining the various mirrors has always complicated the process of developing the websites, but was important to ensure redundancy. Now that we’re serving the sites from EMBL-EBI, we can take advantage of EMBL-EBI’s duplicate, independent data centres in London to provide resilience. We’ve therefore taken this opportunity to simplify things and reduce the burden on all of the consortium sites by bringing everything “under one roof”.
If you have links or bookmarks to the Pfam or Rfam websites, either at Sanger or one of the mirrors, now is the time to update them. The only change that you should need to make is, for example, changing “sanger.ac.uk” or “janelia.org” to “xfam.org”; everything else should remain the same. If you have problems or questions though, do let us know.
We’re aware that the change to *.xfam.org, although transparent for browsers, may cause problems for users of our RESTful interface. If you use tools such as “curl” to access data, you’ll find that you need to tell curl explicitly to follow redirects, using the “-L” flag. Other tools, and possibly scripts, may need similar changes.
We’re aware that interactive sequence searches are a bit slower than they were previously and we will be resolving this performance issue in the near future. Batch searches, conversely, may be somewhat quicker. All of our searches now use the EBI web services framework, so you can now use the same underlying HMMER, pfam_scan.pl and Infernal tools that we use, either via a web form or using SOAP or RESTful interfaces.
Maintaining documentation and keeping it up to date is always a difficult job. We’re aware that a lot of the documentation in our help pages refers to the Sanger sites and we’ll be going through those pages to bring everything up to date soon.
Posted by John.