Newsroom Archive

A library of Scientific Computing and Data announcements, in publications, and in the news

Announcements

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

2022

October 5, 2022 - MSDW - Leaf and ATLAS Maintenance 10/19

October 5, 2022  – Scheduled maintenance to Leaf and ATLAS is scheduled for Wednesday, October 19, from 5:00-8:00 pm. All system access will be affected and service will be interrupted at that time.

September 28, 2022 - MSDW - Leaf and ATLAS Application Training 10/12

September 28, 2022 – A training session to utilize Leaf and ATLAS will be held Wednesday, October 12, from 1:00-2:00 pm. Click here to register for the remote training; a Zoom link is provided following registration.

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.

July 28, 2022: HPC- Minerva PM for LSF Job Scheduler August 15

July 28, 2022 – A Minerva preventative maintenance (PM) for LSF (Load Sharing Facility) job scheduler upgrade is scheduled for 5 hours, 1:00-6:00 PM, on Monday, August 15, 2022. Click here to read more.

July 26, 2022: MSDW - Updates to Leaf features August 9

July 26, 2022 – Scheduled maintenance for Leaf on Tuesday, August 9, from 10:30 am to 6:30 pm will implement new application features. Click here to read more.

July 19, 2022: HPC - Updates on Minerva Login July 26

July 19, 2022 – We will be changing one of the SSH host keys on the Minerva login notes at 1:00 PM on Tuesday, July 26. Click here to read more.

July 19, 2022: RDS - New Data Ark Data Sets Available

July 19, 2022 –  New genomic data sets are now available on the Data Ark Data Commons. Click here to read more.

July 18, 2022: MSDW - TriNetX Training Sessions in July

July 18, 2022 – TriNetX platform training sessions have been scheduled for the month of July and are open for registration. Click here to read more and to register.

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

Thank you for attending the eRAP Town Hall on May 20! Click here for the slide deck from the Town Hall presentation.

May 20, 2022: RDS - Data Ark Town Hall on May 25

Data Ark Town Hall will be on Wednesday, May 25, at 12:00 PM. Click here to register; Zoom details provided following registration.

May 13, 2022: RDS - eRAP Town Hall on May 20

eRAP Town Hall will be on Friday, May 20, at 1:00 PM. Click here to register; Zoom details provided following registration.

May 13, 2022: MSDW - MSDW Town Hall on May 27

MSDW Town Hall will be on Friday, May 27, at 12:00 PM. Click here to register; Zoom details provided following registration.

May 12, 2022: RDS - REDCap Town Hall on May 26

 REDCap Town Hall will be on Thursday, May 26, at 12:00 PM. Click here to register; Zoom details provided following registration.

May 3, 2022: MSDW - BioMe and IRW 1.0 now in Leaf

Self-service cohort building now available for BioMe and the Imaging Research Warehouse 1.0. Click here for more information.

April 8, 2022: HPC - Introduction and LSF Job Scheduler Training Materials

Thank you for attending Introduction to Minerva (April 1) and LSF Job Scheduler (April 8) training! Session recordings and slides are posted; click here to review.

April 5, 2022: HPC - New A100-80GB GPU Nodes Available on Minerva

New A100-80GB GPU Nodes Available on Minerva. Click here to read more.

March 9, 2022: HPC - Minerva Training Sessions in April 2022

High Performance Computing will be holding 2 information/training sessions this April. These sessions are intended to familiarize you with the Minerva environment. Click here to read more.

January 6, 2022: HPC - Scheduled Maintenance: January 20, 2022

A full Planned Maintenance (PM) is in scheduled for Thursday, January 20, 2022, from 1:00 pm to 8:00 pm. Click here to read more.

2021

December 13, 2021: MSDW - Transition for CQT Effective December 20, 2021

To provide the Mount Sinai Community with the very best data and resources to query the data, the Scientific Computing and Data team has been implementing improved infrastructure in the Mount Sinai Data Warehouse. In 2021, we debuted “MSDW2,” based on the OMOP Common Data Model, containing Epic data from throughout the Mount Sinai Health System, and unveiled two self-service query tools for defining and generating patient cohorts: Leaf and ATLAS. Click here to read more.

November 10, 2021: HPC - Scheduled Maintenance: November 15, 2021

There will be scheduled updates on Monday, November 15, from 3:00 pm to 5:00 pm to update packages on web01 (*.u.hpc.mssm.edu), rstudio-connect, and globus servers. Click here to read more.

September 16, 2021: HPC - Dean Kovatch Chairs Computational Approaches for Cancer Workshop

Patricia Kovatch, Dean of Scientific Computing and Data, will present and will chair sessions at this fall’s Supercomputing 2021 conference. Click here to read more.

September 7, 2021: HPC - CATS Coming Soon

The COVID and Translational Science supercomputer (CATS) was awarded in 2021  to enable new kinds of scientific discovery and translation related to the newly emerged COVID-19 pandemic. CATS will be in production in 4Q21 with 2,640 Intel cores, 82 TB of memory and 17 petabytes of storage. Click here to read more.

August 31, 2021: HPC - Minerva Training/Information Sessions in September 2021

We will host three information/training sessions intended to familiarize you with the Minerva environment. Click here to read more.

July 16, 2021: HPC - Two Interactive V100 GPU Modules Now Live

We have added another V100 GPU node to the dedicated interactive GPU node pool which you can use for your GPU job testing. In total, we have 2 dedicated interactive GPU nodes (lg03a01 & lg03a02 with 4 V100 GPUs on each) in the interactive queue now. Click here to read more.

2020

October 29, 2020: HPC - New high memory compute nodes are open on Minerva

We have completed all the tests on the new high memory compute nodes. Those new nodes are added to both express and premium queues with resource -R himem needed this Thursday. Click here to read more.

September 25, 2020: HPC - Minerva expansion: more storage, high memory nodes, and A100 GPU nodes

Thanks to a donor, we’re happy to announce that we will be expanding Minerva with new high memory nodes, A100 GPU nodes, and high-speed storage.  After the installation, we will have a total of 434 nodes for a total of 20,832 cores, and 21 petabytes of usable storage. Click here to read more.

August 24, 2020: HPC - Rstudio Connect server is available on Minerva

Rstudio Connect server is available on Minerva, where you can publish Shiny, R Markdown and Jupyter for collaborators or others. Click here to read more.

January 7, 2020: HPC - Editors’ Choice Award for Best Use of High Performance Data Analytics & Artificial Intelligence for their development of an AI platform to detect neurodegenerative diseases using machine learning

Researchers at Mount Sinai Hospital collaborated with Minerva HPC and won the Editors’ Choice Award for Best Use of High Performance Data Analytics & Artificial Intelligence for their development of an AI platform to detect neurodegenerative diseases using machine learning. The platform, called the Precise Informatics Platform, analyzed digitized microscopic slides of tissue samples to create a convolutional neural network capable of identifying “tangles” that serve as markers for neurodegenerative diseases. “Thank you @hpcwire for the #hpcwire Editors’ Choice Award,” Minerva HPC tweeted. “We couldn’t be more proud of our researchers and partners @Lenovo who have worked so hard.” Read the full article here.

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.

Nov. 18, 2019: Mount Sinai To Deploy New Supercomputer, Integrating Genomic And Clinical Data

Mount Sinai Health System said today its researchers will be able to explore more complex scientific questions more quickly once the New York City health system builds its second “Big Omics Data Engine” (BODE 2) supercomputer, to be funded through a $2 million grant awarded by the U.S. Department of Health and Human Services. Click here to read more

April 17, 2013: "Minerva" Super Computer Ushers New Era Of Precision Medicine At Mount Sinai

“Minerva” Super Computer Ushers New Era Of Precision Medicine At Mount Sinai – Sophisticated algorithms analyze data to develop predictive models of disease in order to better diagnose and treat patients. Click here to read more.

Publications

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

Read More

See other publications and research made possible through resources from Scientific Computing and Data

We are supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences, National Institutes of Health.

Need assistance?

GooGhywoiu9839t543j0s7543uw1 - pls add laura.dent@mssm.edu to GA account UA-149832711-2 with 'Manage Users and Edit' permissions - date 12/2/22