Related papers: Genomic data processing with GenomeFlow
The increasing availability of cloud computing services for science has changed the way scientific code can be developed, deployed, and run. Many modern scientific workflows are capable of running on cloud computing resources. Consequently,…
In order to improve system performance efficiently, a number of systems choose to equip multi-core and many-core processors (such as GPUs). Due to their discrete memory these heterogeneous architectures comprise a distributed system within…
Distributed dataflow systems like Spark and Flink enable data-parallel processing of large datasets on clusters of cloud resources. Yet, selecting appropriate computational resources for dataflow jobs is often challenging. For efficient…
Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…
Large-scale ad hoc analytics of genomic data is popular using the R-programming language supported by 671 software packages provided by Bioconductor. More recently, analytical jobs are benefitting from on-demand computing and storage, their…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
In present day technology, storing and processing of information occur on physically distinct regions of space. Not only does this result in space limitations; it also translates into unwanted delays in retrieving and processing of relevant…
Many modern applications require real-time processing of large volumes of high-speed data. Such data processing needs can be modeled as a streaming computation. A streaming computation is specified as a dataflow graph that exposes multiple…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
This paper presents a novel application of Genetic Algorithms(GAs) to quantify the performance of Platform as a Service (PaaS), a cloud service model that plays a critical role in both industry and academia. While Cloud benchmarks are not…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Edge-cloud collaborative inference is becoming a practical necessity for LLM-powered edge devices: on-device models often cannot afford the required reasoning capability, while cloud-only inference could be prohibitively costly and slow…
The need for computational resources grows as computational algorithms gain popularity in different sectors of the scientific community. This search has stimulated the development of several cloud platforms that abstract the complexity of…
Motivation: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base construction and protein structure determination all benefit from human input. In…
Domains such as manufacturing and medicine crave for continuous monitoring and analysis of their processes, especially in combination with time series as produced by sensors. Time series data can be exploited to, for example, explain and…
FastFlow is a structured parallel programming framework targeting shared memory multicores. Its layered design and the optimized implementation of the communication mechanisms used to implement the FastFlow streaming networks provided to…
Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed…
Apart from forming the backbone of compiler optimization, static dataflow analysis has been widely applied in a vast variety of applications, such as bug detection, privacy analysis, program comprehension, etc. Despite its importance,…
This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node…
The Internet of Things (IoT) is offering unprecedented observational data that are used for managing Smart City utilities. Edge and Fog gateway devices are an integral part of IoT deployments to acquire real-time data and enact controls.…