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
January 6, 2023 - RDS - REDCap Scheduled Maintenance January 18
January 6, 2023– Scheduled maintenance to REDCap’s production servers will take place on Wednesday, January 18, from 5:00-6:00 PM. Maintenance will implement patching on REDCap servers, which will update security vulnerabilities and apply some bug fixes in critical systems software. Access to the REDCap application and forms will be down during this period. Please plan your work ahead of time and log out of the application during maintenance.
December 28, 2022 - MSDW - Leaf and ATLAS Intro Training Courses in PEAK
December 28, 2022 – Interactive training courses for Leaf and ATLAS are now available in PEAK! “Leaf Application Training: Introduction” provides an overview of Leaf access and functions, and “ATLAS Query Application Introduction Training” navigates step-by-step instructions for beginner ATLAS users.
December 27, 2022 - MSDW - Leaf and ATLAS Maintenance January 11
December 27, 2022 – Leaf and ATLAS will be down for scheduled maintenance on Wednesday, January 11, from 5:00 to 7:00 pm. Click here to read more.
December 19, 2022 - RDS - REDCap Billing Policy Changes
December 20, 2022 – Changes to REDCap’s billing policy will take effect in 2023. Click here to read more.
December 19, 2022 - HPC - Minerva Holiday Schedule for tickets takes effect Thursday, December 22
December 19, 2022 – Minerva Holiday Schedule for tickets takes effect Thursday, December 22 through the end of the year. Click here for more details.
December 12, 2022 - RDS - REDCap Training Session Materials Available
December 12, 2022 – Thank you for attending the REDCap Application Training! To review session materials, including slides and session recording, visit the “REDCap Support Materials” section on the About REDCap page.
December 12, 2022 - RDS - eRAP Town Hall Materials Available
December 12, 2022– Thank you for attending the eRAP Town Hall! To review session materials, including our Town Hall archive, visit the “eRAP Support Materials” section on the About eRAP page.
December 15, 2022 - SCD - Dean Patricia Kovatch awarded the Jacobi Medallion Award from the Mount Sinai Alumni Association.
December 15, 2022 – Dean Patricia Kovatch awarded the Jacobi Medallion Award from the Mount Sinai Alumni Association. Congratulations! Click here to read more.
December 8, 2022 - RDS - REDCap Town Hall Materials Available
December 8, 2022 – Thank you for attending the REDCap Town Hall! To review session materials, including our Town Hall archive, visit the “REDCap Support Materials” section on the About REDCap page.
December 7, 2022 - HPC - Minerva HPC Town Hall Materials Available
December 7, 2022 – Thank you for attending the Minerva HPC Town Hall! To review session materials, including our Town Hall archive, visit the “Training” page.
December 2, 2022 - RDS - Data Ark Town Hall Materials Available
December 2, 2022 – Thank you for attending the Data Ark: Data Commons Town Hall! To review session materials, including the session recording, visit the “Support Materials” section on the About Data Ark page.
November 28, 2022 - RDS - REDCap Application Training: Dec. 9 at 2:00 PM
November 28, 2022 – REDCap Application Training will cover the functions and features of REDCap. Training is scheduled for Friday, December 9, at 2:00 PM over Zoom. Click here to register and receive Zoom details.
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 (MountSinai.org). 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
See other publications and research made possible through resources from Scientific Computing and Data
Supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences, National Institutes of Health.