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.
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.
About the Mount Sinai Health System
Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with more than 43,000 employees working across eight hospitals, over 400 outpatient practices, nearly 300 labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time — discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it.
Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients’ medical and emotional needs at the center of all treatment. The Health System includes approximately 7,300 primary and specialty care physicians; 13 joint-venture outpatient surgery centers throughout the five boroughs of New York City, Westchester, Long Island, and Florida; and more than 30 affiliated community health centers. We are consistently ranked by U.S. News & World Report's Best Hospitals, receiving high "Honor Roll" status, and are highly ranked: No. 1 in Geriatrics and top 20 in Cardiology/Heart Surgery, Diabetes/Endocrinology, Gastroenterology/GI Surgery, Neurology/Neurosurgery, Orthopedics, Pulmonology/Lung Surgery, Rehabilitation, and Urology. New York Eye and Ear Infirmary of Mount Sinai is ranked No. 12 in Ophthalmology. U.S. News & World Report’s “Best Children’s Hospitals” ranks Mount Sinai Kravis Children's Hospital among the country’s best in 4 out of 10 pediatric specialties. The Icahn School of Medicine at Mount Sinai is one of three medical schools that have earned distinction by multiple indicators: It is consistently ranked in the top 20 by U.S. News & World Report's "Best Medical Schools," aligned with a U.S. News & World Report "Honor Roll" Hospital, and top 20 in the nation for National Institutes of Health funding and top 5 in the nation for numerous basic and clinical research areas. Newsweek’s “The World’s Best Smart Hospitals” ranks The Mount Sinai Hospital as No. 1 in New York and in the top five globally, and Mount Sinai Morningside in the top 20 globally.