18 papers · ranked by Valyu relevance
Jonas Weber
Containers as the unit of application delivery are the 'next big thing' in the software development world. They enable developers to create an executable image containing an application bundled with all its dependencies which a user can run inside a controlled environment with virtualized resources. Complex workflows…
Gijs Molenaar, Spheshile Makhathini, Julien N. Girard, O. Smirnov
Kliko is a Docker-based container specification for running one or multiple related compute jobs. The key concepts of Kliko are the encapsulation of data processing software into a container and the formalization of the input, output and task parameters. By formalizing the parameters, the software is represented as…
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…
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…
Marcelo Amaral, Jordà Polo, David Carrera, Iqbal Mohomed + 2 more
'Merve Unuvar' 'Małgorzata Steinder'] Abstract—Microservices architecture has started a new trend for application development for a number of reasons: (1) to reduce complexity by using tiny services; (2) to scale, remove and deploy parts of the system easily; (3) to improve flexibility to use different frameworks and…
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…
Shaun D Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O’Huiginn + 4 more
Setting up a suitable platform for effective bioinformatics analysis can be challenging. Determining the dependencies and version requirements needed to install standard software packages is a barrier before analysis can even begin. Installing a bioinformatics tool requires first installing its dependencies, which…
Jordan Matelsky, Gregory Kiar, Erik Johnson, Corban Rivera + 2 more
'Michael Toma' 'William Gray-Roncal'] Medical imaging analysis depends on the reproducibility of complex computation. Linux containers enable the abstraction, installation, and configuration of environments so that software can be both distributed in self-contained images and used repeatably by tool consumers. While…
Jon Ander Novella, Payam Emami Khoonsari, Stephanie Herman, Daniel Whitenack + 4 more
Computational biologists face many challenges related to data size, and they need to manage complicated analyses often including multiple stages and multiple tools, all of which must be deployed to modern infrastructures. To address these challenges and maintain reproducibility of results, researchers need (i) a…
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…
A. Ingargiola, T. Laurence, S. Weiss, X. Michalet
We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based…
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…
Xu Yang, Masahiro Kasahara
Delivering tools for genome analysis to users is often difficult given their complex dependencies and conflicts. Container virtualization systems such as Singularity isolate environments, helping developers avoid conflicts between tools. However, they lack composability, an easy way to integrate multiple tools in…
Carlo Puliafito, Carlo Vallati, Enzo Mingozzi, Giovanni Merlino + 2 more
The internet of things (IoT) is essential for the implementation of applications and services that require the ability to sense the surrounding environment through sensors and modify it through actuators. However, IoT devices usually have limited computing capabilities and hence are not always sufficient to directly…
Pablo Moreno, Luca Pireddu, Pierrick Roger, Nuwan Goonasekera + 16 more
Making reproducible, auditable and scalable data-processing analysis workflows is an important challenge in the field of bioinformatics. Recently, software containers and cloud computing introduced a novel solution to address these challenges. They simplify software installation, management and reproducibility by…
Authors not listed
In this second part, we present the explicit analytical expression of the framework introduced in Part I. The formulation yields closed-form predictions for capillary rise and depression in cylindrical geometries and extends naturally to a wide range of configurations. It shows that the contact angle, rather than being…
Simon Lambert, Kristin Bartik, Ivan Jabin
The control of the selective transformation of a functional group on a substrate bearing multiple identical reactive functions is a major synthetic challenge. The use of macrocyclic molecular containers as supramolecular protecting units is in this context a promising strategy. We report here on a…
James Scott-Brown, Antonis Papachristodoulou
Using robots to automate laboratory tasks could increase throughput and reproducibility, but requires experimental protocols to be specified in a computer-readable format. We present a new user interface (Lists of Liquids) for specifying experimental protocols by directly manipulating a diagram: rather than having to…