by ·Comments Off on 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

by ·1 Comment

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!)

by ·Comments Off on 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

by ·Comments Off on 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

by ·Comments Off on 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

by ·Comments Off on 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

by ·Comments Off on 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.

by ·Comments Off on 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.

by ·1 Comment


Ensembl just updated the live site and underlying databases to
version 53.

Some new features include ‘Active Tracks’ and a searchable ‘Configure this page’!

Go to any region of the chromosome.

Click ‘Configure this page’ at the left.

‘Active tracks’ allows you to see (and deselect) all tracks that are turned on.

‘Search display’ allows you to search for tracks in the menus. In this example, we searched for UniProt. Tracks from different menus appear.

For more updates, including new species, variations, and Amazon Web Services, see the news.

by ·Comments Off on Ensembl Workshops in March, 2009

In March, explore Ensembl in the following events:

1-3: Presentation at the EURATools Annual meeting in Barcelona
5,6: Browser workshop at the Department of Genetics in Cambridge, UK
10: Browser workshop in Leuven, Belgium
13: Browser workshop at the Faculty of Science, Montevideo, Uruguay
16-19: Ensembl Module in the Open Door Workshop, Montevideo, Uruguay
19: Demo at the Bioinformatics Course, National Genetics Reference Lab, Manchester, UK
20: Browser workshop at the Max Delbrück Center in Berlin, Germany
31: Browser workshop at King’s College, London, UK
31 March, 1 April : Demo and Browser Workshop at the IGC Oeiras, Portugal
2,3 April: Ensembl API workshop at the IGC, Oeiras, Portugal

Check out microorganisms at Ensembl genomes featured in the EBI ‘Sequence to Genes‘ Workshop, EBI, Hinxton, UK

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