15 papers · ranked by Valyu relevance
Tiziano Müller, Nina Mujkanovic, Juan J. Durillo, Nicolay Hammer
Containers offer an array of advantages that benefit research reproducibility and portability across groups and systems. As container tools mature, container security improves, and High-performance computing (HPC) and cloud system tools converge, supercomputing centers are increasingly integrating containers in their…
Huaifeng Zhang, Mohannad Alhanahnah, Ahmed Ali-Eldin
While there has been exponential improvements in hardware performance over the years, software performance has lagged behind. The performance-gap is caused by software inefficiencies, many of which are caused by software bloat. Software bloat occurs due to the ever increasing, mostly unused, features and dependencies…
Luciano Baresi, Giovanni Quattrocchi, Nicholas Rasi
Containerization is a virtualization technique that allows one to create and run executables consistently on any infrastructure. Compared to virtual machines, containers are lighter since they do not bundle a (guest) operating system but they share its kernel, and they only include the files, libraries, and…
Reid Priedhorsky, R. S. Canon, Timothy Randles, Andrew Younge
HPC centers face increasing demand for software flexibility, and there is growing consensus that Linux containers are a promising solution. However, existing container build solutions require root privileges and cannot be used directly on HPC resources. This limitation is compounded as supercomputer diversity expands…
Chaoze Lu, Jianchao Zhou, Qifeng Zou, Jacopo Soldani
Lightweight container technology has emerged as a fundamental component of cloud-native computing, with the deployment of containers and the balancing of loads on virtual machines representing significant challenges. This paper presents an optimization strategy for container deployment that consists of two stages…
Christoph Karfusehr, Markus Eder, Friedrich C. Simmel
DNA origami provides a methodology for the sequence-programmable generation of precisely defined molecular nanostructures with sizes of order 100 nm. A new frontier for the field is the generation of superstructures made from DNA origami subunits, which requires other self-assembly strategies than those used for DNA…
Ling-Hong Hung, Evan Straw, Shishir Reddy, Zachary Colburn + 1 more
Biomedical image analyses can require many steps processing different types of data. Analysis of increasingly large data sets often exceeds the capacity of local computational resources. We present an easy-to-use and modular cloud platform that allows biomedical researchers to reproducibly execute and share complex…
Naweiluo Zhou, Huan Zhou, Dennis Hoppe
2022 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or…
Xu Yang, Masahiro Kasahara
Background Delivering tools for genome analysis to users is often difficult given the complex dependencies and conflicts of such tools. Container virtualization systems (such as Singularity) isolate environments, thereby helping developers package tools. However, these systems lack mutual composability, i.e., an easy…
Moses Openja, Forough Majidi, Foutse Khomh, Bhagya Chembakottu + 1 more
Docker and its related container technologies have become a prominent solution for automating the deployment of modern software systems. This is true due to its numerous desirable features such as isolation, low overhead, and efficient packaging of the runtime environment. Docker container management framework consists…
Varik Hoang, Ling-Hong Hung, David Perez, Huazeng Deng + 4 more
To use the Container Profiler scripts with any container, a Linux-based Docker container that encapsulates a script or job to run inside is required. To configure the Container Profiler tool to profile the container, users can optionally provide an executable script inside the Container Profiler, which is specified…
Mads Ry Vogel Jørgensen, Frederik Holm Gjørup, Meghdad Yazdi-Rizi, Zdenek Matej + 3 more
A standardized HDF5-based data format for azimuthally integrated scattering and diffraction data, developed within the NeXus framework, is presented. This format enables inter-operability across facilities and software, helps support FAIR principles, and simplifies data analysis workflows.
Khaled Atia, Robert Hunter, Meshach Asare-Werehene, Benjamin K. Tsang + 1 more
Raman spectroscopy is a powerful tool for qualitative and quantitative analysis in various scientific and industrial fields. However, the development of multisample automated screening remains relatively unexplored. In this paper, we develop RamanBot, a low-cost, easy-to-assemble, and automated Raman spectroscopy…
Mikhail Y. Kovalyov, Mikhail N. Lukashevich, Erwin Pesch
A problem of optimal mid-term or long-term planning of inspection and repair of freight containers in multiple facilities is introduced and investigated. The containers are of different types and quality levels, which define their repair costs and workforce requirements. The objective function includes the total…
Dustin B. Mullaney, Samantha R. Sgrizzi, David Mai, Ian Campbell + 12 more
Single-cell genomics methods have unveiled the heterogeneity present in seemingly homogenous populations of cells, however, these techniques require meticulous optimization. How exactly does one handle and manipulate the biological contents from a single cell? Here, we introduce and characterize a novel semi-permeable…