Eagle is agnostic when it comes to choosing the tools for the job. Whatever tool works best for the job in hand is the one that is chosen. However, Eagle has built up expertise in a selection of tools that frequently turn up in the solutions that it builds, in order to help customers get every drop of value and functionality out of the software installed.
The majority of the tools in which Eagle specialise are open-source. The open nature of these projects allows Eagle to get to know them in the greatest detail, right down to the individual lines of source code, meaning that almost any customisation or integration request can be made possible. The communities behind many of these open-source tools are also a great source of information and inspiration and Eagle actively supports them by contributing code patches and supporting community events.
Ensembl is one of the leading genome browsers and genome data integration platforms, and Eagle staff are experts in every aspect of it. Several Eagle employees used to work within the Ensembl project team at the EBI and have in-depth hands-on knowledge of the source-code and design philosophy behind the platform.
Ensembl is not just a genome browser. It comprises a set of genomic databases which are loosely connected allowing them to be installed separately or together as required. On top of the databases lies an API written in Perl allowing any piece of software to interrogate and load the data contained within Ensembl in a standard schema-independent manner. The Ensembl web interface sits on top of the API to provide an interactive and highly visual way of navigating the many levels of complex data contained in the databases.
Customisations to the web interface and the API are areas in which Eagle are frequently called upon to assist, along with loading custom data into the databases – anything from novel annotations through to complete new genomes.
eHive, produced by the Ensembl team, is one of Ensembl's best-kept secrets. It is a workflow tool designed specifically for managing the huge task of building Ensembl's comparative genomics datasets (Ensembl Compara). It was written in a modular style and thus can easily be applied to almost any workflow requirement, something which Eagle has taken advantage to apply it to everything from next-generation sequencing (NGS) assembly and analysis to SNP and miRNA prediction and metagenomic analysis of bacterial colonies. Eagle's proprietary extensions to eHive allow it to run natively and scale just as well on Amazon Cloud as it does on SGE/LSF/Condor clusters, making it a great option for cloud migration pilots.
TraitTag is an award-winning sequence-based technique from the John Innes Centre to identify molecular biomarkers that can accelerate crop breeding. It allows breeders to identify these biomarkers quickly and effectively through the identification and scoring of variations across very large sets of plants. The key advantage of TraitTag is that it does not require a full reference genome of the plant. This enables plant breeders to use it even when no prior major research has been done into the genome of the plant species they are working with.
TraitTag is a reusable module that can be integrated into almost any workflow on any platform. It is 100% compatible with eHive, and can also be integrated into Taverna.
Taverna, like eHive, is a workflow engine. Eagle works closely with the University of Manchester to develop enhancements and provide commercial support to end-users of the software. Whilst eHive is best suited to industrial-scale server-side workflows, Taverna works brilliantly for desktop users who need to visualise and modify their workflow designs on the fly using drag-and-drop user interfaces.
Eagle is a regular contributor to and supporter of DebianMed, the bioinformatics software repository for Debian. This repository, an extension to one of the most popular Linux distributions, contains prepackaged versions of numerous bioinformatics allowing end-users to install them and all their dependencies with a single action. Eagle have been working with DebianMed to develop an Ensembl package.
Eagle is an Amazon Web Services Consulting Partner. Eagle uses Amazon power to provide the compute capacity necessary to deliver all kinds of bioinformatics projects. All Eagle computation is done on Amazon resources and we have helped numerous customers pilot and migrate their existing bioinformatics systems across to the cloud.