22 papers · ranked by Valyu relevance
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…
Gong Cheng, Quan Lu, Ling Ma, Guocai Zhang + 3 more
'Zongshan Zhou' 'Jun Chen'] Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the…
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…
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…
D. Morris, S. Voutsinas, N. C. Hambly, Robert G. Mann
We describe preliminary investigations of using Docker for the deployment and testing of astronomy software. Docker is a relatively new containerisation technology that is developing rapidly and being adopted across a range of domains. It is based upon virtualization at operating system level, which presents many…
Brian D. O'Connor, Denis Yuen, Vincent Chung, Andrew G. Duncan + 5 more
'Xiang Kun Liu' 'Janice Patricia' 'Benedict Paten' 'Lincoln Stein' 'Vincent Ferretti'] As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as…
Piyush Agrawal, Rajesh Kumar, Salman Sadullah Usmani, Anjali Dhall + 9 more
In past number of web-based resources has been developed in the field of Bioinformatics. These resources are heavily used by scientific community to provide solution for challenges faced by experimental researchers particularly in the field of biomedical sciences. There are number of challenges in utilizing full…
Gong Cheng, Zongshan Zhou, Ling Ma, Guocai Zhang + 2 more
At present Docker technology is increasing level of attention throughout the bioinformatics community, but Docker technology implementation details have not been mastered by most biologist and applied in biological research, In order to apply this technology in the popularization and sufficient use plenty of free…
Adi Farshteindiker, Rami Puzis, Sotiris Kotsiantis, Alberto Guillén
With the advent of microservice-based software architectures, an increasing number of modern cloud environments and enterprises use operating system level virtualization, which is often referred to as container infrastructures. Docker Swarm is one of the most popular container orchestration infrastructures, providing…
ChangHyuk Kwon, Jason Kim, Jaegyoon Ahn, Joseph Gillespie
Background and Objective Docker is a light containerization program that shows almost the same performance as a local environment. Recently, many bioinformatics tools have been distributed as Docker images that include complex settings such as libraries, configurations, and data if needed, as well as the actual tools.…
Ling-Hong Hung, Trevor Meiss, Jayant Keswani, Yuguang Xiong + 2 more
We present BioDepot-workflow-Builder (BwB), a portable and open-source tool for creating bioinformatics workflows with a simple drag-and-drop graphical user interface. The individual components of the workflows are Docker containers which are available from public repositories or provided by the user. The use of…
Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni + 4 more
Reproducibility of a research is a key element in the modern science and it is mandatory for any industrial application. It represents the ability of replicating an experiment independently by the location and the operator. Therefore, a study can be considered reproducible only if all used data are available and the…
Authors not listed
Molecular docking has become an essential tool in the early stages of structure-based drug discovery, enabling rapid virtual screening of large compound libraries against biological targets. However, the accuracy of binder selection is often limited by the available scoring functions. Here, we present a novel workflow…
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…
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…
Robail Yasrab
It is very easy to run applications in Docker. Docker offers an ecosystem that offers a platform for application packaging, distributing and managing within containers. However, Docker platform is yet not matured. Presently, Docker is less secured as compare to virtual machines (VM) and most of the other cloud…
Venkata Chandrasekhar, Nisha Sharma, Jonas Schaub, Christoph Steinbeck + 1 more
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management.…
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…
Ho-min Park, Jongbum Won, Yunseol Park, Esla Timothy Anzaku + 4 more
CRISPR-Cas-Docker is a web server for in silico docking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted computationally when prokaryotic genomes have multiple CRISPR arrays and Cas systems, as frequently observed in…
Authors not listed
The widespread adoption of open-source cheminformatics toolkits remains constrained by technical implementation barriers, including complex installation procedures, dependency management, and integration challenges. Here, we present Cheminformatics Microservice V3, a significant update to the existing platform that…
Authors not listed
This paper presents GLAS (Git-based Lab Automated Scheduler or Get Lab Automation Simplified), an open-source, robust, and highly expandable Git-based architecture designed for laboratory automation. GLAS can be deployed in both partially and fully automated experimental science laboratories, enabling the development…
Jeff Guo, Jon Paul Janet, Matthias R. Bauer, Eva Nittinger + 6 more
Recently, we have released the de novo design platform REINVENT in version 2.0. This improved and extended iteration supports far more features and scoring function components, which allows bespoke and tailor-made protocols to maximize impact in small molecule drug discovery projects. A major obstacle of generative…