The Ensembl Weblog

Ensembl Genomes Release 10

2011-07-12T09:45:00.003+01:00

The Ensembl Genomes Project is pleased to announce release 10 of Ensembl Genomes.

The main highlights of this release are:

* Software migration to Ensembl 63

* Trypanosoma brucei, a causative agent of Human African trypanosomiasis, or sleeping sickness added to Ensembl Protists.

* Ustilago maydis (Plant-pathogen interaction model), Puccinia triticina (wheat rust fungus) and Nectria haematococca (Plant pathogen) added to Ensembl Fungi.

* Latest 1001 Genomes release included for Arabidopsis thaliana, together with 5 additional gene models from TAIR10. Projection of GO terms from Arabidopsis thaliana and Oryza sativa japonica to other species based on homology, also added for Ensembl Plants.

The Ensembl blog is moving!

2011-02-17T14:55:00.005Z

We have now moved our blog to an independent server that will allow us more control. Forthcoming new features include a workshop calendar, and some content such as our development roadmap will also be moved from the main Ensembl website to the blog site, where they are easier for us to update.

New Ensembl blog

Please update your bookmarks and RSS readers to the new address, as no further posts will be made here.

See you on the new site! You will be redirected in 4 seconds.

New Ensembl Genomes release expands the metazoa

2011-02-09T15:20:00.002Z

I'm going to be blogging a bit more about the recent Ensembl 61 release and the Ensembl Genomes 8 release - lots and lots of goodies in both these releases - web site tweaks (some of the them totally critical for generating good displays), the new "favourite tracks" feature, and impressive content changes.

I'll start today on content changes, and in Ensembl Genomes 8 there are some important genome additions. Some come from Paul Kersey's new collaboration with PhtyoPathDB - more on that in a later post - but top of my excitement has been the diversity in metazoa. The Ensembl Metazoa team has added Sea Urchin, Sea Anemone, the rather weird primitive animal, Trichoplax adhaerens (also called the "carpet" organism) and the blood fluke, Schistosoma mansoni. The motivation of bringing these organisms in is to broaden our phylogenetic tree and comparisons we can provide across all of life. So for example for the drosophila Twist

gene:

Twist Gene

One can now see the deep tree for this across metazoa:

For example, there is a deep ortholog to Trichoplax:

Trichoplax gene

which seems to predate the split of some of these Helix Loop Helix proteins, whereas

there are other members of the family which have paralog in Trichoplax

Trichoplax gene (2)

meaning that there seems a fundamental split in this developmentally key

transcription factor. This is just one of many interesting gene trees that

one can look at using this resource...

Happy browsing/data mining!

Ensembl Genomes Release 8

2011-02-09T08:33:00.002Z

The Ensembl Genomes Project is pleased to announce release 8 of Ensembl Genomes (http://www.ensemblgenomes.org/).

The main highlights of this release are:

Software migration to Ensembl 61

New Pan Compara database consisting a selection of vertebrate genomes from Ensembl 61 and genomes from Ensembl Genomes 8 (incorporating 8 new species), giving a species total of 313.

3 oomycete genomes added to Ensembl Protists, including Phytopthora infestans and Phytopthora ramorum responsible for potato blight and Sudden Oak Death disease respectively.

5 genomes added to Ensembl Metazoa, including Strongylocentrotus purpuratus (Echinodermata) (sea urchin), Apis mellifera (Arthropoda) (honey bee) and Nematostella vectensis (Cnidaria) (sea anemone).

For further details please visit the individual homepages:
http://bacteria.ensembl.org
http://protists.ensembl.org
http://fungi.ensembl.org
http://plants.ensembl.org
http://metazoa.ensembl.org

Favourite tracks in 61

2011-02-02T16:23:00.017Z

Ensembl 61 has gone live. In displays like gene summary and region in detail, favourite tracks can be turned on. To do this, open the configuration panel (click on configure this page in the left hand menu). Activating a star by clicking on it will place that track in the favourites menu (shown by an arrow in the diagram).

Hover over any track name in these views to view information about the data, change the display, or turn the track off. Turning on tracks must still be done with the configuration panel.

We hope this helps ease of navigation. Read about other updates in 61, such as our new species, Turkey, in the news. The Ensembl Team

New genebuild summaries now available

2011-01-28T10:03:00.000Z

We are pleased to announce new documentation, specific for describing the gene annotation methodology and results for particular species.

Ensembl gene annotation is a multi-step process which usually takes several months to complete for one species, and is termed the genebuild. In order to provide our users with more information on the data resources used and decisions made during the genebuilding process, we are introducing a new genebuild summary PDF document for each new genebuild, starting from early February 2011 with Ensembl release 61. Each document includes details on not only the alignment programs and data filtering parameters used, but also statistics on the number of protein/cDNA/EST sequences used at different stages of the genebuild. For example, users will be able to find out how many protein sequences were retrieved from public repositories (RefSeq and UniProt) at the beginning of the genebuilding process, how many of these proteins aligned to the genome by various algorithms at different stages of the build, and how many remain in the final gene set as supporting evidence for genes. For human, mouse and zebrafish, the process of merging Ensembl and Havana annotations is also explained.

The genebuild summary will be available for six species: the Anole lizard, Marmoset, Mouse, Panda, Turkey and Zebrafish. More genebuild summaries will be available in the future when genebuilds of existing species are being updated, or when new species are being annotated. You can download the document via a link found near the bottom of the "Description" page for each species. Just click on the species of interest from the home page, to open its description page.

Ensembl Events in February 2011

2011-01-18T20:48:00.004Z

These are the Ensembl events for February:

10 Feb: Developers workshop at the Korea Genome Organization (KOGO) 2011 Winter Symposium, YongPyong Ski Resort, South Korea
11 Feb: Browser workshop at the Zentrum fuer Humangenetik und Laboratoriumsmedizin Dr. Klein und Dr. Rost, Martinsried, Germany
14 Feb: Developers workshop at Seoul National University, Seoul, South Korea
16 Feb: Developers workshop at the Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
17-18 Feb: Browser workshop at the University of Cambridge, Cambridge, UK
23-25 Feb: Ensembl module in the Bioinformatics Roadshow at the Research Centre for Biodiversity and Genetic Resources (CIBIO), Porto, Portugal

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

New Search - Lucene

2011-01-18T16:24:00.008Z

Ensembl is in the process of moving its site search to the open source Apache Lucene framework. This change should bring several advantages, not only to us, but to all users, the main one being added flexibility; in the short term it will have little impact on web site users, except for making life easier to those maintaining local instances.

From Ensembl release 62 (due out this spring) we will incorporate more data into the search (for example help and documentation) and start to improve how we display results. For developers, note that whilst we are not releasing the webcode for Lucene immediately, we are aiming to do so for release 62.

This powerful platform allows searching of over 3 million genes and gene symbols, over 6 million oligo probes, and over 67 million variations! Our implementation utilises software designed and developed by our colleagues at the European Bioinformatics Institute (used in the EB-eye) which has proven to be fast and flexible.

Lucene is open-source technology that has also been implemented to
provide searches of our mailing lists (i.e. announce and dev), thanks to our colleagues at the Wellcome Trust Sanger Institute.

We hope these improvements will help make browsing Ensembl a more user-friendly experience. Please give your feedback at helpdesk@ensembl.org.

New Ensembl mirror in Asia

2011-01-13T21:23:00.002Z

We are pleased to announce the public availability of an Ensembl mirror in Asia. It can be found at http://asia.ensembl.org/ . This provides a fully functional Ensembl website, but there are some things to note which I've listed below.

Redirection

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://asia.ensembl.org/ to access it.

User logins

If you use the login functionality, your existing login will work on http://asia.ensembl.org/ , and configuration changes will be shared between sites.

Other services

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 an Aisa-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; please use the Helpdesk in the first instance, or contact me directly.

Survey Feedback - Thank You

2011-01-12T10:13:00.006Z

Many thanks to the Ensembl browser users who have given us feedback in our recent survey entitled "Tell Us What You Think"! We learned some valuable points that are being addressed to improve our discoverability, functionality, and overall usability.

We heard back from scientists all over the world- the majority of you were in the UK, Netherlands, the US, and Germany. Represented fields include bioinformatics, basic research, clinical and genetics research, biotechnology and immunology. 50% of respondants work mainly with the computer, while the other half of you do at least some wet-lab biology. We even got responses from mainly wet-lab scientists (15% of respondants)- this is useful to us, as we strive to make Ensembl usable to the largest possible community.

So what did we learn? The use of BioMart and the Perl API by website-users has increased since our last survey a year and a half ago. We have more infrequent users, visiting our browser monthly or less often- though the majority of our users are Ensembl masters (frequent users). We believe that this represents the fact that an ever greater percentage of biological research involves at least some bioinformatics tools and hope this reflects a simpler, more straightforward website that does not need extensive study to use. Finally, 65% of our users take a genome-wide approach, while 20% focus on less than 10 genes.

So what did people like? Our tools are popular, especially the Variant Effect Predictor. The recent addition of sortable columns is also a hit. When you all were asked what other tools are desired, we were pleased to find that some (history) were already being implemented, while others exist, but seem to be hidden. On that note-

Those of you who asked for a record of recent actions in Ensembl, if you login (registration is free) a history of recent genes, transcripts, variations and locations you visit will appear in the tabs. Give it a try!

Many of you asked for tools and functionality that exist, such as CpG islands, (available as a track in Location view) a map of gene structure for all isoforms of a gene, and SyntenyView. To aid in the discoverability of these tools, our main search will be configured to also yield results from help pages. This should help people find what they're looking for, without relying on browsing alone. Also, we will make more use of this blog by posting "Did You Know?" tips that will help you learn about functionalities of Ensembl and BioMart that may not be completely transparent. The archive (older) sites in particular don't appear to be easy to find (the link is a small one, at the bottom of each Ensembl page), we address this in our FAQ section.

As for other requests for functionality we don't yet have, these are being taken on board, and will hopefully lead to exciting new developments in the future.

Thanks again for your feedback!

The Ensembl Team

Ensembl UK shutdown - 8/9th January 2011

2010-12-22T14:23:00.004Z

Owing to problems with our data centre cooling system, the Sanger network will be offline from around 4.30pm on Friday 7th January until the evening of Sunday 9th January (UK time).

This means that all UK-based Ensembl sites, including www.ensembl.org, archives and pre site, will be unavailable from late Friday afternoon until Monday morning.

However, you can still browse the genome using our US (Ensembl west & east) and Asia mirror sites. Services that depend on machines based in the UK, i.e. BLAST/BLAT and user logins, will be disabled during this time.

In the case of bacteria, fungi, metazoa, plants, and protists at www.ensemblgenomes.org, no mirror site is as of yet available. Those services will not be running over the weekend.

Please accept our apologies for any inconvenience caused. A reminder will be sent out to the announce@ensembl.org mailing list, and on our Twitter feed, nearer the time.

Seasons Greetings and Upcoming Features

2010-12-21T13:48:00.003Z

Happy holidays from Ensembl! Here in Hinxton, we are planning new developments for the new year (what else would we do with all this snow!) Some of the highlights planned for early next year include:

The first gene set for turkey in Ensembl, and inclusion of turkey into pairwise (between two species) whole-genome alignments and multiple species alignments (including a new 3-way avian alignment).

Inclusion (merge) of manual curation of the zebra-fish genome by the HAVANA group into the Ensembl gene set.

Update to dbSNP 132 for variations in the human genome.

Sea Urchin (Strongylocentrotus purpuratus) and Honey Bee (Apis mellifera) genomes in the Ensembl Metazoa site. See other upcoming species to Ensembl genomes here.

Don't forget, an overview of upcoming annotation to Ensembl is on our roadmap.

For those of you going on holiday soon, enjoy! We look forward to supporting all your cutting-edge scientific endeavors in 2011.

The Ensembl Team

Ensembl Events in January 2011

2010-12-15T11:34:00.005Z

Merry Xmas and a Happy New Year!

All Ensembl events for 2010 are done .... but we already have lined up quite a few for 2011!

Here are the ones for January:

16 Jan: Demo at the Plant and Animal Genome XIX Conference, San Diego, CA, US
18 Jan: Ensembl module in Primers for Predocs, Hinxton, UK
18-19 Jan: Ensembl module in the Workshop on Comparative Genomics, Europe 2011, Cesky Krumlov, Czech Republic
20-21 Jan: Ensembl module in the EBI workshop at City of Hope, Duarte, CA, US
21 Jan: Developers workshop at the Hubrecht Institute, Utrecht, The Netherlands
24 Jan: Browser workshop at the UCSC Genome Browser Group, Santa Cruz, CA, US
26 Jan: Developers workshop at Stanford University, Palo Alto, CA, US
27 Jan: Browser workshop at Stanford University, Palo Alto, CA, US
27 Jan: Browser workshop at The University of Nottingham, UK

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Beds, Wigs, BAMs and Variants for Flies, Rust, Aphids and 301 other species

2010-12-14T11:49:00.006Z

Now that Ensembl Genomes has moved onto the 60 code base, all the goodies in Ensembl's user data site are available across all 304 species in Ensembl genomes - from tiny bacteria to crazy big plants.

One of these is uploads of BAMs, Wigs, Beds in the location based view. For example, if you have the following file to specify a SNP in Drosophila

2L 356013 356013 C/T

By using the Variant Effect Predictor, accessible from Tools on the top of each page, or the 'Manage your data' link at the left of pages, one can get the effect (synonymous, non synonymous, in a UTR etc) for the variant.

(You click on "Variant Effect Predictor", upload a text file of chr, position, allele and hit go) This can also be run as script using the API (the database is internet accessible so you just need to have an internet connection, Perl, MySQL client libraries and the Ensembl code base installed).

In addition, the full set of visualisation tools for your own data is also now accessible for all Ensembl Genomes species. For example, this bedGraph file:

track type=bedGraph name="BedGraph Format" description="BedGraph format" priority=20

2L 21302000 21302300 -1.0

2L 21302300 21302600 -0.75

2L 21302600 21302900 -0.50

2L 21302900 21303200 -0.25

2L 21303200 21303500 0.0

2L 21303500 21303800 0.25

2L 21303800 21304100 0.50

2L 21304100 21304400 0.75

Will render a nice little variable height picture in the main contigview display. Other options are available (like Bed and Wig format) - many of which people will know from UCSC. Come, try it out, and give us feedback at helpdesk@ensembl.org

Ensembl Genomes Release 7

2010-12-01T11:59:00.001Z

The Ensembl Genomes Project is pleased to announce release 7 of Ensembl
Genomes (http://www.ensemblgenomes.org/).

The main highlights of this release are:

* Software migration to Ensembl 60

* 66 new genomes added  for Ensembl Bacteria and updated functional
genomics databases for Escherichia/Shigella and Staphylococcus

* Puccinia graminis f sp tritic genome added to Ensembl Fungi

* Zea mays and Physcomitrella patens genomes added to Ensembl Plants,
new variation datasets for Oryza sativa and updates to the
functional genomics databases for Oryza sativa indica, Oryza sativa
japonica and Arabidopsis thaliana

* Acyrthosiphon pisum genome added to Ensembl Metazoa

Please see the individual homepages for more detailed information:
http://bacteria.ensembl.org
http://protists.ensembl.org
http://fungi.ensembl.org
http://plants.ensembl.org
http://metazoa.ensembl.org

Ensembl Events in December 2010

2010-11-16T15:26:00.005Z

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.

Beds, Wigs and BAMs

2010-11-16T10:31:00.002Z

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!

In addition, we've spruced up our functionality and documentation on the UCSC file formats of Bed, BedGraph and Wig. Take a look at the "File Upload" and "Attach URL" forms, and the documentation. Now we precisely indicate what attributes you can use in each of these formats. Our goal is to make Ensembl as useful as possible to as broad a set of users as possible, so let us know if you find something confusing and/or you have a Bed/Bedgraph/Wig file that works for UCSC but doesn't work on Ensembl.

This is of course available across all 50 species in Ensembl, and in a couple of weeks, when Ensembl Genomes 7 is out, across another 50 eukaryotes from protists to plants and about 250 different bacteria.

Comments are welcome - either on this blog or email to helpdesk@ensembl.org

US East coast Ensembl mirror now available

2010-11-10T16:24:00.000Z

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.

Redirection

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.

User logins

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.

Other services

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!

Release 60

2010-11-10T10:17:00.003Z

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:
http://www.ensembl.org/info/website/news/index.html

The Ensembl Team

Ensembl workshop (ASHG 2010)

2010-10-28T14:59:00.011+01:00

Our workshop at the ASHG Annual Meeting has been sold out this year!

During this session we will explore the latest assembly of the human genome and show some of the highlights of our genome browser. In order to make things easier for participants, we have put together a document that should allow you to follow the session. Dowload this document from here (429KB).

If you are in DC these days come and visit us (booth #527).

Greetings from Washington.

Ensembl Events in November 2010

2010-10-19T11:18:00.003+01:00

As usual November is a busy month for the Ensembl outreach team:

2 Nov: Ensembl demo at the EBI Open Day, Hinxton, UK
5 Nov: Browser workshop at the American Society of Human Genetics Annual Meeting 2010, Washington DC, US
3-9 Nov: Ensembl module in the Computational & Comparative Genomics course at Cold Spring Harbor Laboratory, NY, US
10 Nov: Browser workshop at the Jackson Laboratory, Bar Harbor, ME, US
11 Nov: Demo for EBI / EMBL PhD students, Hinxton, UK
12 Nov: Browser workshop at Middlebury College, VT, US
16-17 Nov: Ensembl module in The Genome Access Course at Cold Spring Harbor Laboratory, NY, US
16-17 Nov: Ensembl browser workshop at MRC Harwell, UK
18 Nov: Ensembl module in the The Bioinformatics Roadshow at the MRC - National Institute for Medical Research, London, UK
22-24 Nov: Developers workshop for EBI and Sanger Institute employees, Hinxton, UK
23 Nov: Browser workshop at the Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
25 Nov: Browser workshop at University College Dublin, Ireland

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

More database maintenance

2010-10-05T14:40:00.004+01:00

Unfortunately our database storage is still unstable, and all Ensembl dbs are being taken offline this afternoon for emergency maintenance work. Please accept our apologies for any inconvenience caused.

This will affect all UK-based sites, including www.ensembl.org, pre.ensembl.org, Vega and the archives. The US West mirror, uswest.ensembl.org, will be running with reduced functionality (no user logins or BLAST, which depend on Sanger dbs), and the cloud-based useast.ensembl.org should be unaffected.

For detailed web status updates, you can also follow us at twitter.com/ensembl_web.

Ensembl Wants to Know What You Think!

2010-10-05T14:14:00.003+01:00

Dear Ensembl Users,

Our survey is still open. Please consider giving us 10 minutes of your time to let us know what you think of our website. This will help us make Ensembl more usable.

Click on the link, and pass it around! We want to hear from new users as well.

http://www.surveymonkey.com/s/KCR6WN2

Many thanks,
The Ensembl Team

Reduced website functionality on 5th October 2010. - Now postponed

2010-10-04T20:26:00.002+01:00

This work has been postponed and the Ensembl site is now running as normal. We will update the blog informing you when this work is rescheduled.

The Systems team at the Sanger Institute need to carry out emergency maintenance to some of the database servers running the ensembl websites from 9.30 am tomorrow morning. This means that we will be running the live Ensembl site with reduced functionality and the Pre, Vega, NCBI36 and archive sites will temporarily be off line.

Blast, Biomart, user-logins and search will all be unavailable. The entire Ensembl website should be considered as "At risk", however should the main site go down the two mirror sites, uswest.ensembl.org and useast.ensembl.org should still be available although these too will have reduced functionality.

We apologise for inconvenience this may cause and will work to ensure the disruption occurs for the shortest time possible.

Main Ensembl site offline - now fixed (3/10/10 6pm)

2010-10-02T22:49:00.004+01:00

The site is now back.

There is a problem with the storage attached to the database servers which has taken the main Ensembl site offline. Please use one of our two mirror sites http://uswest.ensembl.org and http://useast.ensembl.org. We will update the blog when the main site is working again, we apologise for any inconvenience caused.

Changes to mysqlimport

2010-09-28T09:55:00.002+01:00

Owing to problems with BLOB data in some tables, we have had to change the way these tables are dumped, which in turn means a change to the mysqlimport parameters.

It has been necessary to escape the table fields when dumping the MySQL text files. Hence to import successfully, a field escape parameter needs to be specified when using mysqlimport, e.g.

mysqlimport -h your_host -u write_user -p write_pass -P 3306 --fields_escaped_by=\\ database_name /full/path/to/table_name.txt

Tables affected in Release 59 are:

* homo_sapiens_funcgen_59_37d.result_feature
* mus_musculus_funcgen_59_37l.result_feature
* ensembl_compara_59.conservation_scores

and the meta_conf__xml__dm and meta_template__xml__dm tables in all mart databases.

From release 60, all Ensembl mysql dumps will be done this way, so you will need to use the above parameters on all imports.

Ensembl Events in October 2010

2010-09-24T19:56:00.004+01:00

In October we have the following Ensembl events:

12 Oct: Ensembl module in the EBI Bioinformatics Roadshow, Dokuz Eylul University, Izmir, Turkey
13 Oct: Tutorial for The National Genetics Reference Lab, Manchester, UK
14 Oct: Ensembl module in the EBI Bioinformatics Roadshow, Dokuz Eylul University, Izmir, Turkey
19 Oct: Tutorial for The National Genetics Reference Lab, Manchester, UK
19 Oct: Browser workshop at the Royal Veterinary College, Potters Bar, UK *postponed to 26 Oct*
22 Oct: Browser workshop at the Free University Brussels, Belgium

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Changing to LASTZ

2010-09-21T14:05:00.005+01:00

People following the declarations of intentions for the next release (these are sent to announce@ensembl.org) may have noticed that we are releasing LASTZ pairwise alignments instead of BLASTZ ones. LASTZ is written by Bob Harris from the Penn State University as a replacement of BLASTZ, as BLASTZ is now considered obsolete (read the announcement).

This is the first release where we use LASTZ for the new alignments. We will update the previous alignments in the following releases.

A.mel vs A.mel

2010-09-09T16:16:00.004+01:00

Ensembl is already working on the forthcoming release (e60!). The declaration of intentions have been published and include the new Giant Panda (Ailuropoda melanoleuca) genome.

While I was looking at the alignments we are planing to release, I saw the H.sap-A.mel LASTZ-net alignments. Hey! I thought we banned Apis mellifera from Ensembl long time ago.

Then I realised that the scientific names of both the honey bee and the giant panda start with the same letters. So, don't get confused, one of them eats flowers and makes honey, while the other one eats bamboo and makes very nice teddies!

Tell Us What You Think!

2010-09-01T15:13:00.002+01:00

To new and frequent Ensembl users,

We are continuously striving to improve our web interface at www.ensembl.org.

Please let us know how we're doing!

The survey should take 10-15 minutes.

http://www.surveymonkey.com/s/KCR6WN2

Many thanks,
The Ensembl Team

Ensembl Genomes Release 6

2010-08-31T20:43:00.005+01:00

The Ensembl Genomes Project is pleased to announce release 6 of Ensembl Genomes.

The highlights of this release are:

Software migration to Ensembl 59.
Two new rodent malarial genomes: Plasmodium berghei and Plasmodium chabaudi and an update to the Plasmodium falciparum gene-set in Ensembl Protists.
Variation BioMarts added for Plasmodium falciparum, Saccharomyces cerevisiae (Ensembl Fungi), Arabidopsis thaliana, Oryza sativa indica, Oryza sativa japonica, Vitis vinifera (Ensembl Plants), Anopheles gambiae and Drosophila melanogaster (Ensembl Metazoa).

See the individual homepages for Bacteria, Protists, Fungi, Plants and Metazoa for more information.

Ensembl Events in September 2010

2010-08-25T16:21:00.002+01:00

The Summer seems to have gone (at least here in Britain), so Ensembl outreach activities are picking up again:

7 & 8 Sep: Browser workshops at the University of Toronto, Canada
13-15 Sep: Developers workshop at the Genome Informatics Meeting 2010, Hinxton, UK
16-17 Sep: Browser workshop at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands
17 Sep: Demo at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands
27-28 Sep: Browser workshop at the University of Cambridge, UK

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Ensembl browser workshops Western US January 2011

2010-08-23T10:08:00.005+01:00

The Ensembl Outreach team is currently looking into the possibility of giving some 1-day Ensembl browser workshops in the Western US in the period directly before or after the Plant and Animal Genome Conference in San Diego, which takes place from 15-19 January 2011. Hosting institutions would only have to pay the instructor's expenses (accommodation and subsistence) and would share the domestic travel costs, but we would not otherwise charge for the workshops.

For more information about our browser workshops, please have a look here.

Interested? Please contact me for more details at bert@ebi.ac.uk.

Networks problems at the Sanger site

2010-08-19T16:12:00.004+01:00

The Systems team at the Sanger Institute have resolved the network problems and http://www.ensembl.org is now back up and running as normal.

The Sanger Institute is currently experiencing networks problems which have taken the main Ensembl site offline. Please use one of our two mirror sites http://uswest.ensembl.org and http://useast.ensembl.org We will update the blog when the main site is working again, we apologise for any inconvenience caused.

Maintenance Finished

2010-08-18T10:42:00.003+01:00

Hi Ensembl Users,

The work is finished, and search is working on archives again.

Just a warning. Maintenance work this afternoon (18 Aug, 2:45 to 5 PM in the UK) could affect the live site. If this is the case, please try our mirror site at uswest.ensembl.org

Search will be temporarily disabled on the archive sites for versions 55-57. If BioMart queries are slow, please use the interface at www.biomart.org.

Regards,
The Ensembl Team

Ensembl in Toronto

2010-08-16T15:36:00.004+01:00

Ensembl will be training at the Terrence Donnelly Centre for Cellular and Bio-molecular Research, University of Toronto this coming month of September, where we will be running two workshops (7 & 8 September).

In these workshops we will provide an overview of recent and future developments in the Project, as well as focus on some particular topics such as variation or gene annotation. As always, we encourage participants to come with their own research questions. Note that participants have to come with their own laptop, other than that you only need some general knowledge of molecular biology/genomics and familiarity with web browsers. If you have any additional questions you can get information from the organisers. In addition to the University of Toronto, this course is sponsored by the OICR, CIHR-IRSC, and EMBL-EBI.

Regulatory Build now Cell Type specific

2010-08-16T10:01:00.003+01:00

Since release 58, the Ensembl Regulatory Build has been cell type specific. Regulatory Features are defined as sites of open chromatin which are potentially involved in gene regulation. These are built using data from different cell types, resulting in differing structures, attributes and classifications across the various cell types.

Release 59 also boasts greater coverage due to the incorporation of more data sets (see previous blog post), and a new 'projection' methodology. Projection allows Regulatory Features to be built on cell lines with sparse data, and also consolidates existing higher quality builds. The result of these changes is an increase in the number of Regulatory Features per cell type, as well as an improvement in the number of features which are assigned a classification e.g. Gene Associated or Promoter Associated etc.

The 'Regulation' panel has also been updated to reflect the new cell type specific nature of the build e.g. ENSR00000515919. The 'Details by cell line' view is now split into several sections, each showing data for a specific cell line. The uppermost section details a species 'MultiCell' cell line, showing data used to define the core regions of the given Regulatory Feature. More information on this view can be found here. We are always looking at ways to improve our Regulatory Build process, some areas we are currently considering are listed in our development road map.

New ChIP-Seq data and visualisation

2010-08-13T13:21:00.010+01:00

Over the last 3 releases we have significantly increased the content of the functional genomics databases, by including data from large public projects such as ENCODE and The Epigenomics Roadmap. In release 59 we have over 200 human data sets representing 10 cell types, 41 histone modifications and 14 transcription factors. These numbers will steadily increase in the forthcoming releases as more data is incorporated.

These data sets are now available in 'Region In Detail'. Cell type tracks can be turned on via the 'Functional genomics' menu of the configuration panel - click on 'configure this page' on the left to access it. These are split into 'Core' and 'Other' evidence types, reflecting how we deal with these data within the Regulatory Build. Display options include a peak track, with the underlying raw data is available as a 'multi-wiggle' track. Further configuration is available via the 'Cell/Tissue' tab, where individual feature types can be turned on or off.

Work is ongoing to improve the flexibility of these displays.

Human GRCh37 assembly patches

2010-08-05T17:16:00.004+01:00

Ensembl release 59 includes the first human assembly patches released by the Genome Reference Consortium (GRC).

The goal of the GRC is to ensure that the human reference assembly is biologically relevant by closing gaps, fixing errors and representing complex variation. Their ongoing efforts are made available to the community via minor releases called patches. The patches do not change the chromosome coordinate system but do provide either a new alternate haplotype (novel patch) or provide a preview of the chromosome tiling path for that region in the next major release (fix patch).

The patched update GRCh37.p1 affects only 2 regions of the reference assembly.The patch update GRCh37.p1 includes:

Fix Patch: HG79_PATCH (GL339450.1) on chromosome 9, correction for the ABO gene. Click here for an example region.

Novel Patch: HSCHR5_1_CTG1 (GL339449.1) on chromosome 5. This patch provides an alternative region (haplotype). Click here for an example region.

The two patched regions have undergone preliminary gene annotation. Human cDNAs with their annotated ORFs were aligned to the genome using the Exonerate cdna2genome model to generate coding transcripts.

We expect future patch releases on a quarterly basis.

Ensembl Events in August 2010

2010-07-28T11:11:00.003+01:00

Although it's Summer vacation time, there are still a few Ensembl events scheduled the coming month:

18 Aug: Ensembl module in the EURASNET Workshop on Structural Bioinformatics of RNA & RNP at the Adam Mickiewicz University, Poznan, Poland
29 Aug: Ensembl module at the ESF European Meeting on Next Generation Sequencing at Leiden University Medical Center, The Netherlands

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Changes to Ensembl Mailing Lists

2010-07-27T13:45:00.001+01:00

In the near future, we will be changing the way that the ensembl-dev and ensembl-announce mailing lists are managed.

The move to new hardware and list management software will increase responsiveness on the lists (ensembl-dev in particular has suffered from slow deliveries for some time), and in time will also allow us to provide a searchable archive of past posts.

The list addresses will change with the move:

ensembl-dev@ebi.ac.uk becomes dev@ensembl.org
ensembl-announce@ebi.ac.uk becomes announce@ensembl.org

The new addresses are active now.

All subscribers to the old lists have been moved to the new lists. Posts to the old list addresses will be automatically forwarded for a short time, but please update your email address books and any spam filters to reflect the new address list.

Information about the new lists, including details on how to subscribe and unsubscribe, can be found at http://lists.ensembl.org/.

As before, dev@ensembl.org is an open list which any subscriber can post to. Posting to announce@ensembl.org is restricted to Ensembl people.

All sites up and running

2010-07-07T12:08:00.001+01:00

All Ensembl sites are up and running - the outage referred to in the previous post only lasted for about 20 minutes.

Site problems - further details and temporary alternatives

2010-07-02T10:09:00.000+01:00

As Anne mentioned, at approximately 03:00 UK time on 2 July, the Sanger Institute Data Centre suffered a power failure. The effects of this have taken taken the main Ensembl web site and other resources off line. We are working to get the services restored.

In the mean time, we have two US mirror sites available:

http://useast.ensembl.org is recently launched and provides genome browsing and search facility.

http://uswest.ensembl.org provides genome browsing, but search relies on the main site in the UK.

Please note that BLAST services require the main site at Hinxton and will not be available until the systems have been restored.

Thank you for your patience and we apologise for any inconvenience caused.

More power failures

2010-07-02T10:03:00.004+01:00

We are currently experiencing further system problems caused by a generator failure at approximately 3am UK time. Our IT staff are working to restore service, and we apologise for any inconvenience caused.

Our US mirror, uswest.ensembl.org, is still available, although features that depend on Sanger services (user accounts, BLAST) will not be working.

Ensembl Genomes browser workshops

2010-06-24T15:00:00.003+01:00

The Ensembl project has focused on vertebrate organisms for the past ten years. Since Jan 2009, a sister project has formed, Ensembl Genomes, extending analysis to invertebrates, protists, plants, fungi and bacteria.

We do now offer separate workshops on both Ensembl and Ensembl Genomes. Though the browsing is similar, specifics can vary. For example, the genes in most non-vertebrate genomes are determined using different rules than in vertebrate genomes.

So, if you are thinking of hosting a browser workshop and you know your audience will mainly consist of researchers working on non-vertebrate genomes, the Ensembl Genomes browser is the right choice for you!

For more detailed information on the Ensembl Genomes browser workshops please have a look here.

Power failure

2010-06-22T14:00:00.001+01:00

We are currently experiencing a power failure which has taken the main Ensembl site offline. Our mirror site uswest.ensembl.org is still running so please use this until we have the main site back online.

Ensembl Developers Workshop at Genome Informatics 2010

2010-06-21T13:23:00.003+01:00

Ensembl announces a workshop for developers that will take place at the Wellcome Trust Genome Campus, Hinxton, UK. The workshop runs in the week of the Genome Informatics conference, from Monday 13 September until midday Wednesday 15 September 2010, and will cover the same content as in previous years.

Ensembl developers will present sessions on how to create your own core database, including the loading of a genome assembly into a database and the running of simple analyses using the Ensembl genebuild pipeline.

As this workshop is aimed at developers, we will be exploring the underlying code-base of the Ensembl Software System. The workshop comprises presentations around Ensembl as well as practical sessions. We would like to point out that this is not a 'learning how to program in Perl' workshop.

For the successful completion of the workshop exercises, participants will be expected to have comprehensive experience in PERL programming and a background in object oriented programming techniques. Familiarity with Perl, a Unix/Linux environment, databases and structured query languages (MySQL) are needed to follow the workshop and the programming examples. Knowledge of the Ensembl core API is essential. The workshop is suitable for people who have access to small- to large scale compute resources, and who plan to run genome-wide analyses on large-scale data sets.

The workshop will be given by:

• Bronwen Aken (Ensembl Genome Annotation team)
• Jan-Hinnerk Vogel (Ensembl Genome Annotation team)

Additional presenters will attend depending on the number of participants registering.

At the end of this course, attendees will

• have a good understanding of Ensembl's annotation pipeline
• have hands-on experience with loading a genome assembly
• have hands-on experience with the annotation pipeline

There is no registration fee to attend this course for non-industry participants, but we ask you to register in advance because the number of attendees is limited by the size of the training venue.

Please note that the workshop runs before the conference, so don't forget to arrange additional accommodation for the workshop days.

The aim of the Ensembl Developers Workshop is to promote the academic use of the Ensembl Analysis and Ensembl pipeline system used by the Ensembl Genome Annotation Group.

To register your interest to attend, please send an email to Bert Overduin (bert@ebi.ac.uk), together with a brief outline of the relevance of this workshop to your work and your details.

The registration deadline for this workshop is August, 15th. Notification of places will be as soon as possible.

We will circulate an agenda amongst participants in due time.

Ensembl Events in July 2010

2010-06-21T11:24:00.002+01:00

As usually July is one of the quietest months of the year, but we still have a few workshops:

1-2 July: Ensembl module in the EBI Bioinformatics Roadshow at the Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
13 July: Browser workshop at the University of Glasgow, Scotland

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

SNPs in high LD

2010-06-11T10:33:00.005+01:00

A new section has been added to the variation page in Ensembl 58 that allows you to find other variations in strong linkage disequilibrium with the SNP you are viewing.

Clicking on "Linked variations" from the menu on the left hand side of the variation page takes you to a view like this one for rs1333049. Linkage disequilibrium values are calcuated on the fly and presented in one table for each population.

The table shows both r² and D' values, along with the distance between the linked and current variations, any overlapping genes and any phenotypes associated with the linked variations. The table can be sorted by any of these columns by clicking on the column header (see previous post). The view is extensively configurable - clicking on Configure this page allows you to select populations to be displayed, change the distance over which linked variations are looked for, and filter the variations returned.

This view is currently only available for Ensembl Human, and is limited to variations with enough associated genotypes to calculate linkage disequilibrium values.

New Features to Aid Browsing

2010-06-08T15:50:00.014+01:00

With the recent release of version 58, we are pleased to announce a few features designed to make genome browsing simpler. Have you noticed the search function in the individual tables? For example, in the Gene tab: "Variation Table", search for a variation ID.

Have a look at our sortable tables. In this example, we can sort by ID, Type, location, allele, source, or validation status. Use the arrows next to the column title to choose a new column to sort by. Searchable, and sortable, tables can also be found for orthologues, variations across individuals or strains, protein motifs and domains, and more.

If you are browsing a genomic region, you may have noticed that the Location tab: "Region in detail" view has a sliding zoom bar. Zoom out to view neighbouring genes and features, or zoom in to your favourite exon.

Zebrafish RNA-seq gene models

2010-06-02T09:27:00.013+01:00

We have been developing a pipeline to build gene models using only RNA-seq data. For release 58 we have added a preliminary set of Zebrafish RNA-seq gene models with an intention to integrate this new source of evidence into a full genebuild soon.

Zebrafish transcriptome data from 9 tissues were used to build a set of genes and splice variants. For each loci we chose the variant with the highest read support to display, further details on the process are available here.
To display the genes, go to the Region in Detail, or Region Overview. Use the "Configure this page" button and select "RNASeq Genes" from the "Genes" menu. The "Supporting DNA Alignments" menu contains supporting exon and intron features from each of the nine tissues. Clicking on these features in Ensembl location pages shows a simple read count for the intron features and RPKM values for transcripts and exons, (reads per kilobase of model per million mapped reads, from Mortazavi Nature Methods 2008).

This is a first attempt at visualising tissue specific read depth and alternative splicing, which we hope to develop further in the future.

Ensembl Genomes Release 5

2010-06-01T15:54:00.002+01:00

The Ensembl Genomes Project is pleased to announce release 5 of Ensembl Genomes.

The main highlights of this release are:

Software migration to Ensembl 58

Total of 6 new bacterial genomes for Escherichia/Shigella and Staphylococcus collections for Ensembl Bacteria; pairwise alignments added for all collections.

2 new genomes, Phaeodactylum tricornutum and Thalassiosira pseudonana, for Ensembl Protists; pairwise alignments added.

A. fumigatus A1163 genome added to Ensembl Fungi.

Pristionchus pacificus genome from Wormbase and updates to the Drosophilia variation database added to Ensembl Metazoa.

Updates to the variation databases for A.thaliana, O.sativa japonica and V.vinifera in Ensembl Plants.

For further details regarding this release please visit:
http://ensemblgenomes.org/releases/release5_notes

GERP constrained elements via DAS

2010-05-28T15:38:00.004+01:00

It is now possible to get the GERP constrained elements via the DAS protocol. For instance the DAS command to get all the GERP elements on the BRCA2 gene (Human chr 13: 32889611-32973347) is:
http://www.ensembl.org/das/Homo_sapiens.GRCh37.constrained_element/features?segment=13:32889611,32973347

By default, you obtain both the constrained derived from our 16-way amniote alignments and the 33-way placental mammals ones (these include all the low-coverage genomes). You can filter the elements you want by using the argument type:
http://www.ensembl.org/das/Homo_sapiens.GRCh37.constrained_element/features?segment=13:32889611,32973347;type=33_eutherian_mammals

Read more on DAS or on the multiple alignments and constrained elements.

Ensembl Events in June 2010

2010-05-25T09:43:00.002+01:00

In June we will have the following Ensembl events:

2-4 June: Ensembl module in the EBI Bioinformatics Roadshow at Charles University, Prague, Czech Republic
10 June: Browser workshop at Gothenburg University, Sweden
11 June: Browser workshop at Gothenburg University, Sweden (satellite of the European Human Genetics Conference 2010)
12-15 June: Presentation at the European Human Genetics Conference 2010
14-18 June: Ensembl module in the Joint EBI - Wellcome Trust Bioinformatics Summer School, Hinxton, UK
22-23 June: Browser workshops at the German Cancer Research Center (DKFZ), Heidelberg, Germany
23 June: Browser workshop at Trinity College Dublin, Ireland
25 June: Browser workshop at the Ludwig-Maximilians University, Munich, Germany
30 June - 1 July: Browser workshop at the University of Ljubljana, Slovenia

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Which whole-genome multiple aligner? Pecan!

2010-05-24T11:47:00.005+01:00

Comparing and assessing the quality of whole-genome multiple alignments is a difficult task. In the protein world, many mathematical models are available. They are based on synonymous and non-synonymous substitutions and the physicochemical similarities among the aminoacids. None of this can be applied to non-coding sequences, the 99% of the human genome.

There are two main trends for whole-genome alignments. Authors have either used genomic features like ancestral repeats or have developed phylogenetic models to generate synthetic sequences for which the "real" alignment is known.

Two articles have been published recently, one proposing a new method based on artificial sequences (Kim & Sinha, BMC Bioinformatics 2010, 11:54) and the other one looking at the coverage, agreement and accuracy of the alignments in the ENCODE pilot regions (Chen & Tompa, Nature Biotechnology 2010, doi:10.1038/nbt.1637).

According to both studies, Pecan is the strongest contender, showing the clear advantage of using a consistency-based approach (see Paten et al., Genome Res. 2008, 18:1814-28) to align the sequences.

Musing about Fish Alignments.

2010-05-21T13:10:00.002+01:00

Release 57 saw the release of a 5-way EPO alignment across the telost fish - Zebrafish, Stickleback, Medaka, Tetraodon and Fugu. Just recently I've spent some time browsing through them. They are very interesting, with the ancestral duplication in Fish showing more complex homology relationships than in mammals. Here's a nice, clean example

Simple Fish multiple alignments

Here is a far more complex region, when ENREDO has clearly picked up the ancestral duplication but is struggling to make it colinear across the entire region

Complex Fish multiple alignments

One thing which I don't think most people appreciate is the incredible phylogenetic depth in the telost linage. In terms of "millions of years of evolution" or "sequence divergence" actually the deepest splits in the telosts - such as ZebraFish to Stickleback - are almost as deep as telosts to mammals - certainly deeper than birds to mammals. So this is asking alot to find good, clearly co linear stretches, in particular when you think of the draft nature of these genomes.

Chatting to Javier, it might be much better to also look at a 4-way EPO on the "Stickleback" side of the telost linage, in other words, Medaka/Stickleback/Fugu/Tetraodon. This I think will come together better (in fact most of the "nice" regions in the 5-way EPO are actually regions without ZebraFish) and we might be able to look at taking that ancestral chromosome ordering and perhaps sequence in comparisons to Zebrafish.

Ensembl, Xfam and HMMs

2010-05-14T16:27:00.003+01:00

This week, Albert Vilella and myself participated in the Xfam consortium meeting. The meeting focussed on protein, domains and ncRNA classification, and on the new developments of the HMMER package.

Although Ensembl is not part of Xfam, we share many interests. We are getting increasingly interested in the use HMMER models, especially since the release of HMMER3.0. Also, in the forthcoming release (version 58), Ensembl will provide gene trees for ncRNAs. Most of these ncRNA genes are annotated using Rfam models.

Stay tuned for more!

Neandertal Genome Browser

2010-05-11T00:17:00.002+01:00

In collaboration with the Neandertal Genome Project, we have created an Ensembl-style browser of the Neandertal data available at http://projects.ensembl.org/neandertal. A draft sequence of the Neandertal genome was published in the May 7 issue of Science.

The Neandertal browser includes the ability to visualise the Neandertal data using the new Resembl code developed in collaboration with Illumina. The Resembl code will be introduced in the 1000 Genomes browser later this month and in Ensembl over the summer.

Data include:
- Neandertal sequencing reads from all 6 Neandertal fossils
- Neandertal contigs/consensus from all individuals combined
- Modern human sequencing reads to put the divergence of the Neandertal genomes into perspective
- Selective sweep scan to detect positive selection in early modern humans
- A catalog of changes consisting of Neandertal alleles for positions of non-synonymous difference between human and chimpanzee

Full details of the data types and instructions for using our new display tools are available on the data information page.

Links are also provided from the Neandertal Browser home page to the raw sequence data stored at the EBI for the Neandertal genome project and the modern human genome data.

Further information about the project is available from the project page at Max Planck Institute for Evolutionary Anthropology, from the genome paper and from other companion papers in the same issue of science.

We thank Janet Kelso, Ed Green and Udo Stenzel at the MPI for assistance and Eugene Kulesha at the EBI for work to create the Neandertal browser.

SNPedia in Ensembl

2010-05-06T10:36:00.006+01:00

Ensembl is always extending the variation pages to include more information. Did you know that the latest data from SNPedia is now available?

SNPedia is a wiki-style resource for human genetics with public annotation of over 11,000 SNPs, released under a Creative Commons style license. We have integrated it into Ensembl, so you can view these SNP reports along with our other information including variations, genotype and allele frequencies from dbSNP, and SNPs from other sources including UniProt, Affymetrix and Illumina chipsets and phenotype annotations from several genome-wide association studies.

You need to configure the page to view SNPedia. From the variation page, e.g. rs1333049, click on "Configure this page" and then click on "External Data" to select SNPedia to appear in the left hand side menu of all variation pages via DAS. As this information comes directly from SNPedia via DAS it is always up-to-date.

Eyjafjallajökulled?

2010-04-28T12:35:00.003+01:00

This could be come a new word in English is it becomes more frequent... well whilst most of Europe was grounded (and some colleagues from Ensembl stranded throughout the world) we only had to postpone one workshop... And our tour of Australia continued (we only had domestic flights and these weren't disrupted), coming to an end this week (I'm flying to Canberra where the ANU is hosting the last of the series).

Great feedback (thanks for filling those surveys, guys!), and our SNP Effect Predictor tool is becoming very useful, this trip also gave us a a chance to test (first hand) the speed of access to the browser and API from Australia.

This coming month, as Bert has already posted, we are attending a couple of conferences in France, if you are attending the Paris workshop (it may not be too late to register if you plan to be in town) you will have to clear security (it's hosted at the UNESCO at the end of the day), so come early (with your passport or ID card), we are also running a workshop in Montepellier (thanks to HUGO and specially Cathy for this one).

Back to Europe soon,

ǝsoX

Ensembl Events in May 2010

2010-04-23T17:03:00.004+01:00

In May we will have the following Ensembl events:

3-4 May: Ensembl module in the EBI Bioinformatics Roadshow at the Dana-Farber Cancer Institute & Harvard School of Public Health, Boston, MA, US
6 May: Demo for the National Genetics Reference Lab, Manchester, UK
10 May: Browser workshop at the 3rd Variome Project Meeting, Paris, France
10-12 May: Ensembl module in the Wellcome Trust Open Door Workshop - Working with the Human Genome Sequence in Hinxton, UK
11 May: Ensembl Genomes module in the EBI Bioinformatics Roadshow at the Scottish Bioinformatics Forum, Edinburgh, UK
17 May: Browser workshop at the Human Genome Meeting 2010, Montpellier, France
18-20 May: Ensembl module in the EBI Bioinformatics Roadshow at the CSC - IT Center for Science, Helsinki, Finland
18-20 May: Ensembl Genomes module in the EBI Bioinformatics Roadshow at the CSC - IT Center for Science, Helsinki, Finland
27-28 May: Browser workshop at the University of Cambridge, UK

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Shortcut addresses for Ensembl versions

2010-04-23T15:45:00.002+01:00

Want to be sure you are going to the right version of Ensembl? Whilst our archives can be accessed through the link at the bottom of each page, if you want to cite a particular version or access it directly, you previously needed to know the month and year of release to find the archive site (e.g. may2009.archive.ensembl.org).

Now, for the convenience of our users, we have introduced shortcuts that include the version number instead of the date. For example, typing:

e54.ensembl.org

into your browser will redirect you to the same May 2009 archive.

We have put these redirects in as far back as e30 - if the archive no longer exists, you will be directed to the next most recent one (unless doing so would mean a change of assembly, in which case you are redirected back to the last archive on your chosen assembly, if available).

P.S. Don't forget the 'e' at the beginning - we can't use plain numbers as it causes problems with DNS servers

¡ə Ensembl Down Under

2010-04-12T12:38:00.006+01:00

Ensembl is running a series of workshops in Oz, starting today in Melbourne at the VLSCI (tomorrow we have a couple of seminars at the WEHI and Peter MacCallun). Later this week we will have a further workshop in Adelaide, to continue next week in Sydney, Brisbane and Canberra. So if you are in the area, why don't you come around?

Furthermore, we took this opportunity to finished the details of another coming workshop in Paris hosted by the Human Variome Project where in addition to Ensembl we will discuss other EBI resources such as EGA. There are still some seats available if you happen to be in Paris in May

Greetings from Melbourne.

Ensembl Events in April 2010 - Ensembl goes Down Under

2010-03-25T14:25:00.007Z

When we show during workshops a map of the world with the places that have been visited by the Ensembl Outreach team, people are often surprised that we never have been to Australia yet. Well, coming month this is going to change as two of my colleagues will travel to Down Under for a whole series of workshops:

12 Apr: Browser workshop at the University of Melbourne
15-16 Apr: Browser workshop at the University of Adelaide, Adelaide
21-22 Apr: Browser module in the PANDA workshop at the University of New South Wales, Sydney
23 Apr: Developers workshop at the University of New South Wales, Sydney
27-28 Apr: Browser module in the PANDA workshop at the University of Queensland / Griffith University, Brisbane
29 Apr: Developers workshop at the University of Queensland / Griffith University, Brisbane
29-30 Apr: Browser workshop at the Australian National University, Canberra

Aside from that there are many more Ensembl events in other parts of the world this month:

7-9 Apr: Browser module in the EBI Bioinformatics Roadshow at the University of Florence, Florence, Italy
15-16 Apr: Browser workshop at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands
19 Apr: Browser workshop at the VIB Flanders Interuniversity Institute of Biotechnology, Leuven, Belgium
20 Apr: Browser workshop at the VIB Flanders Interuniversity Institute of Biotechnology, Ghent, Belgium
20-21 Apr: Browser module in the EBI Bioinformatics Roadshow at the Dana-Farber Cancer Institute, Boston, MA, US *postponed to 3,4 May*
21 Apr: Developers workshop at the Hubrecht Institute, Utrecht, The Netherlands
22-23 Apr: Browser module in the EBI Bioinformatics Roadshow at the Harvard School of Public Health, Boston, MA, US *postponed to 3,4 May*
26-27 Apr: Browser module in the EBI Bioinformatics Roadshow at Northwestern University, Chicago, IL, US
28-30 Apr: Developers workshop at the University of Cambridge, Cambridge, UK
29-30 Apr: Browser module in the EBI Bioinformatics Roadshow at the University of Pennsylvania, Philadelphia, PA, US

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Genomics and Transcriptomics in Mexico

2010-03-19T14:07:00.009Z

As part of the EBI Roadshow training programme, Ensembl teamed up with ArrayExpress to run workshops for students, postdocs, and professors at ITESM, UNAM, and CIBNOR in these bioinformatic tools. The response was very positive. Feedback from 86 participants includes comments such as:

"I am an undergraduate student, and know little about bioinformatics. In the future, I will be able to use EBI as my primary resource."

"It is a really good opportunity to now get all these tools, to help facilitate understanding and analysis of scientific data"

"An excellent course, and very useful tools!"

Ensembl and ArrayExpress were ranked by 99% of participants as being useful to their work. Not only are people made more aware of individual projects through these workshops, EBI resources are publicised. 31% of our participants were unaware of EBI resources before the workshop, which contrasts to 95% responding that after this workshop, they would most likely use EBI resources. 88% of participants would like more training in these resources and others; specifically mentioned were ontologies, proteomics, and genome sequencing as topics to learn more about. This reflects a need for bioinformatics courses in the life sciences in that part of the world, if not in all the world.

And finally, an after-effect of the workshops was to prove that there is a lot of interest in bioinformatics. This from our host at CIBNOR:

"CIBNOR is in a growing stage, we have a project for an Innovation and Technology Park and I am trying to convince people about the need for a Bioinformatics Unit. I am sure that things like this course will help us a lot."

We greatly enjoyed training in Mexico, because of all the keen interest, energy, and the evenings on the sand dunes. We took the course into the field, discovering a pufferfish and spine on the beach, in honor of vertebrate genomes!

Orthologues on the trees

2010-03-11T13:09:00.002Z

We have added a little trick for orthology-lovers. Starting from the orthologues page, you can choose to switch to the GeneTree. This will highlight the orthologue of interest, as well as the ancestral node that relates both genes.

Another useful feature added in Ensembl 57 is the possibility to display a set of genes (up to 10) using the Multi-Species view. Click on an internal node and select the "Jump to Multi-species view" option. This will show each of these genes in their respective genomic location, with genomic alignments when available.

New avian and new fish mutliple alignments

2010-03-11T05:37:00.005Z

Ensembl 57 includes the turkey genome, the third bird in Ensembl. We are now providing a 3-way avian multiple alignments (chicken, turkey and zebra finch) together with GERP constraint analysis. The image shows amniote and bird constrained elements on the chicken genome.

We have also added a new set of fish multiple alignments (stickleback, medaka, takifugu, tetraodon and zebrafish). GERP constraint analysis is available on fish genomes as well.

Gene Trees now have intron ticks.

2010-03-10T20:56:00.003Z

The gene tree images now have little intron "ticks" on them showing how the intron position is placed relative to the protein sequence. An example is shown above. Each tick is a little black line on each side of the green protein bars, on the right. As intron positions have been remarkably stable on the "chordate" side of the metazoan tree (ie, the deutrosomes), one should expect that the introns line up - if they do, it is good evidence that the alignment is right.

There are some interesting things. Ensembl models small frameshifts to create open reading frames around erroneous data as tiny introns. In this code you cannot distinguish these two classes of introns, but as these errors normally come in patches, a run of intron ticks unique to a genome is probably a set of errors (an example is in Gorilla). I've enjoyed browsing around some of my favourite genes to check out that the introns make sense.

There is some more to go here. The fact that the intron ticks disappear on collapsed nodes is a bit frustrating - it would be nice to see "consensus" intron positions (though this is a bit complex to execute underneath).

Ensembl browser workshop at ESHG 2010

2010-03-09T11:09:00.004Z

The Ensembl Outreach team is pleased to offer a 1-day Ensembl browser workshop as a satellite to the European Human Genetics Conference 2010 that is held from 12-15 June in Gothenburg, Sweden. The workshop will be held on Friday 11 June at Gothenburg University and is free of charge for conference participants. Places are limited to 30 participants. More details can be found here.

Ensembl Genomes Release 4

2010-02-24T14:18:00.002Z

We are pleased to announce the fourth release of Ensembl Genomes.

Ensembl Genomes is a companion project to Ensembl designed to provide access to genome scale data for non-chordate species of scientific interest.

Features of the new release include the addition of new databases for the bread mould Neurospora crassa to the Ensembl Fungi division, the slime mould Dictyostelium discoideum (built with the assistance of dictyBase) to Ensembl Protists, and the body louse Pediculus humanus (containing data provided by VectorBase) to Ensembl Metazoa.

The release also includes new variation databases for Drosophila melanogaster (using data from the Drosophila Population Genomics Project) and Plasmodium falciparum; the update of existing variation databases for Arabidopsis thaliana and Vitis vinifera in Ensembl Plants; and the addition of three new clades to Ensembl Bacteria.

Ensembl Genomes is available at http://www.ensemblgenomes.org

Ensembl Events in March 2010

2010-02-15T09:47:00.005Z

In March we will have the following Ensembl events:

1-2 Mar: Ensembl module in the EBI Bioinformatics Roadshow at ITSEM, Mexico City, Mexico
3-5 Mar: Ensembl module in the EBI Bioinformatics Roadshow at UNAM, Mexico City, Mexico
4 Mar: Ensembl demo at the EBI Open Day in Hinxton, UK
8-12 Mar: Ensembl module in the EBI Bioinformatics Roadshow at CIBNOR, La Paz, Baja California, Mexico
9-12 Mar: Ensembl module in the Wellcome Trust Open Door Workshop - Working with the Human Genome Sequence at the Instituto de Higiene, Montevideo, Uruguay

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Ensembl Developers workshop 28-30 April 2010 in Cambridge, UK

2010-02-01T16:50:00.004Z

From Wednesday April 28th till Friday April 30th 2010 we will give another Ensembl Developers workshop at the Genetics Department of the University of Cambridge in the UK. This 3-day workshop will cover the Ensembl Core API as well as two other APIs, which will be chosen from the Compara, Variation and Functional Genomics APIs, depending on the majority interest of the participants. For the workshop some experience with coding in Perl is required. There are no costs for the workshop (and organiser David Judge will even provide lots of free coffee, tea, orange juice, water, cookies, fruit etc. to keep you going ....).

To register for this workshop, please go here.

If you have any questions about the workshop you can mail me.

Calling all Americans (and Australians/NZ/Pacific Rim...)

2010-01-25T16:12:00.003Z

For about 3 weeks now researchers in the US have had their default Ensembl go to our US west mirror (uswest.ensembl.org) automatically - if you just go to www.ensembl.org you brower gets automatically redirected. The US joined Japan and Canada who we switched in late 2009.

From our perspective, this is all working fine; the usage of uswest has gone up, and IP tracking on that shows far more US IP addresses (so the redirect is working fine!). We get some 3,000 odd visits a day, with some 50,000 pages delivered from our uswest site - about 20% of our total hits. Brilliant.

What is slightly more surprising is that we're not getting any queries on this. Given the usage, we think this means the default browser, content and other functionality must be working well (or Americans are very shy about complaining... but that doesn't sound like a good description of all Americans...). But we'd also like to hear from American users - have you noticed ensembl "go faster?". Are there any glitches?

Another issue we are unclear about is whether we should automatically shift other users on the Pacific Rim to automatically go to uswest - in terms of usage, the biggest country would be Australia, but New Zealand, Phillipines and other Pacific Rim countries would also be candidates. It's quite hard for us to assess whether our Europe (Cambridge UK) based servers or US west servers are best for this - both latency and throughput changes on different routes, and the time zone shift makes things complex to assess systematically in an easy way.

So - feedback welcome - either on this post or to helpdesk@ensembl.org about what your experience is, either from the US or from the pacific rim.

Ensembl Events in February 2010

2010-01-22T04:40:00.004Z

In February we will have the following Ensembl events:

3-4 Feb: Ensembl module in the EBI Bioinformatics Roadshow at the University of Aberdeen, Aberdeen, UK
11 Feb: Browser workshop for the NHS at Western General Hospital, Edinburgh, UK
11-12 Feb: Browser workshop at the University of Cambridge, Cambridge, UK
16-18 Feb: Ensembl module in the EBI Bioinformatics Roadshow at the Jozef Stefan Institute and University of Ljubljana, Ljubljana, Slovenia
22-26 Feb: Ensembl API module in the Hands-on training at EBI - Programmatic Access To Biological Databases (Perl), Hinxton, UK

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Ensembl Events in January 2010

2009-12-16T09:46:00.003Z

For the beginning of the new year we have the following Ensembl events lined up:

9-13 Jan: Ensembl & Ensembl Genomes demo at the Plant and Animal Genome Conference XVIII, San Diego, CA, US
19-20 Jan: Ensembl module in the EBI Bioinformatics Roadshow at City of Hope, Duarte, CA, US
25-27 Jan: Ensembl module in the EBI Tools for Genomics and Proteomics workshop at the Moroccan Society of Bioinformatics, Tangier, Morocco
28 Jan: Browser workshop at the University of Nottingham, Nottingham, UK

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

New on Pre!

2009-12-10T13:09:00.010Z

Updated elephant and gorilla genomes are now available on the Ensembl Pre! site.

They will be released in full with annotated gene sets in Ensembl 57 (due spring 2010). The new gorilla assembly (gorGor2) includes short-read and capillary sequences. The elephant genome (Loxafr3.0) was also updated, and is at 7x coverage. The 57 release will present new genebuilds for both species.

Release 57 rescheduled

2009-12-08T15:09:00.001Z

Ensembl release 57 has been rescheduled for mid to late February 2010.

We had originally planned for release 57 to be this week, but our final quality checks identified a significant error in the unreleased data set. Because of this, we feel that our users would be better served by rescheduling the release to ensure that we provide the best possible data resources for the community.

On behalf of everyone in the project, thank you for your continued support of Ensembl and we wish you all the very best for the holiday season and the new year.

BLAST problems

2009-11-27T10:09:00.002Z

BLAST should be available again - following the recent scripting, the server hard drive had filled up, so that it was unable to process any more requests. We have cleared some space, so the server is now able to accept tickets once again.

Please accept our apologies for the continued downtime.

SNP consequences

2009-11-24T11:04:00.004Z

Did you know that you can use the ensembl API to predict the consequences of your own SNP positions? This is a really popular question and there is some example code on the website to guide you through this. See an example here. This functionality is available from ensembl release 56 but we have also recently patched release 54 in case you need to use the NCBI 36 human assembly.
Soon there will be a page on the website where you can upload your data and we will project SNP consequences for you.

BLAST back online

2009-11-24T09:22:00.002Z

Our BLAST/BLAT service has been re-enabled, following a problem with the server hosting the BLAT logs which has now been fixed. Thank you for your patience.

Ensembl Events in December 2009

2009-11-23T12:48:00.006Z

After two extremely busy months things are getting quieter again on the Ensembl training front. For December we have the following events scheduled:

3 Dec: Browser workshop for Master's students at University College London, London, UK
9 Dec: Browser workshop at Addenbrookes Hospital, Cambridge, UK

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

BLAST unavailable

2009-11-20T16:54:00.002Z

We have had to disable BLAST temporarily owing to excessive load on the servers. The service will be enabled as soon we have analysed the problem.

BLAST back online

2009-11-17T11:51:00.002Z

We have now repaired the BLAST database and the service is once more available. We will be monitoring the situation, but hopefully no further action will be required.

Please accept our apologies for any inconvenience caused.

BLAST unavailable

2009-11-16T09:57:00.002Z

We regret that owing to problems with our BLAST server, we have had to disable this feature temporarily, as issues with tickets were bringing down the whole Ensembl website. We will endeavour to have BLAST back online as soon as possible; please accept our apologies for any inconvenience caused.

Ensembl Events in November 2009

2009-10-22T18:34:00.005+01:00

October was quite a busy month for the Ensembl Outreach team, but November is even busier:

2 Nov: Developers workshop at the German Cancer Research Center (DKFZ), Heidelberg, Germany
4-10 Nov: Ensembl module in the Computational & Comparative Genomics course, Cold Spring Harbor, NY, US
5-6 Nov: Ensembl Genomes module in the EBI Roadshow at the University of Szeged, Hungary
9 Nov: Browser workshop at the German Cancer Research Center (DKFZ), Heidelberg, Germany
10 Nov: Browser workshop at the German Cancer Research Center (DKFZ), Heidelberg, Germany
12-13 Nov: Browser workshop at the University of Cambridge, Cambridge, UK
12 Nov: Browser workshop at the Jackson Laboratory, Bar Harbor, ME, US
13 Nov: Browser workshop at the Jackson Laboratory, Bar Harbor, ME, US
13 Nov: Presentation at the Jackson Laboratory, Bar Harbor, ME, US
16 Nov: Browser workshop at Harvard Medical School, Boston, MA, US
17-18 Nov: Ensembl module in The Genome Access Course, Cold Spring Harbor, NY, US
18 Nov: Presentation for EBI/EMBL Ph.D. students, Hinxton, UK
24 Nov: Browser workshop at the Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
26-27 Nov: Developers workshop at the Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
26 Nov: Browser workshop at the Royal Veterinary College, London, UK
28 Nov: Browser workshop at CEINGE Biotecnologie Avanzate, Naples, Italy
30 Nov - 1 Dec: Ensembl module in the Wellcome Trust Open Door Workshop - Working with the Human Genome Sequence, Hinxton, UK
30 Nov - 2 Dec: Developers workshop at the University of Cambridge, Cambridge, UK

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Aloha ASHG

2009-10-19T07:36:00.002+01:00

From this little corner of the world Ensembl will be delivering an Interactive Workshop on Friday (October 23rd) from noon (12.00) in Room 315 in the Convention Center. If you want to attend, let us know as seating is restricted and we are allocating seats until the room is full. You must bring a laptop with a wireless card (and a fully charged battery).

Furthermore, you can also visit us on booth 432 where we will be happy to help you and get any feedback.
Mahalo

Ensembl Genomes Release 3

2009-10-08T09:05:00.001+01:00

We are pleased to announce the third release of EnsemblGenomes, which includes the first release of two new Ensembl-based portals, Ensembl Plants and Ensembl Fungi.

These complete the span of Ensembl Genomes portals across the taxonomic space, complementing the coverage of vertebrate genomes available through Ensembl.

Ensembl Plants has been built in collaboration with Gramene and includes the genomes of six monocots and two dicots. Variation databases are available for four of these species.

Ensembl Fungi includes a new build of the Sacchromyces cerevisiae genome using the latest data from SGD, including variation data derived from the Saccharomyces Genome Resequencing Project; and Ensembl databases for Schizosaccharomyces pombe (built in collaboration with GeneDB_Spombe) and eight species of Aspergillus (built in collaboration with the Central Aspergillus Database Repository, CADRE).

User upload databases are now operational for Ensembl Protists, Fungi, Plants and Metazoa, allowing users to visualise their own data in the Ensembl environment.

Ensembl Genomes release 3 has been built using Ensembl 55 software. We aim to synchronise with Ensembl with our next release (Ensembl Genomes 4/Ensembl 57), and to stay synchronised thereafter.

Genomewide comparative displays

2009-10-01T12:14:00.007+01:00

When we changed our look and feel almost a year ago, we "left behind" our two main graphical genome-wide comparative genomics displays (our textual comparative genomics displays remains, as did some of the gene centric ones). These were some of the most complex displays, not only in the graphics layout but also in aspects such as configuration - with comparative genomics tracks with up to 30 species, potentially one has the union of all tracks in each species, and doing this consistently required reworking how we thought about the "same" or "different" tracks across species.

It's taken longer than we thought it would, but finally in release 56 these displays are back and better than ever. With more aggressive caching of data items as they head to the web (and, in addition, if you are on the west coast of the US or the Pacific Rim, check out the US west mirror at uswest.ensembl.org) they go far faster, making them far more useable.

We have two fundamentally different ways of thinking about genomic alignments.

In "Multi Sequence View", which works fundamentally as a set of pairwise alignments, we maintain the linear sequence of each genome, and then draw regions which are conserved between them. Check out displays like:

Mouse/Human

And make sure you hit "Configure Page" and in the Comparative Genomics section, switch on blastz. I also like to have genes in "Collapsed, labels" (so alternative splicing doesn't produce excessive displays) and also switch on Regulatory Features.

Now - you get a nice picture of this region in human and mouse. The orthologous gene (PECI) has conserved exons, and the regulatory features at the start of this gene is conserved in human and mouse and both cases classified as a promoter. All as expected.

But a closer look shows that the transcript going by the catchy name of AC123437.5 in mouse, going on the opposite strand has some of its exons overlapping to the human PECI, and Human PECI is duplicated into two local genes here. This is perhaps easier to see as one zooms out in this display (notice you can drag-and-select in the upper panels, or use the + and - bars to change in the lower panels)

Zoom Out

In contrast, the alignment (Image) view, asks you to choose one species as the co-linear
reference, and then the other species are organised specifically by the alignment of that
reference. This is ideal in more linear, orthologous regions. I like using the 10-way EPO alignment for visualisation/gene model comparison, although to go things like conservation analysis, you want to use the 31-way mammalian alignment with the low coverage data

This is gene, well conserved across mammals.

Co Linear

We can look at the precisely the same alignment from the perpsective of Mouse, Rat, Dog, Horse, Human, Pig. In each case, the alignment is unbiased to each species. For example, the Mouse-Rat portion of this multiple alignment still aligns the unique rodent portions.

Here is that same region from the perspective of Cow:

Cow

Notice when you go to human you have a choice of not only 4 different multiple alignments - a 4-way primate alignment, a 10-way mammalian alignment, a 12-way alignment including chicken and 31-way mammalian alignment, but also 40 odd other individual pairwise alignments.

In each case, you can get the alignment out as text - here's a 4-way primate alignment:

Text alignment

or the same region in a 31-way glory

31 one way text

Of course, all this information is also available to download or access through our Perl API. A particularly interesting thing in these alignments is the ability to switch on the ancestral sequence as well (go to the configuration panel).

More on the use and power of comparative genomics later I hope, but for the moment, do enjoy these displays being back, and do both browse around and download/script against them.

Ewan

Release 56

2009-09-29T11:54:00.001+01:00

The Ensembl project is pleased to announce release 56 of Ensembl (http://www.ensembl.org/). Highlights of this release are:

Reintroduction of our multi-species views. Alignments (image), formerly alignsliceview, shows pairwise or multiple alignments from the Ensembl Compara database, highlighting any gaps in the alignment.

Multi-species view, formerly known as multicontigview, displays pairwise alignments without gaps; multiple pairwise alignments can be configured to create a multiple alignment display. As well as genes, other types of features such as regulatory features can be displayed in this view, making this a very useful display for comparative genomic analysis.

A new tab has been added in release 56 based on a Regulatory Feature object. This will enable better display some of the data underlying the Ensembl regulatory build. The new pages are accessed from the gene displays by clicking on the 'Regulation' link in the left-hand menu and then clicking on a regulatory stable ID in either the image popup menus or the table.

From release 56, users can upload wiggle plot data in WIG and bedGraph formats and view this data on various location-based views. At the moment, only a single style, "wiggle", is available on Region in Detail, whereas a selection of density plots are available on whole chromosome and karyotype images. In addition, Region in Detail now supports greyscale rendering of BED scores via the useScore parameter in the file, and rendering of features in different colours via the itemRgb parameter and per-feature values.

New data in this release includes gene sets on two new species (Pig and Marmoset) and a new gene set on the existing Rat Rnor3.4 assembly. Also in this release is an updated human gene set which includes all the Havana manual annotation in the merge with the Ensembl automatic annotation set. This set represents the Encode project GENCODE 3b gene set. Also included is a new human variation database based on dbSNP 130 and mapped to assembly GRCh37.

For more information on these and other new features in this release visit:

http://www.ensembl.org/info/website/news/index.html

Ensembl website downtime

2009-09-28T12:13:00.002+01:00

We are currently in the process of releasing Ensembl 56, and should be back online within an hour or so.

Please note that all Ensembl-based sites will be offline at this time whilst we upgrade our user account database. Affected sites include Vega, Pre, the Ensembl archives and the US mirror. Please accept our apologies for any inconvenience caused.

Thanks!

Ensembl events in October 2009

2009-09-18T15:46:00.006+01:00

In October Ensembl will feature on 4(!) different continents:

7 Oct: Browser workshop at the Centro de Biologia Molecular Severa Ochoa, Madrid, Spain
9 Oct: Browser workshop at the Instituto de Biologia Molecular e Celular, Porto, Portugal
12-15 Oct: Ensembl module in the Wellcome Trust Open Door Workshop - Working with the Human Genome Sequence, Bangkok, Thailand
20 Oct: Demo for the National Genetics Reference Lab, Manchester, UK
20 Oct: Ensembl module in the Hands-on training at EBI - A dip into EBI resources: understanding your data - New resources and Future Directions, Hinxton, UK
22-23 Oct: Browser workshop at the University of the Witwatersrand, Johannesburg, South Africa
23 Oct: Demo at the ASHG 2009 meeting, Honolulu, Hawaii, US
23 Oct: Developers workshop at the Bejing Genomics Institute at Shenzhen, China
27 Oct: Browser workshop at the Centro Nacional de Investigaciones Oncológicas, Madrid, Spain *postponed to 24 Nov*
27-28 Oct: Browser workshop at Cape Biotech, Cape Town, South Africa
30 Oct - 2 Nov: Developers workshop at the CSHL Genome Informatics 2009 meeting, Cold Spring Harbor, NY, US

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

NCBI36 Ensembl Site

2009-09-15T11:58:00.002+01:00

Ensembl announces the release of http://ncbi36.ensembl.org. This Ensembl site is for users who still need access to the NCBI36 human assembly. It is actually a complete copy of the Ensembl 54 release which was the last Ensembl release containing NCBI36.

Although access was already possible through the Ensembl archive sites, the new ncbi36.ensembl.org site will provide better performance because it is running on separate hardware. Also ncbi36.ensembl.org provides Blast/Blat search support which the archives do not.

The main reason we have provided a dedicated site for NCBI36 is for two large projects (Encode and 1000 Genomes) which have some of their data aligned on this assembly. ncbi36.ensembl.org will only be up for as long as there is significant need for it. We will be reviewing usage in Spring 2010 and currently plan to remove the site by Summer 2010. After that time users will still be access the NCBI36 assembly via the archive sites, there just won't be a dedicated site for it anymore.

Ensembl events in September 2009

2009-08-21T14:53:00.010+01:00

The Summer holiday time is almost over, so the Ensembl trainers are getting up to speed again in preparation for Autumn, which will be the busiest time of year for them.

The coming month we will have the following Ensembl events:

7 Sep: Demo for the National Genetics Reference Lab, Manchester, UK
7-10 Sep: Ensembl module in the EBI roadshow at the University of Tartu, Tartu, Estonia
16-17 Sep: Browser workshop at the Erasmus MC Molecular Medicine Postgraduate School, Rotterdam, The Netherlands

For details about these and other upcoming events, please have a look at the complete list of Ensembl training events.

Do you want to attend an Ensembl workshop, but are we never coming to your part of the world? Why not see if you can host a workshop at your own university / institute? For more information have a look here or mail us.

If you are in the Western US, we also may still be able to include your university / institute in our Western US tour coming January. Interested? Please mail me for more details.

EnsemblFungi (beta) now available...

2009-08-19T10:31:00.019+01:00

In addition to Release 2 of Ensembl Genomes early this month, EBI-EMBL would also like to announce the new arrival of Ensembl Fungi (beta).

Release includes:

2 yeast genomes: Saccharomyces cerevisiae and Schizosaccharomyces pombe.

7 Aspergillus genomes A.clavatus, A.flavus, A.fumigatus, A.niger, A.oryzae, A.terreus and Neosartorya fischeri.

If you have any comments or feedback please do not hesitate to contact us at helpdesk@ensemblgenomes.org.

BLAST downtime now over

2009-08-07T19:51:00.003+01:00

To our BLAST users,

BLAST is online again, the maintenance is finished.

Thank you for your patience.

The Ensembl team.

We have scheduled some downtime for our BLAST database servers on Monday 10th August *Postponed to Tuesday, 11 Aug*, in order to install some security patches. We will also be trying out an upgrade path and pushing that out to the main BLAST server if it proves compatible. There will be a downtime of between 30 minutes and 12 hours, depending on how smoothly the maintenance goes. The rest of the Ensembl website should be unaffected.

We suggest that you avoid running BLAST or BLAT searches in the 48 hours preceding the maintenance work as we cannot guarantee that data will not be lost. We will update this post as soon as the maintanance has been finished.

Thank you for your patience,
The Ensembl Team

Ensembl Genomes: Release 2

2009-08-06T10:22:00.003+01:00

EMBL-EBI is pleased to announce release 2 of Ensembl Genomes; extending Ensembl further across the taxonomic space!

Highlights for this release include:

9 new genomes of Escherichia species; 4 new Bacillus and Streptococcus genomes; and additional genomes of Mycobacterium and Staphylococcus genera added to Ensembl Bacteria; taking the total bacteria species/strain count to 134.

Bacillus subtilis now represented using the re-annotation by Barbe et al. (Microbiology 155 2009, 1758-1775).

New Plasmodium falciparum build based on the current release of PlasmoDB, 5.5.

Updated build of Drosophila melanogaster and the inclusion of 11 additional drosophilid species, based on Flybase release FB2008_10

Updated build of Caenorhbditis elegans, and the inclusion of 4 additional Caenorhabditis species, based on WormBase release WS200

Comparative genomic analyses (bacteria, protist, metazoan and pan-taxonomic Compara databases) updated.

Ensembl 54 software

Keep an eye out for Release 3 in September, which will include plants and fungi...

West Coast Mirror

2009-07-21T09:41:00.003+01:00

This year we've invested in our own mirror - maintained by us - on the west coast of the US. This was mainly because assessing the web return time for our users showed a consistent additional 3 to 4 seconds if you were lucky enough to live out on the west coast (worse still if you are in Australia!). Although we did alot last year to improve the general response time of our web pages (for example, compressing our CSS and Javascript down to single files for the whole site, so these are only loaded once and then cach'ed locally), the Ensembl site delivers alot of dynamic content - and nothing but getting closer to the users can help this.

You can reach the site directly at uswest.ensembl.org or alternatively there is a little "world" icon on the top right of the page which switches to the star-and-stripes when you're on the west coast. Having the mirror not only helps our users who are on the west coast but also provides resilience when our main site goes down. As we're responsibile for provisioning it in-sync with our main site (its part of our release process) this mirror will stay current with the main site.

In some sense the mirror should be a low cost "per user" for us having the mirror - if users go to the mirror, it means less load on the main site, and so it's really how we distribute the "web farm" that sits behind Ensembl geographically. However, there are overheads from hiring rack space in the US to making our own release cycle more complex. This means we will need to assess whether running a US mirror makes sense in the long term. Our instinct is yes, but we need hard data on this.

These things need time to pick up, but already we'd be interested in feedback on this - for US users, is this site faster for you - in particular for East coast people who we think are probably still best off on the main site. Does it change with time of day? For Pacific rim users - Japan, Singapore, Korea, Australia - is the west coast site snappier for you? We'll be putting in place our own monitoring schemes, but user feedback is always good...

Ensembl browser workshops Western US January 2010

2009-07-20T15:50:00.003+01:00

The Ensembl Outreach team is currently looking into the possibility of giving some 1-day Ensembl browser workshops in the Western US in the period directly after the Plant and Animal Genome Conference in San Diego, which takes place from 9-13 January 2010. Hosting institutions would only have to pay the instructor's expenses (accommodation and subsistence) and would share the domestic travel costs, but we would not otherwise charge for the workshops.
For more information about our browser workshops, please have a look here.
Interested? Please contact me for more details at bert@ebi.ac.uk.

Release 55

2009-07-15T10:30:00.004+01:00

The Ensembl project is pleased to announce release 55 of Ensembl. Highlights of this release are:

* New GRCh37 human assembly;
* Wallaby 2x genome;
* Ability to display uploaded data on individual chromosomes or whole karyotype.

For more information visit our What's New page.

Ensembl Regulatory Features - now Martable

2009-07-14T17:27:00.004+01:00

Release 55 has lots of goodies - not least the new, coordinated, GRCh37 assembly (more on that later), but one addition is the Martability of Ensembl Regulatory Features. Regulatory features are on by default on Human and Mouse, and each gene has a specific page for the regulatory features (for example http://www.ensembl.org/Homo_sapiens/Gene/Regulation?g=ENSG00000139618). Regulatory Features are developing fast, and the Martability is bringing out the richer information in the functional genomics database - for example, the classification of features into "promoter", "gene associated" and "unclassified". Next release we're hoping to release a more graphical view for each feature, but the present of the regulatory features in Mart allows the large scale users - from Perl, Java, R or just plain-only tab delimited text - to use them.

We're expecting alot of development in this area - the addition of Mouse DNaseI sites has allowed us to develop a Mouse build, and of course, the ENCODE project which is now on line in production mode will provide a far richer, deeper, dataset to work against.

So - watch this space.