Use of application containers and workflows for genomic data analysis

Journal of Pathology Informatics
Wade L SchulzRichard Torres


The rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments. Recent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing. While limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data. With this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.


Jan 14, 2010·Current Protocols in Molecular Biology·Daniel BlankenbergJames Taylor
Nov 9, 2010·Nature Biotechnology·Joel T Dudley, Atul J Butte
Aug 18, 2012·Nature Reviews. Genetics·Anton Nekrutenko, James Taylor
May 3, 2013·The New England Journal of Medicine·UNKNOWN Cancer Genome Atlas Research NetworkGreg Eley
Nov 25, 2014·National Science Review·Jianqing FanHan Liu
Aug 16, 2016·The New England Journal of Medicine·Harlan M Krumholz, Joanne Waldstreicher

❮ Previous
Next ❯


Aug 8, 2018·GigaScience·Pai ZhangKa Yee Yeung
Feb 5, 2019·Journal of Ultrasound in Medicine : Official Journal of the American Institute of Ultrasound in Medicine·Adrian D HaimovichR Andrew Taylor
Aug 14, 2018·Bioinformatics·Jon Ander NovellaOla Spjuth
Nov 29, 2017·F1000Research·Aleksandr AgafonovLars Ailo Bongo
Nov 2, 2017·Journal of the American Medical Informatics Association : JAMIA·Reem AlmugbelKa Yee Yeung
Jun 2, 2020·Journal of Pathology Informatics·Thomas J S DurantWade L Schulz
Jan 8, 2019·BMC Bioinformatics·Indresh SinghKaren E Nelson
Aug 20, 2019·Expert Review of Molecular Diagnostics·Yin Kwan Evelyn WongSze Chuen Cesar Wong

❮ Previous
Next ❯

Methods Mentioned

exome sequencing

Software Mentioned

Docker containers

Related Concepts

Related Feeds

Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is a clinically and genetically heterogeneous disease with approximately 20,000 cases per year in the United States. AML also accounts for 15-20% of all childhood acute leukemias, while it is responsible for more than half of the leukemic deaths in these patients. Here is the latest research on this disease.

AML: Role of LSD1 by CRISPR (Keystone)

Find the latest rersearrch on the ability of CRISPR-Cas9 mutagenesis to profile the interactions between lysine-specific histone demethylase 1 (LSD1) and chemical inhibitors in the context of acute myeloid leukemia (AML) here.

Acute Myeloid Leukaemia & RNA

Acute myeloid leukaemia (AML) is a common hematological type of cancer. As the population ages, there has been a rise in the frequency of AML. RNA expression has been used to see if there are different genetic profiles that exist within AML and whether these may underpin the variations in survival rates. Here is the latest research on AML and RNA.

Related Papers

Journal of Biomedical Informatics
Jeffrey KrisemanValentin Dinu
Clinics in Laboratory Medicine
R R GullapalliW A LaFramboise
Journal of Genetics and Genomics = Yi Chuan Xue Bao
Jun ZhangGenfa Zhang
© 2021 Meta ULC. All rights reserved