by ·Comments Off on Extending Ensembl

Following a recent thread in our ensembl-dev mailing list, we can point our users to a recent post in the Gramene blog (a resources for grass genomes maintained at CSHL). This framework extends Ensembl with a data resource to browse several plant species: maize (Zea mays), rice (Oryza glaberrima and Oryza rufipogon), sorghum (Sorghum bicolor), the model organism Arabidopsis thaliana, grape (Vitis vinifera), and poplar (Populus trichocarpa); with comparative maps for additional species such as wheat (Triticum aestivum), barley (Hordeum vulgare) and oat (Avena sativa).

You can find some sample scripts to load an Ensembl species database from scratch, here.

Thanks to our colleagues at Gramene.

by ·Comments Off on Ensembl 53

We are already working on our next release (out late in February 2009) which will come with the following:

Data

  • New species added to our set: sloth (Choloepus hoffmanni), Anolis lizard (Anolis carolinensis) and zebrafinch (Taeniopygia guttata).
  • Updated marker information for human, cow, dog, horse, chicken, macaque, mouse and Medaka.
  • Updated manual annotation for mouse from VEGA.

Comparative Genomics

  • Pairwise alignments with the new species (human/sloth, zebrafinch/chicken, lizard/chicken).
  • New 31-way eutherian mammal alignment using these 2x genomes (based on the 9-way Enredo-Pecan-Ortheus multiple alignments): elephant (Loxondonta africana) , armadillo (Dasypus novemcinctus), tenrec (Echinops telfairi), rabbit (Oryctolagus cuniculus), guinea pig (Cavia porcelus), hedgehog (Erinaceus europaeus), shrew (Sorex araneus), microbat (Myotis lucifugus), tree shrew (Tupaia belangeri), squirrel (Spermophilus tridecemlineatus), bushbaby (Otolemur garnetii), pika (Ochotona princeps), mouse lemur (Microcebus murinus), cat (Felis catus), megabat (Pteropus vampyrus), dolphin (Tursiops truncatus), alpaca (Vicugna pacos), kangaroo rat (Dipodomys ordii), hyrax (Procavia capensis), tarsier (Tarsius syrichta), gorilla (Gorilla gorilla) and sloth (Choloepus hoffmanni).
  • The current clustering will be replaced by a hierarchical clustering sparse graphs (hcluster) for our trees.

Variation and Functional Genomics

  • An improved array mapping environment integrates genomic and cDNA mappings, supporting multi-species databases.
  • We’ll link to Genome Wide Association from the NHGRI catalogue (Hindorff et al.)
  • Genotype data for mouse (reference strain C57BL/6) will be included.
  • Update of variation for dog, chicken and platypus.

Other

by ·Comments Off on Ensembl at the IMGC

Ensembl is attending the 22nd International Mammalian Genome Conference taking place in Prague (Czech Republic) from 2-5 November 2008. This meeting starts with three bioinformatics workshops on Sunday (2nd November) at the Institute of Molecular Genetics (AS CR). One of these workshops will focus on Ensembl, discussing new developments and featuring a preview of our new interface. We will be starting a 9:00 (Seminar Room 3.102, in the third floor). You can download the workshop materials here (exercises and tutorials). As part of our commitment with the EURATools consortium, we’ll be focusing on rat genomics, but if you work with any other species annotated in Ensembl, you are welcome.
See you in Prague!

by ·Comments Off on Incredible !ndia

The Ensembl team has been involved in several activities in Hyderabad (India) during the last few days, making the most of the latest HUGO’s 13th Human Genome (HGM2008).

A satellite workshop has been organised within the Open Door Workshop framework at the Centre for Cellular and Molecular Biology (CCMB). Over 40 scientists from different countries had the opportunity to learn about different resources freely available on the Internet, providing us with useful feedback.

Following our presence in the HGM2008 in the EBI booth we had the opportunity to make several contacts that hopefully should allow us to organise a series of workshops around India next year. If you were interested to know more about this, or query about possibilities to host one of our workshops, you can contact us.

Greetings from India भारत से नमस्ते

by ·2 Comments

Ensembl is currently migrating to new hardware in conjunction to the development of new webcode for the next release (due in late September). During this period, and due to some technical issues, there might be some downtime of our website. We apologise for any problems this may cause and we are working to minimise its impact in Ensembl.

The Ensembl Team

by ·Comments Off on Ensembl in China

The Ensembl team has recently run a series of workshops in China:

  • In Shanghai we were at Tongji University for a workshop organised by the Shanghai Center for Bioinformation Technology, and

  • In Beijing, we were hosted by Professor Jingchu Luo from the Center of Bioinformatics at Peking University where we also delivered some lectures in the Applied Bioinformatics Course.

    • Following this experience and due to the success of the tour, we are planning to go back to China. So if you were interested in hosting a workshop or you have a collaboration with a Chinese group who might be interested in knowing more about Ensembl, please contact us to discuss dates. We are trying to coordinate our next trip with different hosts.

    The Ensembl Team

    by ·2 Comments

    Ensembl announces a workshop for developers that will take place in the Wellcome Trust Genome Campus in Hinxton (near Cambridge, UK) next September (14th-16th September), following the Genome Informatics meeting.

    In this workshop we will be exploring Ensembl beyond the website. Participants will be expected to have experience in writing Perl programs and a background in object oriented programming techniques. Being familiar with databases (MySQL) and the Ensembl APIs would be an advantage.

    Several Ensembl developers will present uses of our APIs (Application Programming Interfaces) as well as extensions of the Ensembl system. Note this is not a course about how to use the Ensembl APIs.

    At the end of this course, attendees will:

    • have a good understanding of Ensembl’s annotation pipeline;
    • know how to customise a local installation of the Ensembl website;
    • and have hands-on experience with the annotation pipeline.

    In late 2008, the Ensembl Genomes project at the EBI will leverage the Ensembl system to create consistent genome annotation resources focused on a wide variety of eukaryote, as well as prokaryote genomes and thereby continue the activities of the current EBI Integr8 and Genome Reviews projects.

    Thus, there will be a session where the new divisions of Ensembl will be introduced and previewed; the initial data content and future directions will be discussed.

    There is no registration fee to attend this course, but you may need accommodation (or extending your stay in Hinxton Hall: info@wtconference.org.uk), if you could let us know you are planning to attend or wanted more information, please send an eMail to xose@ebi.ac.uk.

    The Ensembl Team

    by ·Comments Off on Ensembl needs you!

    As you know, we are working on a new website design for the Ensembl 50 release. We are currently seeking ‘beta testers‘ who would be happy to take part in a survey and help us shape the look and feel of the new website.

    If you could spare some time we would be very grateful if you could send an eMail to survey@ebi.ac.uk so we can add you to our list of testers.

    We are looking forward to hearing from you.
    The Ensembl Team

    by ·Comments Off on Year of the rat…

    Things are moving within the rat community as this month’s Nature Genetics issue shows with a special on rat genetics exploring the latest developments.

    Featuring:

    • ENU-induced gene targeting in rats;
    • A ‘white paper’ discussing progress and prospects in rat genetics;
    • A brief overview on rat genome resources online;
    • ENU-induced gene targeting in rats;
    • A contribution on dynamics of CNV in rat and their impact in phenotypes;
    • A survey of genetic variation from The STAR Consortium (over 3 million newly identified SNPs and over 20,000 SNPs genotyped across 167 distinct inbred rat strains);
    • and several papers focusing on the identification of genetic variants associated to rat models of human disease…

    The driving force behind these outstanding achievements can be found on a well interliked rat community bridging resources across the Atlantic: RGD and the EURATools Consortium (FP6 contract number LSHG-CT-2005-019015) collaborations are a good example.

    EURATools investigators are developing integrated genome tools (Ensembl is one of the partners of this consortium). Integrating high-throughput sequencing and genotyping with informatics; intensive analysis of phenotypes, gene sequence and gene expression in congenic strains to identify genes and regulatory pathways for a wide range of rat disease phenotypes; and establishing optimised protocols for rat gene targeting are the goals of this ambitious EU funded project.