The distributed computing attempts to improve performance in large-scale computing problems by resource sharing. Moreover, rising low-cost computing power coupled with advances in communications/networking and the advent of big data, now enables new distributed computing paradigms such as Cloud, Jungle and Fog computing.Cloud computing brings a number of advantages to consumers in terms of accessibility and elasticity. It is based on centralization of resources that possess huge processing power and storage capacities. Fog computing, in contrast, is pushing the frontier of computing away from centralized nodes to the edge of a network, to enable computing at the source of the data. On the other hand, Jungle computing includes a simultaneous combination of clusters, grids, clouds, and so on, in order to gain maximum potential computing power.To understand these new buzzwords, reviewing these paradigms together can be useful. Therefore, this paper describes the advent of new forms of distributed computing. It provides a definition for Cloud, Jungle and Fog computing, and the key characteristics of them are determined. In addition, their architectures are illustrated and, finally, several main use cases are introduced.

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Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

Sequence similarity, as a special case of data intensive applications, is one of the neediest applications for parallelization. Clustered commodity computers as a cost-effective platform for distributed and parallel processing, can be leveraged to parallelize sequence similarity. However, manually designing and developing parallel programs on commodity computers is a time-consuming, complex and error-prone process. In this paper, we present a sequence similarity parallelization technique using the Apache Storm as a stream processing framework with a data parallel programming model. Storm automatically parallelizes computations via a special user-defined topology that is represented as a directed acyclic graph. The proposed technique collects streams of data from a disk and sends them sequence by sequence to clustered computers for parallel processing. We also present a dispatching policy for balancing the cluster workload and managing the cluster heterogeneity to achieve more than 99 percent parallelism. An alignment-free method, known as n-gram modeling, is used to calculate similarities between the sequences. To show the cost-performance superiority of our method on clustered commodity computers over serial processing in powerful computers, we simply use UniProtKB/SwissProt dataset for evaluation of the performance of sequence similarity as an interesting large-scale Bioinformatics application.