Related papers: WinBioinfTools: Bioinformatics Tools for Windows H…
To reduce the source of potential exploits, binary debloating or specialization tools are used to remove unnecessary code from binaries. This paper presents a new binary debloating and specialization tool, LeanBin, that harnesses lifting…
Workflows are among the most commonly used tools in a variety of execution environments. Many of them target a specific environment; few of them make it possible to execute an entire workflow in different environments, e.g. Kubernetes and…
In an effort to overcome the data deluge in computational biology and bioinformatics and to facilitate bioinformatics research in the era of big data, we identify some of the most influential algorithms that have been widely used in the…
Machine learning has been gaining traction in recent years to meet the demand for tools that can efficiently analyze and make sense of the ever-growing databases of biomedical data in health care systems around the world. However,…
The amazing advances being made in the fields of machine and deep learning are a highlight of the Big Data era for both enterprise and research communities. Modern applications require resources beyond a single node's ability to provide.…
To face the programming challenges related to heterogeneous computing, Intel recently introduced oneAPI, a new programming environment that allows code developed in Data Parallel C++ (DPC++) language to be run on different devices such as…
Cloud computing recently developed into a viable alternative to on-premises systems for executing high-performance computing (HPC) applications. With the emergence of new vendors and hardware options, there is now a growing need to…
Bioinformatics pipelines depend on shared POSIX filesystems for its input, output and intermediate data storage. Containerization makes it more difficult for the workloads to access the shared file systems. In our previous study, we were…
Multiple matching algorithms are used to locate the occurrences of patterns from a finite pattern set in a large input string. Aho-Corasick and Wu-Manber, two of the most well known algorithms for multiple matching require an increased…
The proliferation of physiological sensors opens new opportunities to explore interactions, conduct experiments and evaluate the user experience with continuous monitoring of bodily functions. Commercial devices, however, can be costly or…
Advances in bioinformatics are primarily due to new algorithms for processing diverse biological data sources. While sophisticated alignment algorithms have been pivotal in analyzing biological sequences, deep learning has substantially…
In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of…
Motivation: The ability to perform operations on encrypted data has a growing number of applications in bioinformatics, with implications for data privacy in health care and biosecurity. The SEAL library is a popular implementation of fully…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
This paper presents a new modeling strategy for joint unsupervised analysis of multiple high-throughput biological studies. As in Multi-study Factor Analysis, our goals are to identify both common factors shared across studies and…
The proliferation of sensor technologies and advancements in data collection methods have enabled the accumulation of very large amounts of data. Increasingly, these datasets are considered for scientific research. However, the design of…
In the fusion community, the use of high performance computing (HPC) has been mostly dominated by heavy-duty plasma simulations, such as those based on particle-in-cell and gyrokinetic codes. However, there has been a growing interest in…
High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
Since the development of the Beowulf project to build a parallel computer from commodity PC components, there have been many such clusters built. The MILC QCD code has been run on a variety of clusters and supercomputers. Key design…