18 papers · ranked by Valyu relevance
Kaiyuan Han, Ting Wang, Shi-Shi Yuan, Cai-Yi Ma + 4 more
Bioinformatics workflows often involve multiple tools and steps, with complex dependencies and environment-specific differences, making results difficult to reproduce across different systems. TAFFISH introduces a moderately engineered framework positioned between raw shell scripts and heavyweight workflow systems. It…
Kaiyuan Han, Ting Wang, Shi-Shi Yuan, Cai-Yi Ma + 5 more
Bioinformatics workflows often involve multiple tools and steps, with complex dependencies and environment-specific differences, making results difficult to reproduce across different systems. TAFFISH introduces a moderately engineered framework positioned between raw shell scripts and heavyweight workflow systems. It…
Jiri Dokulil, Siegfried Benkner
Task-based runtime systems are an important branch of parallel programming research, since tasks decouple computation from the compute units, giving the runtime systems greater flexibility than a thread-based solution. This makes it easier to deal with the ever-increasing complexity of parallel architectures by…
Kyle C. Hale, Conor Hetland, Peter A. Dinda
—The hybrid runtime (HRT) model offers a path towards high performance and efficiency. By integrating the OS kernel, runtime, and application, an HRT allows the runtime developer to leverage the full feature set of the hardware and specialize OS services to the runtime's needs. However, conforming to the HRT model…
Geonbae Na, Jongsu Lim, Sunjun Lee, Jeong Hyun Yi
As interest in Internet of Things environments rapidly increases throughout the IT convergence field, compatibility with mobile devices must be provided to enable personalized services. The security of mobile platforms and applications is critical because security vulnerabilities of mobile devices can be spread to all…
Ayaz Hafiz, Kevin Jin
This paper solves this problem by presenting a cloud-based web service for remote code execution, that is easily extensible to support any number of programming languages and libraries. The service provides a fast, reproducible solution for small software experiments and is amenable to collaboration in a workplace (via…
Aamir Akbar, Peter R. Lewis, Elizabeth Wanner
Backed by the virtually unbounded resources of the cloud, battery-powered mobile robotics can also benefit from cloud computing, meeting the demands of even the most computationally and resource-intensive tasks. However, many existing mobile-cloud hybrid (MCH) robotic tasks are inefficient in terms of optimizing…
Javier E. Pimás, Stefan Marr, Diego Garbervetsky
Object-oriented languages often use virtual machines (VMs) that provide mechanisms such as just-in-time (JIT) compilation and garbage collection (GC). These VM components are typically implemented in a separate layer, isolating them from the application. While this approach brings the software engineering benefits of…
Tazro Ohta, Tomoya Tanjo, Osamu Ogasawara
Improvements in the accuracy and quantity capacity of DNA sequencing technology mean that various sequencing methods are now available to measure different genomic features. Each method produces a massive amount of nucleotide sequence data, which require different data processing approaches . Bioinformatics researchers…
Tazro Ohta, Tomoya Tanjo, Osamu Ogasawara
Container virtualization technologies such as Docker became popular in the bioinformatics domain as they improve portability and reproducibility of software deployment. Along with software packaged in containers, the workflow description standards Common Workflow Language also enabled to perform data analysis on…
Roua Jabla, Maha Khemaja, Félix Buendia, Sami Faiz
With the increasing interest devoted to dynamic environments, a crucial aspect is revealed in context-aware systems to deal with the rapid changes occurring in users' surrounding environments at runtime. However, most context-aware systems with predefined context-aware rules may not support effective decision-making in…
Markus Raab, Gergö Barany
Software tends to be highly configurable, but most applications are hardly context aware. For example, a web browser provides many settings to configure printers and proxies, but nevertheless it is unable to dynamically adapt to a new workplace. In this paper we aim to empirically demonstrate that by dynamic and…
Maria Paasivaara, Philippe Kruchten, Seán Murphy, Leonardas Persaud + 2 more
'William Martini' 'Bill Bosshard'] This paper considers how WASM can be run in different serverless contexts. A comparison of different serverside WASM runtime options is considered, specifically focused on wasmer, wasmtime and lucet. Next, different options for running WASM within two serverless platforms - Openwhisk…
Shixiang Wang
Bioinformatics analyses depend on workflow engines to coordinate dozens of computational tools across complex dependency chains. The most widely adopted engines—Snakemake, Nextflow, the Common Workflow Language (CWL), and the Workflow Description Language (WDL)—run on interpreted or just-in-time (JIT) compiled language…
Thomas Reinbacher, Matthias Függer, Jörg Brauer
We present a runtime verification framework that allows on-line monitoring of past-time Metric Temporal Logic (ptMTL) specifications in a discrete time setting. We design observer algorithms for the time-bounded modalities of ptMTL, which take advantage of the highly parallel nature of hardware designs. The algorithms…
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…
Nicolas Diekmann, Sandhiya Vijayabaskaran, Xiangshuai Zeng, David Kappel + 2 more
Reinforcement learning (RL) has become a popular paradigm for modeling animal behavior, analyzing neuronal representations, and studying their emergence during learning. This development has been fueled by advances in understanding the role of RL in both the brain and artificial intelligence. However, while in machine…
Nickolas Gantzler, Aryan Deshwal, Janardhan Rao Doppa, Cory Simon
Our objective is to search a large candidate set of covalent organic frameworks (COFs) for the one with the largest equilibrium adsorptive selectivity for xenon (Xe) over krypton (Kr) at room temperature. To predict the Xe/Kr selectivity of a COF structure, we have access to two molecular simulation techniques: (1) a…