SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

BMC Bioinformatics

Software

Sarah Killcoyne¹  Chris C Cavnor¹  Bruz Marzolf¹  Stephen A Ramsey¹  David B Burdick¹  Ryan Bressler¹  John Boyle¹  Jeremy Handcock¹  Hector Rovira¹  Jake Lin¹  Ilya Shmulevich¹ 

[1] Institute for Systems Biology, 1441 North 34th Street, 98103, Seattle, WA, USA;

关键词: High Throughput Sequencing;    Data Management System;    Enterprise Architecture;    Software Infrastructure;    Rapid Integration;   

DOI  :  10.1186/1471-2105-11-377

 received in 2009-11-11, accepted in 2010-07-14,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundHigh throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires.ResultsExisting software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code.ConclusionThe system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.

【 授权许可】

CC BY   
© Burdick et al; licensee BioMed Central Ltd. 2010