Fractal MapReduce decomposition of sequence alignment

This work was supported in part by the Center for Clinical and Translational Sciences of the University of Alabama at Birmingham under contract no. 5UL1 RR025777-03 from NIH National Center for Research Resources, by the National Cancer Institute grant 1U24CA143883-01, by the European Union FP7 PNEUMOPATH (HEALTH F3 2009 222983).Background: The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics algorithm development. In some cases an algorithm will find a natural distribution via use of map functions to process vectorized components, followed by a reduce of aggregate intermediate results. However, for some data analysis procedures such as sequence analysis, a more fundamental reformulation may be required. Results: In this report we describe a solution to sequence comparison that can be thoroughly decomposed into multiple rounds of map and reduce operations. The route taken makes use of iterated maps, a fractal analysis technique, that has been found to provide a "alignment-free" solution to sequence analysis and comparison. That is, a solution that does not require dynamic programming, relying on a numeric Chaos Game Representation (CGR) data structure. This claim is demonstrated in this report by calculating the length of the longest similar segment by inspecting only the USM coordinates of two analogous units: with no resort to dynamic programming. Conclusions: The procedure described is an attempt at extreme decomposition and parallelization of sequence alignment in anticipation of a volume of genomic sequence data that cannot be met by current algorithmic frameworks. The solution found is delivered with a browser-based application (webApp), highlighting the browser's emergence as an environment for high performance distributed computing. Availability: Public distribution of accompanying software library with open source and version control at http://usm.github.com. Also available as a webApp through Google Chrome's WebStore http://chrome.google.com/webstore: search with "usm".publishersversionpublishe

Recovery-oriented software architecture for grid applications (ROSA-Grids)

Grids are distributed systems that dynamically coordinate a large number of heterogeneous resources to execute large-scale projects. Examples of grid resources include high-performance computers, massive data stores, high bandwidth networking, telescopes, and synchrotrons. Failure in grids is arguably inevitable due to the massive scale and the heterogeneity of grid resources, the distribution of these resources over unreliable networks, the complexity of mechanisms that are needed to integrate such resources into a seamless utility, and the dynamic nature of the grid infrastructure that allows continuous changes to happen. To make matters worse, grid applications are generally long running, and these runs repeatedly require coordinated use of many resources at the same time. In this thesis, we propose the Recovery-Aware Components (RAC) approach. The RAC approach enables a grid application to handle failure reactively and proactively at the level of the smallest and independent execution unit of the application. The approach also combines runtime prediction with a proactive fault tolerance strategy. The RAC approach aims at improving the reliability of the grid application with the least overhead possible. Moreover, to allow a grid fault tolerance manager fine-tuned control and trading off of reliability gained and overhead paid, this thesis offers an architecture-aware modelling and simulation of reliability and overhead. The thesis demonstrates for a few of a dozen or so classes of application architecture already identified in prior research, that the typical architectural structure of the class can be captured in a few parameters. The work shows that these parameters suffice to achieve significant insight into, and control of, such tradeoffs. The contributions of our research project are as follows. We defined the RAC approach. We showed the usage of the RAC approach for improving the reliability of MapReduce and Combinational Logic grid applications. We provided Markov models that represent the execution behaviour of these applications for reliability and overhead analyses. We analysed the sensitivity of the reliability-overhead tradeoff of the RAC approach to the type of fault tolerance strategy, the parameters of a fault tolerance strategy, prediction interval and a predictor’s accuracy. The final contribution of our research is an experiment testbed that enables a grid fault tolerance expert to evaluate diverse fault tolerance support configurations, and then choose the one that will satisfy the reliability and cost requirements