Neandertal Genome Browser

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

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?

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

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

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

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

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

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

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

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.

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

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

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

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

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...)

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

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

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!

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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...

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

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

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

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

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

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

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.

More about the world of Ensembl

Who is using us?

During the long flight from London to Seoul, where I'm now giving workshops, I had time to do some analysis.

We have recently changed the way we analyse traffic on our website. Urchin Software allows us to pinpoint access to our site with more accuracy. (In a previous post, I showed data where some domains were excluded in the representation).

This month's data (June 2009) is more comprehensive and can be shown with the following heatmap. Again, dark-coloured countries show more use than lightly shaded ones. We can now detect some low level traffic in the African continent missed in previous analyses.

Following a recent thread, I normalised these data taking into account population. (Did I mention how long the flight from London to Seoul actually is?) This puts the Netherlands as the country with the highest ratio of Ensembl users normalised by population, followed by Sweden, Switzerland, the United Kingdom, Finland, Belgium, Iceland, Germany, Denmark and Singapore (the first non European country in the list) pushing the United States (excluding traffic from the US mirror) to the 15th position.

On another matter, I'm glad to see that our user base in this country is well established. Apart from the obvious Seoul, we can also see access from Taejon, Kwangju, Taegu, Pusan, Inchon, Pohang and up to 29 locations in the country, and following these workshops we hope this will increase further.

As they say over here 안녕

Xosé

Go, go, go .... the new Ensembl ontology database and API

Starting with release 55 of Ensembl we provide an ensembl_ontology database. It replaces the older ensembl_go database which used to be loaded straight from the public table dumps provided by the Gene Ontology group (and hence wasn't really an Ensembl database to start with). The associated API is now part of the Ensembl Core API, which should make working with GO terms in Ensembl more straightforward than it was in the past. Available methods include, amongst others, fetching all parent or child terms of a given GO term and fetching all genes, transcripts or translations annotated with a given GO term.

More detailed documentation on both database and API can be found at ensembl/misc-scripts/ontology/README.

Credit for developing the ensembl_ontology database and API goes to Andreas Kahari of the Ensembl Software team.

Colourful gene trees

We have some news for the forthcoming ensembl release. We have added a few more display options for our gene trees. It will be possible to colour the background of the trees based on the taxonomy. It will be much easier to locate orthologues or paralogues in a given clade. For people who prefer more subtle colouring, they can choose to colour the branches instead.

It will also be possible to automatically collapse all the genes for a given clade. In the example shown in this figure, glires and diptera are collapsed. Moreover, the new version will also allow you to hide fish genes for instance or even all genes from low-coverage genomes.

All these options are configurable from the configure panel available through the 'configure page' link in the left panel.

Ensembl Workshops in July

The summer is a time for research institutions to focus on research (or go on holiday). This causes a decrease in our Ensembl Outreach and Training (at least, workshop-wise!) However, we are giving a few workshops in July.

2 July: Internal Developer's Course (let's see what the developers themselves have to say about browsing Ensembl!)
6-7 July: Browser modules in EBI roadshow, Poznan Summerschool of Bioinformatics, Poland
9-10 July: Browser workshop in Seoul, Korea (Korea National Institute of Health)
13 July: Browser workshop in Daejeon, Korea (KRIBB)
13 July: Browser workshop at Wellcome Trust Genome Campus, for campus employees
14-15 July: Browser workshop in Pusan, Korea (Pusan National University)

Don't forget, we have loads of training videos on our tutorials page (and YouTube channel!)

US Mirror

Ensembl is pleased to announce the release of its West Coast US mirror (uswest.ensembl.org). This is a full mirror of the current Ensembl 54 release. We are providing this mirror to improve performance for users in the US, particularly on the West coast. It includes full search, BioMart and BLAST support (BLAST searching is actually run at Sanger with results passed back to the mirror).

This mirror is managed directly by the Ensembl web team, and we will aim to update it along with the main site, to keep it current. Credit for gettting this mirror up goes to James Smith and Eugene Bragin from the web team, with support from the Sanger systems team, particularly Peter Clapham, John Nicholson and Dave Holland.

Future plans: We will improve the mirror in the near future by allowing users to switch between the main and mirror site. Currently, we do not suggest logging in to the mirror. All user data must be retrieved by the main site at the Wellcome Trust Genome Campus. Speed is optimal if login is not used, however this will be improved in the future.

Many thanks,
The Ensembl Team

A view of the world from Ensembl

Following our recent post updating you with feedback from our recent user survey, I wanted to share with you the following data. I've been data mining our web logs to get a picture of worldwide access to Ensembl (this is page impressions) and I put them on a heat map representing access to our browser (this doesn't include either BioMart or direct access of our public databases). I filtered out commercial IP addresses (i.e. all those .com, and .net) to simplify the analysis. Countries are shaded according to how much they accessed the Ensembl browser in the month of May. Dark countries use the Ensembl browser more, light countries, less. And this is what you get:

Can you see your country here? If not, consider running a browser workshop in order to join our wide community of Ensembl users!

This map should help us to monitor the success of our workshops (at this moment I'm writing this from Venezuela which hopefully should appear in future heat maps!) Although there are still some gaps in the map, we are happy to see that Ensembl is used globally and our efforts are recompensed. Training leads to more in depth understanding of how to use the browser, and we think our worldwide workshops are helpful in using Ensembl to guide and enhance research.

Greetings from Venezuela, or as you would say here... ¡Hasta la próxima

Xosé

Thanks for your feedback!

Dear all,

Thanks to all of you who participated in our Ensembl browser survey, which closed at well over 150 respondents. We appreciate hearing from users worldwide, and our responses came from Europe, the Americas, Asia, India, New Zealand and Australia.

We will be able to move forward based on the feedback, in order to make the browser smoother and easier to use.

Some of the things we learned.

How often do you use Ensembl?

The majority of our users (83%) access the Ensembl browser multiple times per week. (See pie chart above). A similar survey run by Ensembl in 2007 reflected a much lower figure: only 32% of users browsed as frequently, with the majority of respondents accessing the browser once a month or less. Genome browsers appear to have moved from being tentative, browse-for-interest curiousities to comprehensive resources that can be integrated into daily research.

We were pleased to see our users are accessing many types of Ensembl data, from transcripts to variations to comparative genomics. Most respondents found the tabs in our new interface to be intuitive, so we won't change those! Many users scroll through views using the buttons on each page, so again, we will keep those in place.

More of you are finding the Pre! and Archive! sites helpful. And 65% of users voted that the most important aspect was good information.

Things we will work on?

In addition to custom data and user upload advances, we are focusing on graphical display of our comparative data. These improvements are already in our pipeline. We did get some new ideas from the survey, for example, some of our respondents could not find the Pre! or Archive! pages. We will think about how to make these links more obvious.

Speed of the browser could be faster. We will keep you posted on the Ensembl mirror on the US west coast.

Finally, more users are finding our help pages and videos, including a new YouTube channel. and we will be constantly adding to the tutorials page. If you have ideas about videos or tutorials you would like to see, please send your comments to our helpdesk. We find it immensely helpful to hear feedback from our user community.

Thanks again for the view of Ensembl from our users! We will be polling again next year.

The Ensembl Team

Give us your feedback!

Hello all,

We are curious as to how our users are finding the current Ensembl web browser. We opened a survey in the current Ensembl (version 54). The survey will close in one week's time (Friday, 5 June). Thank you to everyone who has already entered their feedback.

For users who have not yet replied to the survey, we ask that you spare 10 minutes or so of your time to do so. Please give us your thoughts and feedback by clicking on the link below:

http://tinyurl.com/cv67vs

The feedback centers on the web browser, specifically the new interface launched in Nov, 2008.

Many thanks for your time.

Regards,
The Ensembl Team

Ensembl Events in June 2009

For June we have the following Ensembl events:

4-5 June : Browser workshop at the University of Cambridge, Cambridge, UK
11 June: Demo for the National Genetics Reference Lab, Manchester, UK
15-16 June: Browser workshop at the Facultad de Ciencias de la Universidad de Los Andes, Mérida, Venezuela
18-19 June: Developers workshop at the Facultad de Ciencias de la Universidad de Los Andes, Mérida, Venezuela
22 June: Browser workshop for NHS Molecular Genetics Laboratories at Liverpool Women's Hospital, Liverpool, UK
24-26 June: Ensembl module in the Bioinformatics for Vascular Biology course at the EBI, Hinxton, UK
29 June: Browser workshop at the Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany

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

Pre, Archive, and Vega downtime

Next week, 18-24 May, an upgrade is scheduled that will affect the following sites:

Archive sites versions 48-53 (Dec 2007-May 2009) (Downtime will start Monday 18 May)

BLAST and User Upload on Pre! sites (Wednesday 20 May)

BLAST and User Upload on the Vega site

We ask our users to plan to use these sites after the upgrade, if possible.

Regards,
The Ensembl Team

Ensembl 55

We are currently working on our next release which is due at the end of June 2009 and will contain the following:

Data

Human GRCh 37
We will be releasing a new genebuild for human based on the lastest assembly GRCh37 from the Genome Reference Consortium. A preliminary version of this assembly is available now in Ensembl Pre! Due to the new assembly we will have:

• Updated repeat masking
• New probeset mappings
• cDNA update
• A new ensembl-vega merge delivering a new gene set
  

Wallaby
Ensembl 55 includes the 2X genome for Tammar Wallaby (Macropus eugenii), this will be a projection build similar to our other 2X species.

C. elegans
We will also include an import of the WormBase release WS200 database for C. elegans.

Anole lizard - A gene patch incorporating the gene set provided by Chris Ponting at Oxford University means that we have a new gene set for the green anole lizard (Anolis Carolinensis).

Mouse - The mouse cDNA alignments have been updated.

Zebrafinch - There will be an updated gene set for the 6X zebra finch genome.

Zebrafish - Non-coding RNAs will be added to the Zv8 zebrafish assembly and there will also be some changes to protein coding gene models and new repeats and expression patterns.

Core

Schema Changes

• Patch to update versions (patch_54_55_a.sql). * Add the missing types to go_xref (patch_54_55_b.sql).
• Add new table dependent_xref (will hold the dependencys for the xrefs, i.e. if an EMBL entry come from a uniprot entry this relationship will be in the table)( patch_54_55_d.sql).
• Add new tables for alternative splicing/transcript events (patch_54_55_c.sql).
• Add new column 'is_constitutive' to the exon table (patch_54_55_e.sql)
  

Xrefs
Xrefs will be run for Human, Macacca, Opossum, Chimp, Chicken, Dog and Mouse (including Fantom Xrefs).

Ontology database schema and tools
The ensembl_go_NN databases are no longer being built. Instead we are replacing this with the ensembl_ontology_NN database which may be connected to using the core API.

Assembly mapping
Some of the databases will contain mapping coordinates between current and previous assemblies:

• human: mapping from current GRCh37 to NCBI36, NCBI35 and NCBI34
• mouse: mapping from current NCBIM37 to NCBIM36, NCBIM35 and NCBIM34
  

Other changes

• API support for alternative transcripts/splicing events will be added
• API support for constitutive exons will be added
• Deprecated API modules will be removed
• All slices will be created using the new_fast method from the SliceAdaptor to improve performance
• seq_region seq edit support will be added. Seq_edits can already be stored and retrieved but these were not used in getting the sequence data. This will be changed so that "_rna_edit" attributes in the seq_region_attrib table will be used and the sequence changed.
• MySQL and FASTA dumps will be copied to Amazon Public Datasets project
  
• Gene name and xref projections
  
  

Mart

• New functional genomics mart * A new Probe section added to Ensembl mart
• New ontology mart
• Constitutive exon information will be re-added to Ensembl mart
  

Variation

• There will be a new human variation database generated by mapping NCBI36 coordinates to GRCh37 (using dbSNP 129)
• Illumina array data for SNP/CNV is to be added
• Transcript variations for Zebrafish and Zebrafinch will be reculated to include information from the new gene sets
• Schema change - added a call to get consequence_type
  

Functional genomics

• Human Regulatory Build will be updated using the GRCh37 assembly
• Probe alignment and transcript annotation for all species will migrate from the core datbases to the functional genomics databases, this includes Affymetrix, Illumina, Codelink and Phalanx
• Schema change, an is_current filed is to be added to the coord_system table
  

Comparative genomics

Alignments - The new human assembly means that the following alignments will be regenerated:

• 9 eutherian mammals EPO multiple alignments
• 31 eutherian mammals EPO multiple alignments
• 12 amniota vertbrates Pecan multiple alignments
• 4 catarrhini primate EPO multiple alignments
• Pairwise BLASTZ-NET alignments of human against each of the other 9 and 31 eutherian mammals
• Additional pairwise BLASTZ-NET alignments will be run for human-opossum, human-platypus, human- chicken and human-wallaby
• Translated BLAT-NET will be regenerated for human against fugu, X.tropicalis, C.intestinalis, C.savignyi, stickleback, medaka, chicken, zebrafish, tetraodon, zebrafinch and anole lizard
  

Synteny will be recalculated for: rat vs. huamn, chicken vs. human and human vs. macaque, dog, chimpanzee, platypus, opossum, mouse, orangutan, horse and cow

Homologies amd families

• 50 way GeneTrees and homologies with new/updated genebuilds and assemblies
• Clustering using hcluster_sg
• Multiple Sequence Alignments using consistency-based MCoffee meta-aligner (mafftgins + muscle + kalign + probcons) and new exon-skipping aware "skipper" algorithm.
• New 'putative gene split' and 'distant paralog' homology types
• Pairwise gene-based dN/dS calculations for high coverage species pairs
• Updated MCL families including all Ensembl transcript isoforms and newest Uniprot Metazoa
• Multiple sequence alignments with MAFFT
• Stable IDs for GeneTrees (ENSGT00550NNNNNNNNN) and MCL Families (ENSFM00550NNNNNNNNN).
  

SNPs and ancestral alleles

The new Ensembl release includes a new view for SNPs and other genomic variations. It shows the alignment of the polymorphic position together with 10 base pairs of sequence up- and downstream. The user can choose among all available multiple alignments. Polymorphic positions in the other species are also shown.

This is very useful for looking at ancestral alleles, especially in combination with our EPO alignments as they include the inferred ancestral sequence. Although dbSNP provide predicted ancestral alleles for human SNPs, these are based on the chimp sequence only. In several cases, the ancestral sequence inferred from the multiple alignment is in disagreement with the chimp sequence like in this example. Using multiple alignments gives better results and more confidence to the calls.

Release 54 and pre.ensembl.org

The Ensembl project is pleased to announce release 54 of Ensembl. Highlights of this release are:

• New Zv8 zebrafish assembly;
  
• Comparative alignment text displays for variations and regions;
  
• Ability to add personal notes to any Gene or Transcript.

For more information visit:

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

Along side this release we are also releasing a new version of the pre site. This now includes:

• The GRCh37 human assembly released in February 2009, with preliminary analyses included;
• The callJacc3 marmoset assembly.
  

The eFG Array Mapping Environment

The Ensembl Functional Genomics (eFG) environment has been expanded to incorporate array mapping functionality. Historically, arrays from different vendors have been processed in similar, but non-identical ways due to differing array designs, with the output being stored in the core database. The 'arrays' environment unifies this process within the eFG database to provide a new standardised array mapping procedure for all array formats. This involves a two step process whereby probe sequences are aligned both to genomic and transcript sequences, and then subsequently transcripts are annotated with xrefs(DBEntries) dependant on the quality of the probe alignments around a given transcript locus.

The 'arrays' environment provides easily accessible and interactive command line functions to help run and administer the array mapping pipeline. Recent developments include broader array format support and multi-species capability, along with capture of much more detailed mapping information. This data has yet to be seen in the Ensembl browser, but from release 55 we will start redirecting the web displays to use the eFG data, with a view to developing a more detailed 'Probe' panel at some point later in the year.

We will endeavour to provide alignments and mappings of all popular arrays, for all others we invite you to try out the eFG 'arrays' environment. For more information check out(literally):

ensembl-functgenomics/docs/array_mapping.txt

Or see it online here.

If you have any questions, please mail ensembl-dev@ebi.ac.uk

Browser Training in Vienna on 22 May

The Ensembl Genome Browser project is pleased to announce a workshop on 22 May as a satellite meeting of the European Human Genetics Conference in Vienna, Austria. This full-day workshop is aimed at geneticists and life scientists, and will explore genes, variations, and comparative information using the browser's new interface released Nov, 2008. An introduction to large-scale data retrieval with BioMart will be included. We will also feature brief introductions into the European Genotype Archive (EGA) and the 1000 Genomes Project. The format of our browser workshops are described on our outreach page.

The course on 22 May is held at a central location- the Vienna University Computer Service.

The workshop is free, however limited places are available. Please register if you will be attending.

Ensembl Events in May 2009

For May we have the following Ensembl events:

29 April - 1 May: Ensembl Developers workshop at the University of Cambridge, Cambridge, UK
8 May: Browser workshop at Imperial College, London, UK
11-13 May: Ensembl module in the Wellcome Trust Open Door Workshop - Working with the Human Genome Sequence, Hinxton, UK
11-15 May: Ensembl module in the EBI hands-on training A walktrough EBI Bioinformatics Resources, Hinxton, UK
12-13 May: Ensembl module in the EBI roadshow at the Université Victor Segalen Bordeaux 2, Bordeaux, France
19-21 May: Ensembl module in the EBI roadshow at the Universidade de Santiago de Compostela, Santiago de Compostela, Spain
22 May: Browser workshop at the European Human Genetics Conference, Vienna, Austria
26 May: Ensembl Developers workshop at the VIB Flanders Interuniversity Institute of Biotechnology, Ghent, Belgium
27-28 May: 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.

Ensembl Genomes live!

Today the long-awaited Ensembl Genomes went live! This is a 'sister project' focusing on those species that aren't part of Ensembl, i.e. non-vertebrates. Please have a look at what the Ensembl Genomes team have to say about it themselves:

"We are delighted to announce the forthcoming release of Ensembl Bacteria, Ensembl Protists and Ensembl Metazoa, the first sites to be launched as part of the EBI's "Ensembl Genomes" project to extend the use of the Ensembl browser to non-vertebrate genomes.

These following site are available:

http://bacteria.ensembl.org
http://protists.ensembl.org
http://metazoa.ensembl.org

Additional sites for fungi and plants are in development and will be launched during the summer of this year.

In the Ensembl Genomes project, we are aiming to do two things: firstly to work with particular communities to support the bioinformatic analysis of genome-scale data; and secondly, to provide an integrative portal to data from species of scientific interest from across the taxonomic space. In pursuit of both these aims, we will re-use and extend the proven Ensembl software system, that has been developed by EBI and the Wellcome Trust Sanger Institute in the context of vertebrate genomics.

As with Ensembl, Ensembl Genomes will provide access to DNA and protein sequence, positional and functional annotation of protein-coding and non-protein coding genes, repeat analysis and other features and statistics. An interesting feature made available with the release of Ensembl Genomes is the inclusion of a multi-way comparative genomic analysis performed using a selection of species from bacteria to humans, and the production of gene trees showing the inferred ancestral relationships within deeply conserved protein families. Comparative resources are also provided at a narrower level (for example, DNA and protein-based analyses of individual bacterial clades). In partnership with collaborators, we are working on capturing gene expression, and population-scale variation data, in a number of contexts. More generally, we anticipate the ongoing enrichment of these resources through the integration of increasing quantities of high throughput data now becoming routinely available for all species.

Ensembl Genomes will provide access to data through the usual routes supported for vertebrate data; web-based browser, FTP site, programmatic API, DAS, and BioMart-style data warehouse; as well as text and sequence-based search.

We look forward to working with you as future producers and consumers of data. More information about the project is available at http://www.ensemblgenomes.org. We will be happy to receive any feedback you might wish to offer us at helpdesk@ensemblgenomes.org."

Ensembl Tips: Navigating the Browser

Though the overall response has been good, a few Ensembl users are finding it difficult to switch from the old interface to the new browser launched Nov, 2008. For those users, functionality has not been lost. You should still be able to do the same tasks as before in a faster interface.

We will post a series of tips to show you how to make the switch from the old interface to the new. If you still have trouble, please watch our video tutorial: Browsing Ensembl.

TIP: I want to use ExonView. Where is this now?

To view the full genomic sequences, exons and introns, go to any transcript. (Exons are transcript information. To see the exons page, go to a transcript tab, not the gene tab.) Click on the 'Exons' link under 'Sequence' at the left of any transcript page.

To show the full introns, click on 'Configure this page' at the left. Select 'Show full intronic sequence'. Click 'Save and Close' at the top right corner of the menu window.

Still can't find what you're looking for? Email us at helpdesk@ensembl.org.