ASHG 2013 logoEnsembl will be at the ASHG meeting in Boston this year. Look out for Paul Flicek (head of EBI Vertebrate Genomics, including Ensembl) and Emily Pritchard (Ensembl Outreach Officer) at the conference.

Photo of Paul Flicek

Paul Flicek – Head of EBI Vertebrate Genomics

We’ll be holding a 90 min workshop entitled Ensembl Highlights Interactive Workshop: Intermediate/Advanced Users, taught by Emily. This workshop will look at some of the advanced access features in Ensembl, including BioMart, the Ensembl Perl APIs and custom data upload, as well as some of the new features in Ensembl, the Variant Effect Predictor, the REST API and sharing data. This course will only provide a very brief introduction to Ensembl itself: before the course you may wish to get up-to-date on what Ensembl is and the kind of data it provides using our Quick Tour. If you’re already registered for ASHG, you can register for the course through the ASHG conference website and there is a small charge of US$25.

Photo of Emily Pritchard

Emily Pritchard – Ensembl Outreach Officer

If you would like to meet up and chat informally about Ensembl at ASHG, Emily will be happy to speak to you. Do you have any specific questions about Ensembl, or would like to solve some your Ensembl problems by speaking to us? We can walk through the Ensembl website to see if we can solve your problems. Please bring along any data or information we’d need. Perhaps you’re also interested in hosting an Ensembl workshop at your institute and would like to find out more about it? We can discuss what a workshop would entail, how to organise it and maybe pencil in some dates.

You can book an appointment to meet Emily using our booking system, then we’ll arrange somewhere to meet up. Appointments are free, but please state briefly what you would like to chat about when you book. There may also be a limited number of slots to speak to Paul. There will be lots of people on the Workshop, so don’t assume that you’ll be able to ask your questions then; it may just be too busy. Even if you’re going to the Workshop, you might still want to book an appointment to talk about your specific issue.

If you’re at the Biocuration conference currently happening in Washington DC, feel free to swing by the poster of Amonida Zadissa to learn about the Ensembl gene set (poster number P.87).

Ensembl Genebuild members will also be attending:

5th International Conference on Primate Genomics Bronwen Aken
17-19 April 2012
Houston, Texas, USA

Recomb 2012  Thibaut Hourlier, Poster 276
First session, 21st April, 18:30-20:00
Conference on Research in Computational Molecular Biology
21-24 April 2012
Barcelona, Spain

 

 

Greetings from San Diego!

If you are at the Plant and Animal Genome (PAG) conference, please come and visit the posters by Susan Fairley (P0941: Genome Annotation in Ensembl), Paul Kersey (P0942: Ensembl Plants: An Integrating Resource for Plant Genomics and Variation) and our friends from the Havana group (P0620: Production of a reference gene set for the porcine sex chromosomes). For any questions regarding Ensembl and Ensembl Genomes you can also visit the EBI booth (302).  Just ask!

ICHG 2011The Ensembl team will be delivering a couple of workshops in the 12th International Congress of Human Genetics today and tomorrow. Please come along if you were interested to know about the latest improvements to our browser.

  • Today (Friday 14th October) our workshop will take place at the Palais des Congrès de Montréal (Convention Center, room 524 level 5 from 18.15 to 20.00. We will be exploring Ensembl beyond the browser, highlighting some new features to those more experienced with Ensembl. We will distribute a DVD to those interested to have a virtual machine with the latest APIs installed.
  • Tomorrow 12.30 to 13.30 (room 524, level 5) we will provide a more basic workshop for newcomers or people interested in catching up with genome browsers.

If you want to learn how Ensembl can help you on your research, or perhaps you have some questions, please come along. You are welcome to come with your laptop and join us today and/or tomorrow.

À bientôt!

We are looking for projects that use aspects of the Ensembl code (for example, the webcode, the genebuild pipeline, or comparative analyses).  If you want to be added to our list, please reply to this blog post, or email our helpdesk with your project name, url, and what aspect of the code you are using.

In addition to the projects on our powered by Ensembl page, we have heard from:

Let us know about your project!

 

This year the Human Genome Meeting has brought us to Dubai (in the United Arab Emirates) for a very interesting conference focusing on the genomics of human genetics. Ensembl is featured in one of the satellite events organised, The Open Door Workshop, offering us a unique opportunity to present the latest develoments in the project to participants from 12 countries (Australia, Brazil, India, Indonesia, Iran, Pakistan, Saudi Arabia, Slovenia, Spain, Sri Lanka, Sudan and obviously our host country UAE) with a broad range of interests ranging from clinical genomics to database management.

We have received very positive feedback on some of the latest goodies hidden in our favourite genome browser, such as the possibility of streaming BAM files to display NGS data alongside the Ensembl annotation (undoubtely we should be posting some tips on this very soon).

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.

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