Genomics as a service: A joint computing and networking perspective

Reali, Gianluca; Femminella, Mauro; Nunzi, E.; Valocchi, Dario

doi:10.1016/j.comnet.2018.08.005

Cited by 9 publications

(6 citation statements)

References 116 publications

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“…Only reads with at least 100 nucleotides (nt) were retained and then primer sequences were detected, clipped, and oriented into forward-reverse primer orientation. The forward and reverse paired-end reads were imported and analyzed by using Qiime2 platform [38] in a genomic cloud-computing environment based on [39,40] and oriented for biological nano-communication systems in blood vessels for early medical tumor diagnosis [41]. At first, paired-end sequences were denoised, dereplicated, and filtered by any phiX reads and chimera (consensus) by using q2-dada2 quality control method [42] for detecting and correcting (where possible) Illumina amplicon sequence data.…”

Section: Metagenomicsmentioning

confidence: 99%

A Shifted Composition of the Lung Microbiota Conditions the Antifungal Response of Immunodeficient Mice

Nunzi

Renga

Palmieri

et al. 2021

IJMS

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The microbiome, i.e., the communities of microbes that inhabit the surfaces exposed to the external environment, participates in the regulation of host physiology, including the immune response against pathogens. At the same time, the immune response shapes the microbiome to regulate its composition and function. How the crosstalk between the immune system and the microbiome regulates the response to fungal infection has remained relatively unexplored. We have previously shown that strict anaerobes protect from infection with the opportunistic fungus Aspergillus fumigatus by counteracting the expansion of pathogenic Proteobacteria. By resorting to immunodeficient mouse strains, we found that the lung microbiota could compensate for the lack of B and T lymphocytes in Rag1–/– mice by skewing the composition towards an increased abundance of protective anaerobes such as Clostridia and Bacteroidota. Conversely, NSG mice, with major defects in both the innate and adaptive immune response, showed an increased susceptibility to infection associated with a low abundance of strict anaerobes and the expansion of Proteobacteria. Further exploration in a murine model of chronic granulomatous disease, a primary form of immunodeficiency characterized by defective phagocyte NADPH oxidase, confirms the association of lung unbalance between anaerobes and Proteobacteria and the susceptibility to aspergillosis. Consistent changes in the lung levels of short-chain fatty acids between the different strains support the conclusion that the immune system and the microbiota are functionally intertwined during Aspergillus infection and determine the outcome of the infection.

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Section: Metagenomicsmentioning

confidence: 99%

A Shifted Composition of the Lung Microbiota Conditions the Antifungal Response of Immunodeficient Mice

Nunzi

Renga

Palmieri

et al. 2021

IJMS

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“…The reason is that these types of data sets are stored at distant (remote) databases and their transmission is supported by IP-based Internet. Therefore, similar genomic data sets are needed to be sent across the remote location several times [69,70]. Consequently, several problems are created regarding transmission of genomic data sets in which bandwidth, congestion, delay, and high resource consumption is maximized.…”

Section: Future Directionsmentioning

confidence: 99%

Compound Popular Content Caching Strategy in Named Data Networking

et al. 2019

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The aim of named data networking (NDN) is to develop an efficient data dissemination approach by implementing a cache module within the network. Caching is one of the most prominent modules of NDN that significantly enhances the Internet architecture. NDN-cache can reduce the expected flood of global data traffic by providing cache storage at intermediate nodes for transmitted contents, making data broadcasting in efficient way. It also reduces the content delivery time by caching popular content close to consumers. In this study, a new content caching mechanism named the compound popular content caching strategy (CPCCS) is proposed for efficient content dissemination and its performance is measured in terms of cache hit ratio, content diversity, and stretch. The CPCCS is extensively and comparatively studied with other NDN-based caching strategies, such as max-gain in-network caching (MAGIC), WAVE popularity-based caching strategy, hop-based probabilistic caching (HPC), LeafPopDown, most popular cache (MPC), cache capacity aware caching (CCAC), and ProbCache through simulations. The results shows that the CPCCS performs better in terms of the cache hit ratio, content diversity ratio, and stretch ratio than all other strategies.

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“…The simulation results indicate a downward trend in latency and overall network traffic. In [37], the authors discuss various insights of caching or replicating genome data set to provide guidelines for the improvement and optimization of genome content distribution. The authors analyze the main genome processing applications, and classify genome workflow computation alternatives as either a location machine or a distributed cloud.…”

Section: Related Workmentioning

confidence: 99%

Optimal Content Caching in Content-Centric Networks

Qazi

Khalid

Rais

et al. 2019

Wireless Communications and Mobile Computing

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Content-Centric Networking (CCN) is a novel architecture that is shifting host-centric communication to a content-centric infrastructure. In recent years, in-network caching in CCNs has received significant attention from research community. To improve the cache hit ratio, most of the existing schemes store the content at maximum number of routers along the downloading path of content from source. While this helps in increased cache hits and reduction in delay and server load, the unnecessary caching significantly increases the network cost, bandwidth utilization, and storage consumption. To address the limitations in existing schemes, we propose an optimization based in-network caching policy, named as opt-Cache, which makes more efficient use of available cache resources, in order to reduce overall network utilization with reduced latency. Unlike existing schemes that mostly focus on a single factor to improve the cache performance, we intend to optimize the caching process by simultaneously considering various factors, e.g., content popularity, bandwidth, and latency, under a given set of constraints, e.g., available cache space, content availability, and careful eviction of existing contents in the cache. Our scheme determines optimized set of content to be cached at each node towards the edge based on content popularity and content distance from the content source. The contents that have less frequent requests have their popularity decreased with time. The optimal placement of contents across the CCN routers allows the overall reduction in bandwidth and latency. The proposed scheme is compared with the existing schemes and depicts better performance in terms of bandwidth consumption and latency while using less network resources.

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Genomics as a service: A joint computing and networking perspective

Cited by 9 publications

References 116 publications

A Shifted Composition of the Lung Microbiota Conditions the Antifungal Response of Immunodeficient Mice

A Shifted Composition of the Lung Microbiota Conditions the Antifungal Response of Immunodeficient Mice

Compound Popular Content Caching Strategy in Named Data Networking

Optimal Content Caching in Content-Centric Networks

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