Abstract

Accepted manuscript version. The final publication is available at Springer via "a href=http://dx.doi.org/10.1007/978-3-319-24462-4_22"http://dx.doi.org/10.1007/978-3-319-24462-4_22"/a". Biological data analysis is typically implemented using a deep pipeline that combines a wide array of tools and databases. These pipelines must scale to very large datasets, and consequently require parallel and distributed computing. It is therefore important to choose a hardware platform and underlying data management and processing systems well suited for processing large datasets. There are many infrastructure systems for such data-intensive computing. However, in our experience, most biological data analysis pipelines do not leverage these systems. We give an overview of data-intensive computing infrastructure systems, and describe how we have leveraged these for: (i) scalable fault-tolerant computing for large-scale biological data; (ii) incremental updates to reduce the resource usage required to update large-scale compendium; and (iii) interactive data analysis and exploration. We provide lessons learned and describe problems we have encountered during development and deployment. We also provide a literature survey on the use of data-intensive computing systems for biological data processing. Our results show how unmodified biological data analysis tools can benefit from infrastructure systems for data-intensive computing. Document type: Part of book or chapter of book

Abstract

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-54420-0_31 A large up-to-date compendium of integrated genomic data is often required for biological data analysis. The compendium can be tens of terabytes in size, and must often be frequently updated with new experimental or meta-data. Manual compendium update is cumbersome, requires a lot of unnecessary computation, and it may result in errors or inconsistencies in the compendium. We propose a transparent file based approach for adding incremental update ca-pabilities to unmodified genomics data analysis tools and pipeline workflow managers. This approach is implemented in the GeStore system. We evaluate GeStore using a real world genomics compendium. Our results show that it is easy to add incremental updates to genomics data processing pipelines, and that incremental updates can reduce the computation time such that it becomes prac-tical to maintain large-scale up-to-date genomics compendia on small clusters. Document type: Part of book or chapter of book