Ensembl Genomes Release 10

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!

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

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.