Eric Sobie
Mount Sinai Hospital
6 Papers
14 Citations
Eric Sobie is an academic researcher from Mount Sinai Hospital. The author has contributed to research in topics: Software & Thread (computing). The author has an hindex of 4, co-authored 6 publications. Previous affiliations of Eric Sobie include Icahn School of Medicine at Mount Sinai.
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Papers
Building Containerized Workflows Using the BioDepot-workflow-builder (Bwb)
Ling-Hong Hung,Jiaming Hu,Trevor Meiss,Alyssa Ingersoll,Wes Lloyd,Daniel Kristiyanto,Yuguang Xiong,Eric Sobie,Ka Yee Yeung +8 more
TL;DR: The BioDepot-workflow-builder (Bwb) as mentioned in this paper allows users to create and execute reproducible bioinformatics workflows using a drag-and-drop interface.
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Building containerized workflows for RNA-seq data using the BioDepot-workflow-Builder (BwB)
TL;DR: The BioDepot-workflow-builder (Bwb), a software tool that allows users to create and execute reproducible bioinformatics workflows using a drag-and-drop interface, is presented.
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Holistic optimization of an RNA-seq workflow for multi-threaded environments.
Ling-Hong Hung,Wes Lloyd,Radhika Agumbe Sridhar,Saranya Devi Athmalingam Ravishankar,Yuguang Xiong,Eric Sobie,Ka Yee Yeung +6 more
TL;DR: This work presents a unique molecular identifier (UMI) RNA sequencing pipeline consisting of 3 steps: split, align, and merge, and demonstrates that optimization of all three steps yields a 40% increase in speed when executed using a single thread.
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Software Solutions for Reproducible RNA-seq Workflows
TL;DR: It is shown here that the analysis of mRNA-seq data can depend on the computing environment, and it is demonstrated that software containers represent practical solutions that ensure the reproducibility of RNAseq data analyses.
Holistic optimization of an RNA-seq workflow for multi-threaded environments
Ling-Hong Hung,Wes Lloyd,Radhika Agumbe Sridhar,Saranya Devi Athmalingam Ravishankar,Yuguang Xiong,Eric Sobie,Ka Yee Yeung +6 more
TL;DR: A Unique-molecular-identifier (UMI) RNA sequencing pipeline consisting of 3 steps: split, align, and merge is demonstrated, which shows that optimization of all three steps yields a 40% increase in speed when executed using a single thread.