DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing technologies have led to the high-throughput production of sequence data (reads) at low cost. However, these reads are significantly shorter and more error-prone than conventional Sanger shotgun reads. This poses a challenge for the <it>de novo </it>assembly in terms of assembly quality and scalability for large-scale short read datasets.</p> <p>Results</p> <p>We present DecGPU, the first parallel and distributed error correction algorithm for high-throughput short reads (HTSRs) using a hybrid combination of CUDA and MPI parallel programming models. DecGPU provides CPU-based and GPU-based versions, where the CPU-based version employs coarse-grained and fine-grained parallelism using the MPI and OpenMP parallel programming models, and the GPU-based version takes advantage of the CUDA and MPI parallel programming models and employs a hybrid CPU+GPU computing model to maximize the performance by overlapping the CPU and GPU computation. The distributed feature of our algorithm makes it feasible and flexible for the error correction of large-scale HTSR datasets. Using simulated and real datasets, our algorithm demonstrates superior performance, in terms of error correction quality and execution speed, to the existing error correction algorithms. Furthermore, when combined with Velvet and ABySS, the resulting DecGPU-Velvet and DecGPU-ABySS assemblers demonstrate the potential of our algorithm to improve <it>de novo </it>assembly quality for <it>de</it>-<it>Bruijn</it>-graph-based assemblers.</p> <p>Conclusions</p> <p>DecGPU is publicly available open-source software, written in CUDA C++ and MPI. The experimental results suggest that DecGPU is an effective and feasible error correction algorithm to tackle the flood of short reads produced by next-generation sequencing technologies.</p

Piergiuseppe Morone and Richard Taylor: Knowledge diffusion and innovation: modelling complex entrepreneurial behaviours

In recent years, knowledge and networks have become key concepts in the economics of innovation and evolutionary economics. The book by Piergiuseppe Morone and Richard Taylor, “Knowledge diffusion and innovation: modeling complex entrepreneurial behaviors”, is an important contribution to an emerging literature that, through agent-based modeling, tries to enlighten the complex mechanisms underlying knowledge diffusion in networks

Towards the derivation of an integrated process cost-modelling technique for complex manufacturing systems

Cost modelling is used to support business decisions, especially, when the objective is to remain competitive on price and be able to realise outputs at low cost. Many researchers and industrialists have proposed and experimented with different cost-modelling techniques with a view to influencing design and production decisions at an early stage of the development process. This has led to cost-modelling methods which have been broadly classified in this paper as qualitative and quantitative. The paper identifies current best practice cost-modelling techniques and their performance in complex and dynamic manufacturing environments. The review served as a platform to support the recommendation for an integrated cost-modelling methodology. The integrated methodology is based on the strengths of cost engineering, enterprise modelling, system dynamics and discrete event simulation modelling techniques. The method can help in the redesign and re-engineering of products and processes for better cost and value indications; support investment decision analysis; help determine appropriate business and manufacturing paradigms; influence ‘make, buy or outsourcing’ decisions and serve as a key process improvement tool