Related papers: S3Mirror: Making Genomic Data Transfers Fast, Reli…
Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…
Observability helps ensure the reliability and maintainability of cloud-native applications. As software architectures become increasingly distributed and subject to change, it becomes a greater challenge to diagnose system issues…
In past years, the world has switched to many-core and multi-core shared memory architectures. As a result, there is a growing need to utilize these architectures by introducing shared memory parallelization schemes to software…
The problem of data synchronization arises in networked applications that require some measure of consistency. Indeed data synchronization approaches have demonstrated a significant potential for improving performance in various…
The deployment of 3D detectors strikes one of the major challenges in real-world self-driving scenarios. Existing BEV-based (i.e., Bird Eye View) detectors favor sparse convolutions (known as SPConv) to speed up training and inference,…
Motivation: Our goal was to combine the capabilities of Spark and GOR into a single computing framework for use in analysis of large scale genome data. Results: We have created a relational query engine that unites SparkSQL and GORpipe into…
The reproducibility of computational pipelines is an expectation in biomedical science, particularly in critical domains like human health. In this context, reporting next generation genome sequencing methods used in precision medicine…
Serverless functions provide high levels of parallelism, short startup times, and "pay-as-you-go" billing. These attributes make them a natural substrate for data analytics workflows. However, the impossibility of direct communication…
Fourier and related transforms is a family of algorithms widely employed in diverse areas of computational science, notoriously difficult to scale on high-performance parallel computers with large number of processing elements (cores). This…
Software Defined Networking (SDN) not only enables agility through the realization of part of the network functionality in software but also facilitates offering advanced features at the network layer. Hence, SDN can support a wide range of…
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…
Modular data centers (MDCs) that can be placed right at the energy farms and powered mostly by renewable energy, are proven to be a flexible and effective approach to lowering the carbon footprint of data centers. However, the main…
The FFT of three-dimensional (3D) input data is an important computational kernel of numerical simulations and is widely used in High Performance Computing (HPC) codes running on a large number of processors. Performance of many scientific…
Large scale initiatives such as the Human Genome Project, Structural Genomics, and individual research teams have provided large deposits of genomic and proteomic data. The transfer of data to knowledge has become one of the existing…
The need for high availability and performance in data management systems has been fueling a long running interest in database replication from both academia and industry. However, academic groups often attack replication problems in…
Embedded Linux processors are increasingly used for real-time computing tasks such as robotics and Internet of Things (IoT). These applications require robust and reproducible behavior from the host OS, commonly achieved through immutable…
In modern computing, RDBMS are great to store different types of data. To a developer, one of the major objectives is to provide a very low cost and easy to use solution to an existing problem. While commercial databases are more easy to…
Consus is a strictly serializable geo-replicated transactional key-value store. The key contribution of Consus is a new commit protocol that reduces the cost of executing a transaction to three wide area message delays in the common case.…
Recent advances in transformer architectures have revolutionised natural language processing, but their application to healthcare domains presents unique challenges. Patient timelines are characterised by irregular sampling, variable…
Leadership computing facilities around the world support cutting-edge scientific research across a broad spectrum of disciplines including understanding climate change, combating opioid addiction, or simulating the decay of a neutron. While…