March 3, 2017

Eagle Genomics' symposium 3rd abstract

The third abstract of one of the talks which will be held at our 2nd Symposium: "The Next 10 Years of Genome Content Management" on 29th March held at Cambridge, Babraham Research Campus.

The title is: Just Enough Developed Infrastructure

Presented by: Dan MacLean, Head of Bioinformatics, Sainsbury Laboratory

  "The Sainsbury Laboratory is a small independent research lab of approximately 80 researchers, we concentrate on Plant/Pathogen interactions with a focus on the genetics and genomics of a wide and frequently shifting line-up of organisms under study. A large proportion of our projects are focussed on a relatively modest goal, for example identifying Resistance genes in a novel model, rather than producing a gold-standard annotated genome. Recently we have made the decision to abandon our own compute cluster in favour of merging with larger users ie TGAC in an 'Access is more important than ownership model'. Similarly, we have found that many existing tools for genome sequence and feature annotation management, while great in their own way, can be too large and more difficult to manage than is useful for our projects and personnel profile. I'll describe the sequencing pipelines and hardware that feed into our data store as background for the core of our management structure, our lightweight sequence and feature versioning tool Gee Fu. Gee Fu interacts with our assembly and annotation pipelines from the command-line and from our Galaxy installation. It acts simultaneously as a store and annotation editor that has appropriate interfaces for users with a wide range of computing skills and can be used to share data externally via its RESTful interface and a web based front end."

 

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Topics: Babraham Research Campus, Bioinformatics, Bioinformatics, Bioinformatics events, Dan MacLean, Eagle Genomics symposium, March science event, Sainsbury Laboratory, The next 10 years Genome Content Managemen