Centralizing Bioinformatics via High-Performance Computing: Applications, Opportunities, and Challenges in the Era of Large-scale -Omics Data

The beginning of the 21^st century has seen an increased interest in the approaches to data analysis in scientific computing as essentially every field is seeing an exponential increase in the size of the data deluge. The data sizes imply that high-performance computing is becoming essential to process the information in a timely fashion. For example, executing large number of independent tasks or tasks that perform minimal inter-task communication in parallel is a common requirement in many domains. In computational biology / bioinformatics, the global market continues to experience double-digit growth and so is the deluge of bigdata, especially with the advances in recent sequencing technologies creating Terabytes of -omics based datasets. Despite this data globalization, the data / algorithmic complexity, heterogeneous data sources and nomenclatures, impractically excessive runtimes, etc. make the data exploration and mining a huge challenge. It is thus obvious that comprehensive studies to understanding complex biological organisms will require computational processing power and alternative paradigms for efficient data integration, replication and organization.

At UCR’s high-performance computing | bioinformatics facility, we have developed a series of parallel-, multi-core-CPU-based open-source pipelines for large-scale -omics data analysis, which enables efficient and parallel analysis of multiple datasets in a short time. The facility provides access to high-performance compute resources, data analysis, hosting, programming expertise, backups and storage. The resources serve scientists at UC Riverside and external academia / industry partners to master the informatics needs of their research in a proficient and cost-effective manner. Our unit has been contributing to different research projects by providing, (i) Support and expertise in programming and advanced data analysis, focusing primarily on high-throughput genomics technologies including microarrays, genotyping and next-generation sequencing (RNA-seq, ChIP-seq, SNP-seq, etc.), (ii) Virtual server environments, secure and public web portals, and a large suite of open source applications, (iii) Instruction of hands-on tutorials and workshops on a wide variety of informatics topics, (iv) Custom data analysis and consultation services, and (v) Establishment of research collaborations with experimental scientists from different departments. The facility is open to all researchers, UCR as well as to external users anywhere in the world. Detailed information about the services, research, manuals developed, etc. is available at http://facility.bioinformatics.ucr.edu/.