相关论文: META-pipe - Pipeline Annotation, Analysis and Visu…
As immunotherapies become standard cancer treatments, it is increasingly important to identify a patient's immune profile, which encompasses the activity of immune cells within the tumor microenvironment and the presence of specific…
Climate change and other anthropogenic factors have led to a catastrophic decline in insects, endangering both biodiversity and the ecosystem services on which human society depends. Data on insect abundance, however, remains woefully…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Computational engineering generates knowledge through the analysis and interpretation of research data, which is produced by computer simulation. Supercomputers produce huge amounts of research data. To address a research question, a lot of…
The constant growth in the number of malware - software or code fragment potentially harmful for computers and information networks - and the use of sophisticated evasion and obfuscation techniques have seriously hindered classic…
One of the major challenges providing large databases like the WFCAM Science Archive (WSA) is to minimize ingest times for pixel/image metadata and catalogue data. In this article we describe how the pipeline processed data are ingested…
A bioinformatics platform is introduced aimed at identifying models of disease-specific pathways, as well as a set of network measures that can quantify changes in terms of global structure or single link disruptions.The approach integrates…
This paper presents the Container Profiler, a software tool that measures and records the resource usage of any containerized task. Our tool profiles the CPU, memory, disk, and network utilization of containerized tasks collecting over…
We develop a tool called PipeGen for efficient data transfer between database management systems (DBMSs). PipeGen targets data analytics workloads on shared-nothing engines. It supports scenarios where users seek to perform different parts…
The growing number of pretrained models in Machine Learning (ML) presents significant challenges for practitioners. Given a new dataset, they need to determine the most suitable deep learning (DL) pipeline, consisting of the pretrained…
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…
To turn environmentally derived metabarcoding data into community matrices for ecological analysis, sequences must first be clustered into operational taxonomic units (OTUs). This task is particularly complex for data including large…
From medical charts to national census, healthcare has traditionally operated under a paper-based paradigm. However, the past decade has marked a long and arduous transformation bringing healthcare into the digital age. Ranging from…
Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Artificial intelligence (AI) is showing promise in improving clinical diagnosis. In breast cancer screening, recent studies show that AI has the potential to improve early cancer diagnosis and reduce unnecessary workup. As the number of…
The assessment of microbial species biodiversity is essential in ecology and evolutionary biology (Reaka-Kudla et al. 1996), but especially challenging for communities of microorganisms found in the environment (Das et al. 2006, Hillebrand…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
Anthropogenic methane (CH4) point sources drive near-term climate forcing, safety hazards, and system inefficiencies. Space-based imaging spectroscopy is emerging as a tool for identifying emissions globally, but existing approaches largely…
Artificial intelligence (AI), especially deep learning, requires vast amounts of data for training, testing, and validation. Collecting these data and the corresponding annotations requires the implementation of imaging biobanks that…