We describe Globus Genomics, a system that we have developed for rapid analysis of large quantities of next-generation sequencing (NGS) genomic data. This system achieves a high degree of end-to-end automation that encompasses every stage of data analysis including initial data retrieval from remote sequencing centers or storage (via the Globus file transfer system); specification, configuration, and reuse of multi-step processing pipelines (via the Galaxy workflow system); creation of custom Amazon Machine Images and on-demand resource acquisition via a specialized elastic provisioner (on Amazon EC2); and efficient scheduling of these pipelines over many processors (via the HTCondor scheduler). The system allows biomedical researchers to perform rapid analysis of large NGS datasets in a fully automated manner, without software installation or a need for any local computing infrastructure. We report performance and cost results for some representative workloads.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4203657 | PMC |
| http://dx.doi.org/10.1002/cpe.3274 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Case Report: A novel hemizygous missense variant in a Vietnamese boy with pyruvate dehydrogenase E1-alpha deficiency.
Front Pediatr
December 2024
Institute of Genome Research, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.
A pyruvate dehydrogenase complex deficiency causes a reduction in adenosine triphosphate production and energy insufficiency, leading to neurological disorders. An abnormal E1-alpha protein originating from the gene with pathogenic variants is unable to communicate with E1-beta for the formation of the E1 enzyme, decreasing pyruvate dehydrogenase complex activity. In this study, we report a Vietnamese boy with lethargy, severe metabolic acidosis, increased serum lactate, hyperalaninemia, lactic acidosis, and globus pallidus lesions.
View Article and Find Full Text PDFNovel pathogenic variant in a mild case of type B molybdenum cofactor deficiency: case report and literature review.
BMC Med Genomics
December 2024
Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
Background: Molybdenum cofactor deficiency (MoCD) is a rare metabolic disorder caused by pathogenic variants in the highly conserved biosynthetic pathway of molybdenum cofactor (MoCo), resulting in sulfite intoxication. MoCD may present in a clinically severe, fatal form marked by intractable seizures after birth, hyperekplexia, microcephaly and cerebral atrophy, or a later onset form with a more varied clinical course. Three types of MoCD have been described based on the effected gene along the MoCo synthesis pathway: type A (MOCS1); type B (MOCS2 or MOCS3) and type C (GPHN).
View Article and Find Full Text PDFExploring PDE5A upregulation in bipolar disorder: insights from single-nucleus RNA sequencing of human basal ganglia.
Transl Psychiatry
December 2024
Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
Basal ganglia is proposed to mediate symptoms underlying bipolar disorder (BD). To understand the cell type-specific gene expression and network changes of BD basal ganglia, we performed single-nucleus RNA sequencing of 30,752 nuclei from caudate, putamen, globus pallidus, and substantia nigra of control human postmortem brain and 24,672 nuclei from BD brain. Differential expression analysis revealed major difference lying in caudate, with BD medium spiny neurons (MSNs) expressing significantly higher PDE5A, a cGMP-specific phosphodiesterase.
View Article and Find Full Text PDFThe PRIDE database at 20 years: 2025 update.
Nucleic Acids Res
November 2024
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Article Synopsis
- The PRIDE database is a premier repository for mass spectrometry-based proteomics data and plays a key role in the ProteomeXchange consortium, facilitating research sharing.
- Over the past three years, PRIDE has made significant advancements, including a new file transfer protocol and an automatic dataset validation process, resulting in approximately 534 datasets submitted monthly.
- Recent innovations include the introduction of a PRIDE chatbot for user support and enhanced efforts to integrate high-quality data with resources like UniProt and Ensembl.
Causal influences of testosterone on brain structure change rate: A sex-stratified Mendelian randomization study.
J Steroid Biochem Mol Biol
January 2025
Department of Urology, Second Hospital of Shanxi Medical University, Male Reproductive Medicine Center, 382 Wuyi Road, Taiyuan 030001, China. Electronic address:
The impact of testosterone levels on changes in brain structure has been reported. However, it is still unclear which specific brain region could be affected. This study approached Mendelian randomization method to reveal the causal relationship between testosterone levels and the rate of longitudinal structural changes in the brain.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!