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…
Roy Cruz Candelaria, Wouter Deconinck, Aman Desai, Guillermo Fidalgo Rodríguez + 9 more
We present the material and resources developed for training physicists on containerization technologies enabled by Apptainer. In the context of analysis preservation using Apptainer's capabilities, we have developed examples that execute common tools in High Energy Physics (HEP) and Nuclear Physics within containers.…
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…
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…
W. Li, Rodney S. Lafuente Mercado, Jaime Peña, Ross E. Allen
—We present Syndeo: a software framework for container orchestration of Ray on Slurm. In general the idea behind Syndeo is to write code once and deploy anywhere. Specifically, Syndeo is designed to addresses the issues of portability, scalability, and security for parallel computing. The design is portable because the…
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…
Gregory J. Hunt, Johann A. Gagnon-Bartsch
In recent decades the analysis of data has become increasingly computational. Correspondingly, this has changed how scientific and statistical work is shared. For example, it is now commonplace for underlying analysis code and data to be proffered alongside journal publications and conference talks. Unfortunately…
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…
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…
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…
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…
Karol Chlasta, Paweł Sochaczewski, Grzegorz M. Wójcik, Izabela Krejtz
'Izabela Krejtz'] In this study, we explore the simulation setup in computational neuroscience. We use GENESIS, a general purpose simulation engine for sub-cellular components and biochemical reactions, realistic neuron models, large neural networks, and system-level models. GENESIS supports developing and running…
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…
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.…
Jinghui Geng, Kateryna Voitiuk, David F. Parks, Ash Robbins + 15 more
Electrophysiology offers a high-resolution method for real-time measurement of neural activity. Longitudinal recordings from high-density microelectrode arrays (HD-MEAs) can be of considerable size for local storage and of substantial complexity for extracting neural features and network dynamics. Analysis is often…
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.…
Anthony Sonrel, Almut Luetge, Charlotte Soneson, Izaskun Mallona + 16 more
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and…
Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck + 2 more
Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for…
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.…