Newsroom Archive

December 15, 2022 – Dean Patricia Kovatch awarded the Jacobi Medallion Award from the Mount Sinai Alumni Association. Congratulations! Click here to read more.

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 – 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 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 – Thank you for attending the Minerva HPC Town Hall! To review session materials, including our Town Hall archive, visit the “Training”  page.

November 16, 2022 – Scientific Computing is helping researchers to gain access to major cloud providers such as Google Cloud Platform (GCP), Amazon Web Services (AWS) and Microsoft Azure under the NIH Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative. Click here to read more.

October 31, 2022 – You are invited to Scientific Computing and Data’s Open House on Tuesday, November 1, from 2-3 PM in Goldwurm Auditorium. Click here to read more.

October 10, 2022 – Thank you for attending the Minerva training sessions this fall: Introduction to Minerva, LSF Job Scheduler, and Containerized Environment on Minerva. To review session recordings and slide decks, click here! These materials, and an archive of past training sessions, are located on our Training page.

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.

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

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

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

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 – 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’s 2022 charge rate is $180/hour for Custom MSDW Data Requests. Click here to read more.

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 – 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 – 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 – TriNetX application training sessions for the month of June are open for registration. Click here for session details and registration information.

June 8, 2022 – Web01 and Rstudio Scheduled Maintenance on Thursday, June 9. Click here to read more.

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 – 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 – Thank you for attending the Data Ark town hall on May 25! Click here for the slide deck from the Town Hall presentation.

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

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

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

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

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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