Scientific Computing

The mission of the Scientific Computing division of the Icahn School of Medicine at Mount Sinai (ISMMS) is to accelerate scientific discovery by providing researchers with high-performance computational and data services along with the human expertise for efficient and effective use of these resources. We collaborate with both internal and external scientists on innovative research to pursue new scientific opportunities and program growth, and we actively strive for broader engagement with the local and state communities for education and workforce development.

To help accomplish the mission the Scientific Computing division consists of three groups:

  • High Performance Computing (HPC),
  • Mount Sinai Data Warehouse (MSDW),
  • Research Data Services

Collectively, the Scientific Computing groups serve over 2,000 users at 150 institutions in 21 countries. The HPC resources consist of 12,672 compute cores, 160 terabytes of flash and 20 petabytes of parallel file system storage.  MSDW is a collection of clinical, financial and operational data from over 20 data sources at the Mount Sinai Hospital from 2003. It is updated daily with data from >8 million patients, >2 billion facts and >4,000 data points per patient.  Research Data Services designs and maintains electronic data capture system for clinical trials; and is home to the eRAP Rapid Database Generator (eRAP RDG).

Our mission is to accelerate scientific discovery at Mount Sinai by providing researchers with a scalable high performance computational and data infrastructure along with human expertise for efficient and effective use of these researchers.

We partner with internal and external scientists on innovative research to pursue new scientific opportunities and actively strive for broader engagement and industrial partnerships with the local and state communities for education and workforce development. 

Our 2,200-square foot data center grants us a unique opportunity to operate an on-site supercomputer and data infrastructure in New York City using the latest “green” technologies. This location makes it easy to integrate new resources into our existing facilities and ultimately, provide an easier access model for faculty, especially those with large data sets. The size of the data center empowers us to build an infrastructure of unprecedented size for scientists and researchers at the Icahn School of Medicine. This new infrastructure has allowed researchers to run computer simulations of disease processes with increased fidelity, complexity and scalability. The Hess Center has made it possible for us to deploy massive computational and data systems that empower our researchers to tackle scientific problems that are far larger than ever before.

Minerva

Scientific Computing’s supercomputer, Minerva, is named after the Roman goddess of wisdom and medicine and provides more than 100 million core hours of computation per year with a peak speed of more than 200 teraflops. Minerva is comprised of over 12,000 cores connected via Infiniband, 60 terabytes of RAM, 160 terabytes of flash memory, and 10 petabytes of raw storage capacity. In addition to its computational and data capabilities, Minerva also hosts web, database, Matlab, archival storage, visualization and high-speed data transfer services.

In addition to providing computing power, Scientific Computing also offers domain-specific computational experts to assist researchers in making the most efficient and effective use of the supercomputer with code optimization and other services.

Access to Minerva is open to all Icahn School of Medicine and external affiliated researchers; and accounts can be requested here. In addition to providing computing power, Scientific Computing also offers domain-specific computational experts to assist researchers in making the most efficient and effective use of the supercomputer with code optimization and other services.

The Mount Sinai Data Warehouse (MSDW) consists of clinical, operational, and financial data derived from patient care processes of The Mount Sinai Hospital and the Mount Sinai Doctors Faculty Practice Associates. Detailed inpatient and outpatient data are extracted from transactional systems, transformed and loaded into MSDW nightly. MSDW contains data since 2003, sourced from 20 transactional systems, encompassing over three million patients and approaching one billion facts. Learn more about the Mount Sinai Data Warehouse.

MSDW is compliant with HIPAA and New York State privacy and security regulations and with Mount Sinai IRB policy regarding protection of human subjects and participation in research. Researchers planning new studies or grant applications can quickly search the de-identified Data Warehouse to quantify eligible cohorts. For IRB-approved research or CQI projects, datamarts tailored to specific eligibility and data analysis requirements are prepared. Datamarts may be de-identified, or may contain PHI with appropriate approvals.

Mount Sinai’s Research Data Services department provides services and resources for data management, specimen management, scheduling for shared resource facilities, and data mining and data marts. We provide both self-service and custom electronic data capture systems for clinical trial.

Electronic Research Application Portal (eRAP)

The eRAP Rapid Database Generator (eRAP RDG) is a 21 CFR Part 11 compliant web-based interactive tool for data entry and reporting. We can rapidly develop custom databases for longitudinal single and multi-site studies. Services include: reporting tools, randomization engine, data upload, and file upload. In addition, eRAP is integrated with other Mount Sinai Health System clinical systems, such as EPIC, Mount Sinai Data Warehouse, Specimen management Systems (Freezerworks and IPM LIMS) and SCC Labs, making sharing data between systems more efficient. Learn more about eRAP.

We offer a diverse array of education and training events including graduate classes in Scientific Computing and workshops with academic and industrial partners.

Masters of Science in Biomedical Informatics

The Masters of Science in Biomedical Informatics will empower graduates to accelerate biomedical scientific discovery and healthcare translation through teaching and applying informatics approaches and methods. The Mount Sinai program will offer a unique, practical approach focused on tackling biomedical questions with relevant computational and data analytic skills. Our goal is to train individuals with Computer Science and/or Bioscience backgrounds to be immediately productive in biomedical research and clinical teams by teaching practical computational and data science skills. The program has been designed to interact with academic, non-profit and industrial partners to enable students to get real-life experience to accelerate job search and placement.

Community Research Education and Engagement for Data Science

The Community Research Education and Engagement for Data Science (CREEDS) will advance research education by providing an intensive, practical spring school in RNA sequencing for postdocs and early career faculty; an intensive, practical summer school experience in computational genomics for graduate students; and DREAM Challenges and problem solving to tackle real-life biomedical questions for graduate students.