Seamless Coarse Grained Parallelism Integration in Intensive Bioinformatics Workflows

To be easily constructed, shared and maintained, complex in silico bioinformatics analysis are structured as workflows. Furthermore, the growth of computational power and storage demand from this domain, requires workflows to be efficiently executed. However, workflow performances usually rely on the ability of the designer to extract potential parallelism. But atomic bioinformatics tasks do not often exhibit direct parallelism which may appears later in the workflow design process. In this paper, we propose a Model-Driven Architecture approach for capturing the complete design process of bioinformatics workflows. More precisely, two workflow models are specified: the first one, called design model, graphically captures a low throughput prototype. The second one, called execution model, specifies multiple levels of coarse grained parallelism. The execution model is automatically generated from the design model using annotation derived from the EDAM ontology. These annotations describe the data types connecting differents elementary tasks. The execution model can then be interpreted by a workflow engine and executed on hardware having intensive computation facility

Strengthening measurements from the edges: application-level packet loss rate estimation

Network users know much less than ISPs, Internet exchanges and content providers about what happens inside the network. Consequently users cannot either easily detect network neutrality violations or readily exercise their market power by knowledgeably switching ISPs. This paper contributes to the ongoing efforts to empower users by proposing two models to estimate -- via application-level measurements -- a key network indicator, i.e., the packet loss rate (PLR) experienced by FTP-like TCP downloads. Controlled, testbed, and large-scale experiments show that the Inverse Mathis model is simpler and more consistent across the whole PLR range, but less accurate than the more advanced Likely Rexmit model for landline connections and moderate PL

Grid Analysis of Radiological Data

IGI-Global Medical Information Science Discoveries Research Award 2009International audienceGrid technologies and infrastructures can contribute to harnessing the full power of computer-aided image analysis into clinical research and practice. Given the volume of data, the sensitivity of medical information, and the joint complexity of medical datasets and computations expected in clinical practice, the challenge is to fill the gap between the grid middleware and the requirements of clinical applications. This chapter reports on the goals, achievements and lessons learned from the AGIR (Grid Analysis of Radiological Data) project. AGIR addresses this challenge through a combined approach. On one hand, leveraging the grid middleware through core grid medical services (data management, responsiveness, compression, and workflows) targets the requirements of medical data processing applications. On the other hand, grid-enabling a panel of applications ranging from algorithmic research to clinical use cases both exploits and drives the development of the services

Parallelization of dynamic programming recurrences in computational biology

The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained parallelism in dynamic programming kernels using field-programmable gate arrays: FPGAs). We advocate a high-level synthesis approach, using the recurrence equation abstraction to represent dynamic programming and polyhedral analysis to exploit parallelism. We suggest a novel technique within the polyhedral model to optimize for throughput by pipelining independent computations on an array. This design technique improves on the state of the art, which builds latency-optimal arrays. We also suggest a method to dynamically switch between a family of designs using FPGA reconfiguration to achieve a significant performance boost. We have used polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four Xilinx Virtex 4 FPGAs outperforms 198 3 GHz Intel Core 2 Duo processors. Furthermore, our design running on a single FPGA is an order of magnitude faster than competing implementations on similar-generation FPGAs and graphics processors. Our work is a step toward the goal of automated synthesis of hardware accelerators for dynamic programming algorithms