Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.
Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach.
NEC Labs China, Beijing 100084, China. Electronic address: liu_bo@nec.cn.
Bo
B
Liu
Computation Institute, University of Chicago, Chicago, IL, USA; Mathematics and Computer Science Division, Argonne National Lab, IL, USA.
Ravi K
RK
Madduri
Computation Institute, University of Chicago, Chicago, IL, USA.
Borja
B
Sotomayor
Computation Institute, University of Chicago, Chicago, IL, USA.
Kyle
K
Chard
Computation Institute, University of Chicago, Chicago, IL, USA.
Lukasz
L
Lacinski
Computation Institute, University of Chicago, Chicago, IL, USA.
Utpal J
UJ
Dave
School of Software Engineering, Beijing University of Technology, Beijing 100022, China.
Jianqiang
J
Li
NEC Labs China, Beijing 100084, China.
Chunchen
C
Liu
Computation Institute, University of Chicago, Chicago, IL, USA; Mathematics and Computer Science Division, Argonne National Lab, IL, USA.
Ian T
IT
Foster
D019295:Computational Biology; D016247:Information Storage and Retrieval; D017421:Sequence Analysis / Q000295:instrumentation*
Bioinformatics; Cloud computing; Galaxy; Scientific workflow; Sequencing analyses