Scientific Computing and Data announcements, in publications, and in the news

Scientific Computing and Data News

High Performance Computing (HPC), Research Data Services (RDS), and Mount Sinai Data Warehouse (MSDW) impact the research community in contributions to science


Events, updates, and news from HPC, RDS, and MSDW

September 20, 2022 - MSDW - Quarterly Update: Upgrade Releases for Leaf and ATLAS

September 20, 2022 – Quarterly upgrade releases for Leaf (October 4, 2:00-5:00 pm) and ATLAS (October 5, 2:00-5:00 pm) are scheduled and system access will be affected. Click here to read more.

September 16, 2022 - HPC - Minerva Preventative Maintenance September 22

September 16, 2022 – A Minerva preventative maintenance (PM) for upgrading the globus server with the new trust root is scheduled for Thursday, September 22, from 1:00-5:00 PM. The globus server will be offline and all data transfer/share through globus will be interrupted at that time.

September 13, 2022 - HPC - Minerva Training and Information Sessions This Fall

September 13, 2022 – Minerva information and training sessions (Introduction to Minerva, LSF Job Scheduler, and Containerized Environment on Minerva) are scheduled for this fall. Click here to read more and to register.

September 1, 2022: MSDW - TriNetX Trainings in September

September 1, 2022 – TriNetX platform training sessions have been scheduled for the month of September. Click here to read more and to register.

August 26, 2022: MSDW - New BioMe Biobank Cohorts to MSDW Available

August 26, 2022 – Three new BioMe Biobank cohorts to MSDW and its Leaf and ATLAS cohort query tools are now available. Click here to read more.

August 23, 2022: MSDW - New Cancer Patient Cohort is Available

August 23, 2022 – A new Cancer Patient cohort available in MSDW, Leaf, and ATLAS. Click here to read more.

August 18, 2022: MSDW - Leaf Maintenance August 22

August 18, 2022 – Scheduled maintenance for Leaf on Monday, August 22, from 12:00 to 1:00 pm will implement a newly “pre-calculated” cancer patient cohort for use in Leaf queries. Click here to read more

August 3, 2022: MSDW - TriNetX Trainings in August

August 3, 2022 – TriNetX platform training sessions have been scheduled for the month of August. Click here to read more and to register.

In The News

Reports and news events for Scientific Computing and Data

July 26, 2022: The Mount Sinai Hospital Is Recognized in U.S. News & World Report “Best Hospitals” Rankings

The Mount Sinai Hospital was ranked in the top 20 in 10 specialties and improved its ranking in seven of those specialties. Specialties with significant rank improvements include:

  • Orthopedics, which had the biggest gain, rising to No. 8 from No. 14. Two years ago, the hospital ranked No. 24.
  • Pulmonology & Lung Surgery, which rose to No. 17 from No. 20. Two years ago, it ranked No. 27.
  • Cancer, which rose to No. 28 from No. 32. Two years ago, the hospital ranked No. 49.


Other departments to achieve top national honors include:

  • Cardiology/Heart Surgery, ranked No. 6
  • Neurology/Neurosurgery, ranked No. 9
  • Rehabilitation, ranked No. 13
  • Gastroenterology/GI Surgery, ranked No. 13
  • Diabetes/Endocrinology, ranked No. 14
  • Urology, ranked No. 14 (tie)
  • Ear, Nose & Throat, ranked No. 35 (tie)

Click here to read more.

Dec 1, 2021: Mount Sinai Named a Lead Site for Enrollment in Nationwide Study on the Long-Term Effects of COVID-19

Mount Sinai Named a Lead Site for Enrollment in Nationwide Study on the Long-Term Effects of COVID-19 ( Click here to read more.


Scientific Computing and Data resources utilized in publications

Abstract: Quantitative chest computed tomography combined with plasma cytokines predict outcomes in COVID-19 patients

by P. Kovatch, S. Nirenberg, et al. 2022 August | Background: Despite extraordinary international efforts to dampen the spread and understand the mechanisms behind SARS-CoV-2 infections, accessible predictive biomarkers directly applicable in the clinic are yet to be discovered. Recent studies have revealed that diverse types of assays bear limited predictive power for COVID-19 outcomes. Here, we harness the predictive power of chest computed tomography (CT) in combination with plasma cytokines using a machine learning and k-fold cross-validation approach for predicting death during hospitalization and maximum severity degree in COVID-19 patients. Patients (n = 152) from the Mount Sinai Health System in New York with plasma cytokine assessment and a chest CT within five days from admission were included. doi: 10.1016/j.heliyon.2022.e10166.

Science Stories: Pharmacology - Computer-Aided Structural Biology and Drug Discovery, Dr. Marta Filizola

Preserving Data: Who’s Got Your Back(up)? by Patricia Kovatch

Data management has become an essential part of research. Scientists need to be able to rely on their data infrastructures to recover data in case of disaster or to assist with reproducibility of their results. Ensuring a reliable data infrastructure and backup processes may not be the most exciting part of research, but consequences… Read more

Abstract: Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report

by Hernandez MM. et al. 2021 February | New York City (NYC) emerged as a coronavirus disease 2019 (COVID-19) epicenter in March 2020, but there is limited information regarding potentially unrecognized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections before the first reported case. We utilized a sample pooling strategy to screen for SARS-CoV-2 RNA in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across our NYC health system who were evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We obtained complete SARS-CoV-2 genome sequences from samples collected between late February and early March. Additionally, we detected SARS-CoV-2 RNA in pooled specimens collected in the week ending 25 January 2020, indicating that SARS-CoV-2 caused sporadic infections in NYC a full month before the first officially documented case. medRxiv:2021.02.08.21251303

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