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2024
Churros: a Docker-based pipeline for large-scale epigenomic analysis
DNA Research
2024
Deploying WordPress in Docker: A Scalable and Secure Solution
Qeios
2024
DExplore: An Online Tool for Detecting Differentially Expressed Genes from mRNA Microarray Experiments
Biology
2024
2023
Containers for computational reproducibility
Nature Reviews Methods Primers
2023
Genome annotation: From human genetics to biodiversity genomics
Cell Genomics
2023
The five pillars of computational reproducibility: bioinformatics and beyond
Briefings in Bioinformatics
2022
Containers in Bioinformatics
The Journal of Molecular Diagnostics
2022
QoS-aware online scheduling of multiple workflows under task execution time uncertainty in clouds
Cluster Computing
2022
Methods in Molecular Biology
2022
DockerPedia: A Knowledge Graph of Software Images and Their Metadata
International Journal of Software Engineering and Knowledge Engineering
2022
Artificial intelligence and machine learning in cancer imaging
Communications Medicine
2022
Performance Assessment of Using Docker for Selected MPI Applications in a Parallel Environment Based on Commodity Hardware
Applied Sciences
2021
A quantitative cross‐comparison of container networking technologies for virtualized service infrastructures in local computing environments
Transactions on Emerging Telecommunications Technologies
2021
Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging
Frontiers in Genetics
2021
2021 IEEE 27th International Conference on Parallel and Distributed Systems (ICPADS)
2021
Design considerations for workflow management systems use in production genomics research and the clinic
Scientific Reports
2021
Scheduling multiple scientific workflows using containers on IaaS cloud
Journal of Ambient Intelligence and Humanized Computing
2021
Implementation of human whole genome sequencing data analysis: A containerized framework for sustained and enhanced throughput
Informatics in Medicine Unlocked
2021
The Stroke Neuro-Imaging Phenotype Repository: An Open Data Science Platform for Stroke Research
Frontiers in Neuroinformatics
2021
2021 Third International Conference on Intelligent Communication Technologies and Virtual Mobile Networks (ICICV)
2020
2020 19th International Symposium on Parallel and Distributed Computing (ISPDC)
2020
Lecture Notes in Computer Science
2020
Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity
BMC Genomics
2020
Modeling population heterogeneity from microbial communities to immune response in cells
Cellular and Molecular Life Sciences
2020
Lecture Notes in Computer Science
2020
Lecture Notes in Computer Science
2020
2020 25th IEEE International Conference on Emerging Technologies and Factory Automation (ETFA)
2020
A Guide and Toolbox to Replicability and Open Science in Entomology
Journal of Insect Science
2020
MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations
G3 Genes|Genomes|Genetics
2020
MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome–Host Interactions
Cells
2019
2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)
2019
Proceedings of the 12th IEEE/ACM International Conference on Utility and Cloud Computing Companion
2019
BIGSEA: A Big Data analytics platform for public transportation information
Future Generation Computer Systems
2019
Methods in Molecular Biology
2019
Encyclopedia of Bioinformatics and Computational Biology
2019
2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)
2019
Prioritizing bona fide bacterial small RNAs with machine learning classifiers
PeerJ
2019
2019 15th International Conference on eScience (eScience)
2019
A Novel Approach for Remote Compilation using Docker Containers
International Journal of Computer Communication and Informatics
2019
Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection
GigaScience
2019
2019 IEEE 12th International Conference on Cloud Computing (CLOUD)
2019
NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
BMC Bioinformatics
2019
Container-based bioinformatics with Pachyderm
Bioinformatics
2018
Human Genome Informatics
2018
2018 IEEE 11th International Conference on Cloud Computing (CLOUD)
2018
Container-Based Clinical Solutions for Portable and Reproducible Image Analysis
Journal of Digital Imaging
2018
Advances in Intelligent Systems and Computing
2018
2018 17th International Symposium on Parallel and Distributed Computing (ISPDC)
2018
Transparent Orchestration of Task-based Parallel Applications in Containers Platforms
Journal of Grid Computing
2018
Automating Installation of the Integrating Biology and the Bedside (i2b2) Platform
Biomedical Informatics Insights
2018
Metagenomics
2018
sppIDer: A Species Identification Tool to Investigate Hybrid Genomes with High-Throughput Sequencing
Molecular Biology and Evolution
2018
Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size
The ISME Journal
2018
Scheduling dynamic workloads in multi-tenant scientific workflow as a service platforms
Future Generation Computer Systems
2018
The Scientific Filesystem
GigaScience
2018
DockerBIO: web application for efficient use of bioinformatics Docker images
PeerJ
2018
Docker Container Scheduler for I/O Intensive Applications Running on NVMe SSDs
IEEE Transactions on Multi-Scale Computing Systems
2018
Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools
iScience
2017
Containers for Portable, Productive, and Performant Scientific Computing
Computing in Science & Engineering
2017
BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters
PeerJ
2017
General guidelines for biomedical software development
F1000Research
2017
General guidelines for biomedical software development
F1000Research
2017
Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments
Journal of Biotechnology
2017
Bio-Docklets: virtualization containers for single-step execution of NGS pipelines
GigaScience
2017
Nextflow enables reproducible computational workflows
Nature Biotechnology
2017
GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis
PeerJ
2017
Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform
Journal of Integrative Bioinformatics
2017
Lecture Notes in Computer Science
2017
Comparison of classical multi-locus sequence typing software for next-generation sequencing data
Microbial Genomics
2017
BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
PLOS Computational Biology
2016
2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)
2016
2016 IEEE 35th International Performance Computing and Communications Conference (IPCCC)
2016
Lecture Notes in Computer Science
2016
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
Genome Biology
2016
Translating RNA sequencing into clinical diagnostics: opportunities and challenges
Nature Reviews Genetics
2016
Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers
PLOS ONE
2016
Methods in Molecular Biology
2015
BioShaDock: a community driven bioinformatics shared Docker-based tools registry
F1000Research
2015
2015 IEEE/ACM 8th International Conference on Utility and Cloud Computing (UCC)
2015
PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols
Source Code for Biology and Medicine
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