Related papers: Genomic data processing with GenomeFlow
The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems.…
This article introduces a general processing framework to effectively utilize waveform data stored on modern cloud platforms. The focus is hybrid processing schemes where a local system drives processing. We show that downloading files and…
We assess the potential of quantum computing to accelerate computation of central tasks in genomics, focusing on often-neglected theoretical limitations. We discuss state-of-the-art challenges of quantum search, optimization, and machine…
The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive…
Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…
The ability to process large numbers of continuous data streams in a near-real-time fashion has become a crucial prerequisite for many scientific and industrial use cases in recent years. While the individual data streams are usually…
The proliferation of cloud data center applications and network function virtualization (NFV) boosts dynamic and QoS dependent traffic into the data centers network. Currently, lots of network routing protocols are requirement agnostic,…
Shared memory multiprocessors come back to popularity thanks to rapid spreading of commodity multi-core architectures. As ever, shared memory programs are fairly easy to write and quite hard to optimise; providing multi-core programmers…
Complex workflows play a critical role in accelerating scientific discovery. In many scientific domains, efficient workflow management can lead to faster scientific output and broader user groups. Workflows that can leverage resources…
Whilst computational resources at the cloud edge can be leveraged to improve latency and reduce the costs of cloud services for a wide variety mobile, web, and IoT applications; such resources are naturally constrained. For distributed…
Background: Metabolomics datasets are becoming increasingly large and complex, with multiple types of algorithms and workflows needed to process and analyse the data. A cloud infrastructure with portable software tools can provide much…
The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a…
To increase performance and efficiency, systems use FPGAs as reconfigurable accelerators. A key challenge in designing these systems is partitioning computation between processors and an FPGA. An appropriate division of labor may be…
Cloud computing offers on-demand, scalable computing and storage, and has become an essential resource for the analyses of big biomedical data. The usual approach to cloud computing requires users to reserve and provision virtual servers.…
Recent advances in computing architectures and networking are bringing parallel computing systems to the masses so increasing the number of potential users of these kinds of systems. In particular, two important technological evolutions are…
In many scientific and engineering applications, one has to solve not one but a sequence of instances of the same problem. Often times, the problems in the sequence are linked in a way that allows intermediate results to be reused. A…
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…
Graph partitioning, a well studied problem of parallel computing has many applications in diversified fields such as distributed computing, social network analysis, data mining and many other domains. In this paper, we introduce FGPGA, an…