Posts Tagged ‘xfam’

Moving to xfam.org

May 1, 2014

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. Read the rest of this entry »

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We’ve moved, now the websites

January 30, 2014

In November 2012, we announced that the Xfam groups were moving the few tens of metres from the Wellcome Trust Sanger Institute to the European Bioinformatics Institute. We warned you then, that the websites would also eventually move. Read the rest of this entry »

Who’s who ?

March 22, 2011

It has been some time since we posted a blog, so, to keep you all on your toes, we are going behind the scenes to reveal something about the minds that run Pfam… From the longest-serving member to the newest recruit we have elicited a few key facts in the form of answers to some ‘trivial’ questions. Here are two profiles as they were given.  Can you work out who is who?

Read the rest of this entry »

Job opportunities and staff changes at Xfam

September 1, 2010

We have been very sad to see a few people leave the group recently. Rob Finn has been the dedicated and hard working project leader of Pfam for many years. In fact as a summer student he is credited with preparing most of the families for Pfam 2.0 [1]! We’re expecting to see great things from him at his new post at HHMI’s Janelia Farm. We’ve also seen Jaina Mistry get married and move to another city, fortunately for us she’s still working part-time for Pfam remotely. Jen Daub after her whirlwind trip around the world will also be working part-time on the Rfam project from her luxurious new abode in France.

This means we have a number of opportunities for bright and enthusiastic people. We are looking to recruit a new Project Leader to lead the Pfam group. This is an exciting opportunity for a motivated, enthusiastic and experienced computational biologist, and is an influential position working with a high profile bioinformatic resource. We anticipate the candidate will lead the next phase of database development that will include community annotation and the incorporation of new developments based on the HMMER3 software. We would expect the successful candidate to have their own research ideas
and be able to deliver research outputs with the group.

We are also looking for two Computational Biologists to join the group. The successful candidate will ideally a MSc in bioinformatics or equivalent experience and a strong background in molecular biology, biochemistry, genetics or similar.

We would also like to take the opportunity to welcome Professor John Burke from the University of Vermont. John is taking a one year sabbatical with Rfam to learn about all things bioinformatic. He is already an expert on all things to do with ribozymes and RNA structure, so we expect some major improvements in Rfam in these areas.

Last but not least, we have Chris Boursnell, a refugee from the banking world, who is working us and the fine Recode database
to improve our coverage of frame-shift elements.

Xfam consortium meeting

June 4, 2010

The annual Xfam consortium meeting was held on the 10-11th May 2010 and we have the photographic evidence to prove it.

We spent the two days listening to talks from everyone about the latest developments.  We were particularly interested to hear about new developments in HMMER3 and INFERNAL – fundamental pieces of software that Xfam rely on.  Nucleotide enabled HMMER3 is in development and will be great for Rfam, hopefully replacing the current BLAST pre-filters.  We are also had updates on how the HMMER software scales using multiple threading and/or MPI.

We also had a number of wide ranging discussions.  Erik Sonnhammer unfortunately wasn’t present this time so the usual discussion on Stockholm alignment format was avoided.  However, we had a fulsome discussion of Pfam family naming nomenclature.  It was generally agreed that although there were rules followed for Pfam short names, no one else in the world understood them.  So we will endeavour to add a new section to our documentation about it.  We discussed how much information is actually required before a DUF (domain of unknown function) is renamed to something more meaningful.

We were blessed because the Icelandic ash cloud didn’t intervene.  But one of our number did leave their passport in a car bound for Oxford causing a delay home. We would like to thank all the members of the Pfam and Rfam consortia for coming and also to our other EBI attendees.

Janelia Farm Research Campus: Sean Eddy, Eric Nawrocki, Travis Wheeler, Tom Jones, Diana Kolbe, Michael Farrar

Stockholm Bioinformatics Center: Kristoffer Forslund, Dave Messina

Wellcome Trust Sanger Institute: Alex Bateman, Paul Gardner, Lars Barquist, Jaina Mistry, John Tate, Prasad Gunasekaran, Penny Coggill, Rob Finn

University of Manchester: Sam Griffiths-Jones

University of Oxford: Andreas Heger

University of Helsinki: Liisa Holm

Other friends from EBI: Sarah Hunter, Phil Jones, Craig McAnulla  and  Javier Herrero.

A season of Xfam courses

May 28, 2010

It seems this year Xfam is involved in a lot of courses this year. Here are a few of the dates when you can see Xfam-ers in the flesh! Read the rest of this entry »

Xfam consortium meeting – Have your say

May 5, 2010

The Xfam consortium will be having their annual meeting in Cambridge on the 10th-11th May. Members of the Rfam and Pfam consortia including the developers of HMMER and INFERNAL will be getting together along with some friends from InterPro, ADDA and Ensembl.

This is a time of great planning, strategising, and playing kubb. Its also an opportunity for you to influence the future direction of Rfam and Pfam.  Please let us know if you have great ideas for how you would like to see Xfam develop in the future.

Posted by Alex

Alex wins the Benjamin Franklin award!

April 1, 2010

Our very own Alex Bateman has been awarded the prestigious Benjamin Franklin award! This is an annual award presented to someone in the community who has made significant contributions to promoting open access in the life sciences.

Nominations are made by at least two members of the community and then votes are collected by the good people at bioinformatics.org. Alex faced some stiff competition from many greats in the field yet still managed to win. He is the third Xfam associate who has won the award, joining Ewan Birney and Sean Eddy.

Naturally, all of the Xfam members are very happy with this result and are currently glowing in the reflected glory (or is that the result of the celebratory bubbly or the unseasonal weather).

Posted by: Rob and Paul.

Welcome to the Xfam blog

January 19, 2009

Welcome to the new blog for the Xfam databases ! Xfam is our shorthand for the combination of Pfam and Rfam databases, which we note will also future-proof us, in case we add any further databases to the brand.

We hope that this blog will become a useful point of reference, where our users can learn about what is going on behind the scenes at Xfam central. We will be announcing some important changes that are coming with the eagerly awaited release of HMMER 3. As well as announcing new releases of the data and website, we’ll also try to discuss our philosophy on protein/RNA domains and sequence classification. If there are other topics that you would like to hear more about, why not leave us a comment.