Blaeu: Mapping and navigating large tables with cluster analysis

Blaeu is an interactive database exploration tool. Its aim is to guide casual users through large data tables, ultimately triggering insights and serendipity. To do so, it relies on a double cluster analysis mechanism. It clusters the data vertically: it detects themes, groups of mutually dependent columns that highlight one aspect of the data. Then it clusters the data horizontally. For each theme, it produces a data map, an interactive visualization of the clusters in the table. The data maps summarize the data. They provide a visual synopsis of the clusters, as well as facilities to inspect their content and annotate them. But they also let the users navigate further. Our explorers can change the active set of columns or drill down into the clusters to refine their selection. Our prototype is fully operational, ready to deliver insights from complex databases

Genome sequence analysis with MonetDB: a case study on Ebola virus diversity

Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but results in terabytes of data to be stored and analysed. Biologists are often exposed to excessively time consuming and error-prone data management and analysis hurdles. In this paper, we propose a database management system (DBMS) based approach to accelerate and substantially simplify genome sequence analysis. We have extended MonetDB, an open-source column-based DBMS, with a BAM module, which enables easy, flexible, and rapid management and analysis of sequence alignment data stored as Sequence Alignment/Map (SAM/BAM) files. We describe the main features of MonetDB/BAM using a case study on Ebola virus genomes

Genome sequence analysis with MonetDB - A case study on Ebola virus diversity

Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but yields terabytes of data to be stored and analyzed. Biologists are often exposed to excessively time consuming and error-prone data management and analysis hurdles. In this paper, we propose a database management system (DBMS) based approach to accelerate and substantially simplify genome sequence analysis. We have extended MonetDB, an open-source column-based DBMS, with a BAM module, which enables \textit{easy}, \textit{flexible}, and \textit{rapid} management and analysis of sequence alignment data stored as Sequence Alignment/Map \\(SAM/BAM) files. We describe the main features of MonetDB/BAM using a case study on Ebola virus \\genomes

Computational pan-genomics: Status, promises and challenges

Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different Computational methods and paradigms are needed.We will witness the rapid extension of Computational pan-genomics, a new sub-area of research in Computational biology. In this article, we generalize existing definitions and understand a pangenome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a Computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations