23 papers · ranked by Valyu relevance
Gregory M. Kurtzer, Vanessa Sochat, Michael W. Bauer, Attila Gursoy
Here we present Singularity, software developed to bring containers and reproducibility to scientific computing. Using Singularity containers, developers can work in reproducible environments of their choosing and design, and these complete environments can easily be copied and executed on other platforms. Singularity…
Jorge Gomes, Emanuele Bagnaschi, Isabel Campos, M. David + 5 more
'Luís M. Alves' 'João Pedro Facundo Martins' 'J. Pína' 'Álvaro López García' 'Pablo Orviz'] Containers are increasingly used as means to distribute and run Linux services and applications. In this paper we describe the architectural design and implementation of udocker, a tool which enables the user to execute Linux…
Vaibhav Rastogi, Drew Davidson, Lorenzo De Carli, Somesh Jha + 1 more
'Patrick McDaniel'] Application containers, such as Docker containers, have recently gained popularity as a solution for agile and seamless deployment of applications. These light-weight virtualization environments run applications that are packed together with their resources and configuration information, and thus…
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…
Ilter Taha Aktolga, Elif Sena Kuru, Yiğit Sever, Pelin Angın
The rising use of microservices based software deployment on the cloud leverages containerized software extensively. The security of applications running inside containers as well as the container environment itself are critical infrastructure in the cloud setting and 5G. To address the security concerns, research…
Udit Gupta
Virtualization started to gain traction in the domain of information technology in the early 2000's when managing resource distribution was becoming an uphill task for developers. As a result, tools like VMWare, Hyper-V (hypervisor) started making inroads into the software repository on different operating systems.…
Maria A. Rodriguez, Rajkumar Buyya
Containers, enabling lightweight environment and performance isolation, fast and flexible deployment, and fine-grained resource sharing, have gained popularity in better application management and deployment in addition to hardware virtualization. They are being widely used by organizations to deploy their increasingly…
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…
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…
Cheol-Ho Hong, Kyungwoon Lee, Minkoo Kang, Chuck Yoo
Fog computing is a new computing paradigm that employs computation and network resources at the edge of a network to build small clouds, which perform as small data centers. In fog computing, lightweight virtualization (e.g., containers) has been widely used to achieve low overhead for performance-limited fog devices…
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…
Kavishwar B. Wagholikar, Pralav Dessai, Javier Sanz, Michael E. Mendis + 2 more
'Michael E. Mendis' 'Douglas S. Bell' 'Shawn N. Murphy'] Background Informatics for Integrating Biology and the Bedside (i2b2) is an open source clinical data analytics platform used at over 200 healthcare institutions for querying patient data. The i2b2 platform has several components with numerous dependencies 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…
Thanh Nhan Bui
Over the last few years, the use of virtualization technologies has increased dramatically. This makes the demand for efficient and secure virtualization solutions become more obvious. Container-based virtualization and hypervisor-based virtualization are two main types of virtualization technologies that have emerged…
Ling-Hong Hung, Daniel Kristiyanto, Sung Bong Lee, Ka Yee Yeung + 1 more
'Lennart Martens'] Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact…
Reem Almugbel, Ling-Hong Hung, Jiaming Hu, Abeer Almutairy + 3 more
Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, to allow users to easily…
Pai Zhang, Ling-Hong Hung, Wes Lloyd, Ka Yee Yeung
Using software containers has become standard practice to reproducibly deploy and execute biomedical workflows on the cloud. We demonstrate that hot-starting, from containers that have been frozen after the application has already begun execution, reduces the costs of cloud computing by avoiding repetitive…
Eric Deutsch, Luis Mendoza, David Shteynberg, Michael Hoopmann + 3 more
The Trans-Proteomic Pipeline mass spectrometry data analysis suite has been in continual development and refinement since its first tools PeptideProphet and ProteinProphet were published twenty years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search…
Jiaming Hu, Ling-Hong Hung, Ka Yee Yeung
Data science notebooks, such as Jupyter, combine text documentation with dynamically editable and executable code and have become popular for sharing computational methods. We present nbdocker, an extension that integrates Docker software containers into Jupyter notebooks. nbdocker transforms notebooks into autonomous…
Federico Marotta, Oliver Stolpe, Benedikt Obermayer, January Weiner + 3 more
In many bioinformatic data analysis projects, it is convenient to visualize plots and results through an interactive web app or dashboard. These interactive reports can then be shared with customers, collaborators, or the general public. Publishing and sharing these apps is not straightforward, becoming especially…
Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan + 1 more
Processing of Next-Generation Sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized post-analysis visualization and data mining software. In order to address some of these challenges, developers have…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
Authors not listed
Machine learning models are transforming data-driven research across scientific disciplines, yet their deployment as accessible and reliable web services remains a significant challenge. We introduce the NERDD framework, a scalable, maintainable, and secure microservices platform designed to support the sustainable…