|Title||SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. |
|Publication Type||Journal Article |
|Year of Publication||2010 |
|Authors||Burdick, DB, Cavnor, CC, Handcock, J, Killcoyne, S, Lin, J, Marzolf, B, Ramsey, SA, Rovira, H, Bressler, R, Shmulevich, I, Boyle, J |
|Journal||BMC Bioinformatics |
|Date Published||2010 Jul 14 |
|Keywords||Algorithms, Base Sequence, Computational Biology, Database Management Systems, Internet, Sequence Analysis, DNA, Software |
BACKGROUND: High 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.
RESULTS: Existing 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.
CONCLUSION: The 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.
|Alternate Journal||BMC Bioinformatics |
|PubMed ID||20630057 |
|PubMed Central ID||PMC2916924 |
|Grant List||P50 GM076547 / GM / NIGMS NIH HHS / United States |
R01 CA137442 / CA / NCI NIH HHS / United States
P50GMO76547 / / PHS HHS / United States
R01-1CA1374422 / CA / NCI NIH HHS / United States