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
June 24, 2022: MSDW - ATLAS Scheduled Maintenance on Wednesday, June 29
June 24, 2022 – ATLAS will be down for scheduled maintenance on Wednesday, June 29, from 3:00 to 6:00 pm. All system access will be affected and service will be interrupted at that time. Please plan your work ahead of time and log out of the application during maintenance. Click here for more information.
June 22, 2022: MSDW - MSDW's 2022 charge rate is $180/hour for Custom MSDW Data Requests
June 22, 2022 – MSDW’s 2022 charge rate is $180/hour for Custom MSDW Data Requests. Click here to read more.
June 16, 2022: HPC - Minerva’s 2022 charge rate is $100/TiB per year for high-performance online parallel file system storage.
June 16, 2022 – Minerva’s 2022 charge rate is $100/TiB per year for high-performance online parallel file system storage. This includes all Minerva services, including CPU, GPU and archival storage. Click here to read more.
June 16, 2022: RDS - REDCap’s 2022 charge rate is $200/year per database in production, and $140/hour consulting fee for project-specific development or services
June 16, 2022 – REDCap’s 2022 charge rate is $200/year per database in production, and $140/hour consulting fee for project-specific development or services. Click here to read more.
June 16, 2022: RDS - eRAP’s 2022 charge rate is $140/hour for new project development or changes to existing project functionality
June 16, 2022 – eRAP’s 2022 charge rate is $140/hour for new project development or changes to existing project functionality. Click here to read more.
June 13, 2022: MSDW - TriNetX application training sessions for the month of June are open for registration
June 13, 2022 – TriNetX application training sessions for the month of June are open for registration. Click here for session details and registration information.
June 8, 2022: HPC - Scheduled Maintenance Thursday, June 9: Web01 and RStudio
June 8, 2022 – Web01 and Rstudio Scheduled Maintenance on Thursday, June 9. Click here to read more.
May 31, 2022: MSDW - MSDW Town Hall Slides Available
May 31, 2022 – Thank you for attending the MSDW Town Hal on May 27! Click here for the slide deck from the Town Hall presentation.
May 26, 2022: RDS - REDCap Town Hall Slides Available
May 26, 2022 – Thank you for attending the REDCap Town Hal on May 26! Click here for the slide deck from the Town Hall presentation.
May 25, 2022: RDS - Data Ark Town Hall Slides Available
May 25, 2022 – Thank you for attending the Data Ark town hall on May 25! Click here for the slide deck from the Town Hall presentation.
May 23, 2022: RDS - eRAP Town Hall Slides Available
May 23, 2022 – Thank you for attending the eRAP Town Hall on May 20! Click here for the slide deck from the Town Hall presentation.
In The News
Reports and news events for Scientific Computing and Data
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: Multi-ethnic Investigation of Risk and Immune Determinants of COVID-19 Outcomes
by P. Kovatch, S. Nirenberg, et al. 2022 March | Background: Disparate COVID-19 outcomes have been observed between Hispanic, Non-Hispanic Black, and White patients. The underlying causes for these disparities are not fully understood. Methods: This was a retrospective study utilizing electronic medical record data from five hospitals within a single academic health system based in New York City. Multivariable logistic regression models were used to identify demographic, clinical, and lab values associated with in-hospital mortality. Results: 3,086 adult patients with self-reported race/ethnicity information presenting to the emergency department and hospitalized with COVID-19 up to April 13, 2020 were included in this study. While older age (multivariable OR 1.06, 95% CI 1.05-1.07) and baseline hypoxia (multivariable OR 2.71, 95% CI 2.17-3.36) were associated with increased mortality overall and across all races/ethnicities, Non-Hispanic Black (median age 67, IQR 58-76) and Hispanic (median age 63, IQR 50-74) patients were younger and had different comorbidity profiles compared to Non-Hispanic White patients (median age 73, IQR 62-84; p<0.05 for both comparisons). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between the Non-Hispanic Black population and interleukin-1-beta (interaction p-value 0.04). Conclusions: This analysis of a multi-ethnic cohort highlights the need for inclusion and consideration of diverse populations in ongoing COVID-19 trials targeting inflammatory cytokines. DOI: 10.21203/rs.3.rs-1055587/v1
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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