Mount Sinai Researchers Develop Tool that Analyzes Biomedical Data within Minutes
In a world where Big Data reigns, fast, open, and free analysis is key
Researchers at the Icahn School of Medicine at Mount Sinai have developed a tool that speeds up the analysis and publication of biomedical data from many months or years to mere minutes, transforming the way researchers communicate results of their studies. Until now, the primary method available to share biomedical research data has been through print publication in scientific journals. The new tool, BioJupies, relies on cloud technologies to analyze and visualize large amounts of data, such as that acquired by genome sequencing, as described in the November 2018 issue of Cell Systems.
RNA sequencing is the most common experimental method used to profile cells in biomedical research. In recent years, sequencing technology has revolutionized the way scientists examine genetic data, and this advancement plays a crucial role in drug discovery and development. Traditionally, RNA sequencing analysis requires extensive computer programming skills and access to local high performance computing facilities, slowing down the speed at which biomedical data can be analyzed, shared, and published.
Through the creation of BioJupies, users can now upload and analyze their RNA sequencing data in a fraction of the time as done previously. The platform utilizes a cloud computing pipeline that reduces the cost of RNA-sequencing data processing to less than one cent per sample. BioJupies also produces a complete, open source, interactive report from the processed data allowing for 300,000 publicly available RNA sequencing datasets to be fetched, reanalyzed, and reused to bolster biomedical research.
“As the amount of biomedical data generated continues to climb exponentially, so should the tools used to analyze and share them,” said Avi Ma’ayan, PhD, Director of the Mount Sinai Center for Bioinformatics, Professor, Department of Pharmacological Sciences, faculty of Icahn Institute for Data Science and Genomic Technology, and senior author of the publication. “BioJupies not only accelerates the manner in which we analyze and interpret data, but it also provides a completely new way to share results with the global research community.”
As new genomic technologies have allowed for the collection of massive amounts of biomedical information that can be harnessed for precision medicine efforts, accessibility, interoperability, and reusability of this data has become crucial to scientific research. BioJupies paves the way for researchers with no computational background to perform RNA sequencing analysis without the need to collaborate with bioinformaticians, enabling more medical and scientific advancements to flourish in our data rich world.
BioJupies is freely available as a web-based application at: http://biojupies.cloud. The software was developed during the pilot phase of the NIH Data Commons 180-day production pilot phase.
This work was partially supported by NIH grants: OT3OD025467 and U54HL127624
Paper Cited: Denis Torre, Alexander Lachmann, Avi Ma’ayan. “BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud” Cell Systems.
DOI: 10.1016/j.cels.2018.10.007
About the Mount Sinai Health System
Mount Sinai Health System is one of the nation’s leading integrated academic health systems and one of the largest in the New York metropolitan area. Its comprehensive system includes seven hospitals, more than 400 outpatient practices, over 600 research and clinical laboratories, the Icahn School of Medicine at Mount Sinai, the Graduate School of Biomedical Sciences, and the Mount Sinai Phillips School of Nursing. Together, the Health System comprises approximately 48,000 employees, more than 9,000 physicians, and 8,600 nurses.
As a leading learning health system, Mount Sinai combines clinical expertise with scientific discovery to improve patient care while training the next generation of health care and biomedical leaders. The Health System provides care across every stage of life, from prenatal care through geriatrics, while advancing personalized medicine through artificial intelligence, data science, and biomedical research.
Mount Sinai is consistently recognized among the nation’s leading academic health systems for patient care, research, and education. The Mount Sinai Hospital is ranked No. 1 in New York by Newsweek and No. 5 on the magazine’s World’s Best Hospitals list. The Icahn School of Medicine at Mount Sinai ranks No. 11 among U.S. medical schools and No. 1 among freestanding medical schools for National Institutes of Health funding, reflecting the strength of its scientific enterprise and leadership in biomedical research.
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