23 papers · ranked by Valyu relevance
Kelsey R. Florek, Erin L. Young, Kutluhan Incekara, Kevin G. Libuit + 1 more
'Curtis J. Kapsak'] Bioinformatic software containerization, the process of packaging software that encapsulates an application together with all necessary dependencies to simplify installation and use, has improved the deployment and management of next-generation sequencing workflows in both clinical and public health…
Henry Clausen, Robert Flood, David Aspinall
The design and evaluation of data-driven network intrusion detection methods are currently held back by a lack of adequate data, both in terms of benign and attack traffic. Existing datasets are mostly gathered in isolated lab environments containing virtual machines, to both offer more control over the computer…
Lubomir Urblik, Erik Kajati, Peter Papcun, Iveta Zolotova + 1 more
'Peter Chong'] There is a rapid increase in the number of edge devices in IoT solutions, generating vast amounts of data that need to be processed and analyzed efficiently. Traditional cloud-based architectures can face latency, bandwidth, and privacy challenges when dealing with this data flood. There is currently no…
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…
Mohamed Salim Nasser Al Hinai, Zakira Naureen, Syed Abdullah Gilani
Since, Bioinformatic research is getting attraction that can be seen with sudden increase in development of tools as well as publications. However, there are challenges in bioinformatics which are making the results difficult to obtain while facing reproducibility, scalability, and accessibility of computational…
Prathamesh Muzumdar, Amol Bhosale, Ganga Prasad Basyal, George Thomas Kurian
The cloud computing landscape is rapidly expanding and growing in complexity. It has witnessed the emergence of Cloud Computing as a widely adopted model for efficiently processing large volumes of data by harnessing clusters of commodity computers. This evolution enables the handling of massive data through on-demand…
VP Nagraj, Stephen D Turner, Neal Magee
Containerization enables portable, reproducible, and scalable scientific computing. However, container development, documentation, and deployment practices can vary widely, even within a single domain. Understanding patterns of how containers are implemented in real-world settings can inform community guidelines…
Vamsi Krishna Yepuri, Venkata Kalyan Polamarasetty, Shivani Donthi, Ajay Kumar Reddy Gondi
'Ajay Kumar Reddy Gondi'] Abstract—This project investigates the benefits of containerization technology in modern software development and deployment. The study emphasizes the advantages of using Kubernetes and Docker in the development process, including the easy packaging and deployment of microservices, efficient…
Safaa Hriez, Mohammad Haikal
Introduction The rapid growth of artificial intelligence (AI) has significantly increased computing demand, intensifying the operational strain on the computing environment. While virtualization and containerization are established technologies for resource optimization, their comparative energy efficiency and…
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…
Eric Hitimana, Gaurav Bajpai, Richard Musabe, Louis Sibomana + 2 more
'Kayavizhi Jayavel' 'Antonio Puliafito'] Nowadays, building infrastructures are pushed to become smarter in response to desires for the environmental comforts of living. Enhanced safety upgrades have begun taking advantage of new, evolving technologies. Normally, buildings are configured to respond to the safety…
Eddie Antonio Santos, Carson McLean, Christopher Solinas, Abram Hindle
Virtualization provides a number of benefits when deploying software, such as process isolation and resource control. Process isolation means that software developers can make strong assumptions about the state of the system, including the operating system configuration, and having the exact software dependencies…
Koustabh Dolui, Csaba Király
—Stringent latency requirements in advanced Internet of Things (IoT) applications as well as an increased load on cloud data centers have prompted a move towards a more decentralized approach, bringing storage and processing of IoT data closer to the end-devices through the deployment of multi-purpose IoT gateways.…
Jingwen Bai, Chakradhar Bandla, Jiaxin Guo, Roberto Vera Alvarez + 6 more
BioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community has developed a set of guidelines to standardize the software containers including the metadata, versions, licenses, and/or software dependencies. BioContainers…
V. S. Devi Priya, S. Sibi Chakkaravarthy
Discovering malicious packets amid a cloud of normal activity, whether you use an IDS or gather and analyze machine and device log files on company infrastructure, may be challenging and time consuming. The vulnerability landscape is rapidly evolving, and it will only become worse as more and more developing…
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…
Tomasz Przygodzki
Quantitative analysis of microscopic images has become a standard in basic biological and biomedical research. Deep machine learning provided a powerful tool facilitating this process. However, practical adoption of deep machine learning to image analysis may be difficult for a researcher who lacks basic coding skills.…
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…
Garikoitz Lerma-Usabiaga, Noah Benson, Jonathan Winawer, Brian A. Wandell
Neuroimaging software methods are complex, making it a near certainty that some implementations will contain errors. Modern computational techniques (i.e., public code and data repositories, continuous integration, containerization) enable the reproducibility of the analyses and reduce coding errors, but they do not…
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…
Authors not listed
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, and are packed full of enzyme cargoes and metabolites as they fulfill their function.…
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Effective visualization of complex synthesis routes is critical for computeraided synthesis planning (CASP), yet current solutions are limited in scope, integration flexibility, and chemical intuition. We introduce RouteWise, a versatile, containerized web application designed to address these unmet needs. Its modular…