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Using Data Hubs in Ensembl to display your organisation’s genomic data
February 28th, 2013 by Nick James
Configuring Data Hubs in Ensembl Using data hubs in Ensembl is a great way to view preconfigured tracks displaying internal (or external) genomic data. There is no need for each user to upload their own data. Nor is there any need to do complex configuration within Ensembl. No Ensembl configuration is required and more data…
What is bioinformatics?
August 10th, 2011 by Ivan Karabaliev
What is bioinformatics? Where did it come from? What does it do and what is it used for? I decided to try to answer these questions as part of a series of blogs explaining how bioinformatics is applied in different life science sectors: plant and animal breeding, biofuels, drug discovery, cosmetics. This blog is the…
As R&D Budgets Shrink and Data Grows, Bioinformatics Service Providers Could Gain in Popularity
December 14th, 2010 by Richard Holland
GenomeWeb published an article in BioInform this week giving a great case study of our relationship with local biotech firm Cytocell. It describes the state of the bioinformatics outsourcing market in general and gives examples of a number of firms active in the area. Several quotes from our recent white paper entitled "Ten Steps to Successfully…
Collaboration with EMBL-EBI on Ensembl
November 22nd, 2010 by Richard Holland
Details of a collaboration between Eagle Genomics and EMBL Enterprise Management Technology Transfer GmbH (EMBLEM), acting on behalf of the European Molecular Biology Laboratory’s Bioinformatics Institute.
Ensembl 60 top tip #1
November 10th, 2010 by Richard Holland
Ensembl 60 came out yesterday. For those of you who are technical developers like us who do in-depth hacking of the source code, there's two things that have changed which you need to be aware of: (this information is shamelessly cribbed from the ensembl-dev mailing list – if you need more details, email the Ensembl team…
Importing Ensembl into Amazon RDB
October 21st, 2010 by Richard Holland
Ensembl very kindly distributes their databases on Amazon as public datasets in a variety of forms. The most straightforward to use is the set of MySQL database files that can simply be copied into your MySQL server’s data directory and they will become instantly available. However, the most cloud-like way to use databases within Amazon…
Bio-IT World Europe 2010 slides
October 4th, 2010 by Richard Holland
Here are the slides I just presented at the Cloud Computing Workshop at Bio-IT World Europe 2010 in Hannover, Germany. Other speakers included Dave Powers from CycleComputing, and Glenn Proctor from the EBI, both of whom presented very interesting summaries of how they had been using cloud technology to improve the services that their organisations…
European Conference on Computational Biology, Ghent ( ECCB10)
September 17th, 2010 by Nick James
In a couple of weeks I shall be attending the ECCB10 conference in Ghent. I have just been reading through the talks and needless to say it looks interesting. I shall be presenting a poster this time, on "An Ensembl-based pipeline for microRNA prediction and expression profiling using Next Generation Sequencing data" I've already described this…
Debian Ensembl update
September 10th, 2010 by Richard Holland
Eagle’s DebianMed contribution of a fully-working .deb file to install Ensembl is almost complete. The demonstration version 57 contains only minor issues now that need to be resolved before it can be released through the Debian package management process. Those issues are: Removal of the embedded JALView as it breaks a lot of Debian’s licensing…
ProServer Das, Ensembl and EC2
September 9th, 2010 by Nick James
If you use the ProServer DAS server with some Ensembl-based adaptors ( maybe you want to server data from Ensembl, or maybe you have genomic data and want to serve it with some extra annotation that is in Ensembl ) then you may have come across the ‘mysql has gone away’ timeout error. Basically what…