The last Ensembl events of 2010:
1 Dec: Browser workshop at the Institute of Cancer Research: Royal Cancer Hospital, London
1-3 Dec: Developers workshop at the University of Cambridge, UK
6-7 Dec: Browser workshop at MRC Harwell, UK
7-8 Dec: Browser workshop at the University of Tampere, Finland
7-8 Dec: Ensembl module in the Open Door Workshop - Working with the Human Genome Sequence, Hinxton, UK
9-10 Dec: Browser workshop at the Stazione Zoologica Anton Dohrn of Naples, Italy
14 Dec: Browser workshop at University College London, UK
For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.
16 November, 2010
The last Ensembl events of 2010:
The Ensembl 60 release sees two changes in our data upload capabilities
First off Ensembl can now "attach" a BAM file. BAM is the compressed form SAM - Sequence AlignMent files - which has become the dominant way to package up next-generation sequencing data. A BAM (or SAM file) has both the sequence and the alignment of a set of reads in a compact form (BAM makes it even more compact). Critically you can index a BAM file allowing programs rapid access to particular "Slices" of the reads by genomic position. Alignment tools such as Maq, BWA, SOAP can produce BAM files; a variety of analysis tools are written around BAM files, and now Ensembl can view BAM files.
To make a BAM file viewable you need to have access to a website where you can put files (like you local web space, perhaps an institutional thing). Call MyGreatExperiment.bam. You then need to index the BAM file using one of the tools - samtools is the usual one to do this, making a MyGreatExperiment.bam.bai (BAM index) precisely along side it (The Ensembl code is going to make the assumption that the index is called filename.bai). Then go to "Manage your Data" button on any web page in Ensembl, and go to the "Attach BAM" section. And then browse your RNA-seq, Chip-seq, Exome data to your hearts content!
Posted by Ewan Birney
10 November, 2010
We are pleased to announce the public availability of a second Ensembl mirror in the USA. This can be found at http://useast.ensembl.org/ . This provides a fully functional Ensembl website, but there are some things to note which I've listed below.
We don't automatically redirect users to the new mirror, although we have plans for this in future. So for now you'll need to explicitly visit http://useast.ensembl.org/ to access it.
If you use the login functionality, your existing login will work on http://useast.ensembl.org/ , although configuration changes will not be reflected between sites. We plan to support shared logins very soon.
We don't yet offer the Biomart or BLAST/BLAT services on the new mirror; these will come in the near future. We currently have no plans to offer a US-based MySQL mirror, so you should continue use ensembldb.ensembl.org for MySQL queries.
We're very keen to hear your experiences with this new mirror, particularly from our US users, please use the Helpdesk in the first instance, or contact me directly. We also have advanced plans for mirrors in other parts of the world, so stay tuned!
Posted by Glenn Proctor
The Ensembl project is pleased to announce release 60 of Ensembl. Highlights of this release are:
* New species - Giant Panda
* New assemblies and genebuilds for zebrafish and rabbit
* Improved design of the Variation Table
* New display for GO terms
* Improved navigation on Region in Detail, including autocompletion of gene display names (e.g. HGNC)
For more information visit:
The Ensembl Team
Posted by Ensembl Helpdesk (Giulietta)
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