Benefits for Bioinformatics Managers

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Next generation sequencing (NGS) is transforming genome-based research. Now, more than ever, research organizations need complete management of their sequence data.

GenomeQuest SDM

In particular, bioinformatics managers are often tasked with sharing sequence data and building workflows between an increasing number of discovery tools in their environment, including: mining, visualization, desktop analysis, statistics, LIMS, assemblers, and aligners.

With the coming of NGS, they are finding it intractable to develop and maintain point-to-point interfaces between these tools and, therefore, seek a platform to broadly manage their sequence data and workflows.

Bio IT Challenge: Moving Beyond Point-to-Point Approach

With GenomeQuest and its open platform, bioinformatics managers can:

• Share sequence data throughout their environment
• Establish common management of data and workflows across all tools
• Configure and extend GenomeQuest
• Customize GenomeQuest built-in workflows
• Share compute resources across all discoveries
• Employ a "best-of-breed"/interoperable database strategy
• Generally unify their sequence data environment.
• Achieve these items at NGS volumes

The open platform is based on a comprehensive application programmer interface (API) which provide access to all GenomeQuest data, commands, and compute resources. The data types include administrative, sequence databases, and sequence compares. The commands include administration, database upload/download, sequence search/compare, database joins, database read/writes, and workflows. The APIs are available via URL APIs, web services, and command line APIs.

The open platform requires and interoperates with popular RDBMS's, including Oracle and MySQL. Using a federated, best-of-breed approach, GenomeQuest utilizes the RDBMS to manage all relational data -- including admin, metadata, and user annotations -- while itself efficiently and comprehensively managing all sequence data and reference annotations.

GenomeQuest interfaces with all popular sequencing machines, including 454, Illumina, and SOLiD.

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