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Full-Text Articles in Bioinformatics
Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed
Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed
Parallel Computing and Data Science Lab Technical Reports
Proteogenomics is an emerging field of systems biology research at the intersection of proteomics and genomics. Two high-throughput technologies, Mass Spectrometry (MS) for proteomics and Next Generation Sequencing (NGS) machines for genomics are required to conduct proteogenomics studies. Independently both MS and NGS technologies are inflicted with data deluge which creates problems of storage, transfer, analysis and visualization. Integrating these big data sets (NGS+MS) for proteogenomics studies compounds all of the associated computational problems. Existing sequential algorithms for these proteogenomics datasets analysis are inadequate for big data and high performance computing (HPC) solutions are almost non-existent. The purpose of this …
A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed
A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed
Parallel Computing and Data Science Lab Technical Reports
With the advent of high-throughput next-generation sequencing (NGS) techniques, the amount of data being generated represents challenges including storage, analysis and transport of huge datasets. One solution to storage and transmission of data is compression using specialized compression algorithms. However, these specialized algorithms suffer from poor scalability with increasing size of the datasets and best available solutions can take hours to compress gigabytes of data. In this paper we introduce paraDSRC, a parallel implementation of DSRC algorithm using a message passing model that presents reduction of the compression time complexity by a factor of O(1/p ). Our experimental results show …