Quarterly Update: Upgrade Releases for Leaf and ATLAS

There will be scheduled quarterly maintenance to Leaf and ATLAS for upgrade releases and improvements:

  • Leaf: Tuesday, October 4, from 2:00 pm to 5:00 pm—quarterly updates will include apache & ssh config to fix low- and medium-level security vulnerabilities
  • ATLAS: Wednesday, October 5, from 2:00 to 5:00 pm—quarterly updates will include updating and reformatting Program for Protection of Human Subjects requirements for improved readability within the ATLAS Terms and Conditions

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.

You may contact us with questions by submitting a ticket. For more information on Leaf or ATLAS, click here. Thank you.

Three new BioMe Biobank cohorts to MSDW and its Leaf and ATLAS cohort query tools

The Charles Bronfman Institute for Personalized Medicine (IPM) and the Mount Sinai Data Warehouse (MSDW) team are pleased to announce the addition of three new BioMe Biobank cohorts to MSDW and its Leaf and ATLAS cohort query tools.

These “pre-calculated” cohorts for the BioMe Biobank program represent over 64,000 enrolled participants from diverse ancestral and cultural backgrounds that have genetic, longitudinal epidemiologic, and molecular data available, including over 52,000 participants with microarray data and over 30,000 participants with whole exome sequencing data (WES).

Like the other such patient cohorts in MSDW, these new cohorts are intended to be a convenient base population to which you may apply your own additional inclusion and exclusion criteria. Of course, usage of these cohorts is entirely optional.

The “pre-calculated” patient cohorts in MSDW and available in the Leaf and ATLAS cohort query tools now include the following:

  1. BioMe Biobank
  2. BioMe Biobank Global Diversity Array (Sema4)
  3. BioMe Biobank Global Screening Array (Regeneron)
  4. BioMe Biobank Whole Exome Sequencing (Regeneron)
  5. Cancer Patient Cohort
  6. Cancer Institute Biorepository
  7. Imaging Research Warehouse 1.0

Please visit the Mount Sinai Data Warehouse website for tutorials on Leaf and ATLAS, as well as for more information about requesting help from the Scientific Computing and Data team.

Please visit the Charles Bronfman Institute for Personalized Medicine website for more information on BioMe Biobank program

New Cancer Patient Cohort Available

The Mount Sinai Data Warehouse team is pleased to announce the addition of a new cancer patient cohort to MSDW and its Leaf and ATLAS cohort query tools.

 

This “pre-calculated” cohort comprises all Mount Sinai patients with a diagnosis in Epic that maps to a cancer-related ICD-9, ICD-10, or SNOMED code.

 

Like the other such patient cohorts in MSDW, this new cohort is intended to be a convenient base population to which you may apply your own additional inclusion and exclusion criteria.  Of course, usage of these cohorts is entirely optional.

 

The “pre-calculated” patient cohorts in MSDW and available in the Leaf and ATLAS cohort query tools now include the following:

 

  1. Cancer Patient Cohort
  2. BioMe BioBank
  3. Cancer Institute Biorepository
  4. Imaging Research Warehouse 1.0

 

Please visit the Mount Sinai Data Warehouse website for tutorials on Leaf and ATLAS, as well as for more information about requesting help from the Scientific Computing team.

Notice: New Leaf Release Live August 9

Scientific Computing and Data is pleased to announce a new development for data accessibility: the Leaf query tool will soon deploy a software release, making it easier to query de-identified patient data in the Mount Sinai Data Warehouse.

 

Leaf’s new software release will display maintenance notifications and updates in real time, and will restore the ability to view and export lists of patients from Leaf while adhering to patient privacy regulations regarding small cohorts.

 

The biggest update to Leaf will enable users in the Mount Sinai School or Hospital system to log in to Leaf directly using their secure Mount Sinai credentials. This enhancement will remove the requirement for new users to request Leaf access through the user support ticketing system. With the ability to access data quickly, more researchers across the Mount Sinai system will be able to leverage Leaf for data queries.

 

Scheduled software update to Leaf will take place on Tuesday, August 9 from 10:30 am to 6:30 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 this scheduled downtime.

 

If you have any questions about Leaf, or about querying data in the Mount Sinai Data Warehouse, please click here.

Mount Sinai Data Warehouse (MSDW) Charge Rate – 2022

Finance and Compliance completed their yearly review of Mount Sinai Data Warehouse (MSDW)’s charge rate and determined that the 2021 rate will continue unchanged in 2022.

 

In 2022, a charge rate of $180/hour for this Custom MSDW Data Request service will remain unchanged.

 

To learn more about the Custom Data Request process, click here.

 

To submit a Custom Data Request, click here.

Self-service cohort building now available for BioMe and the Imaging Research Warehouse 1.0

Researchers can now build cohorts specific to the Imaging Research Warehouse (IRW) 1.0 and the BioMe BioBank Program using the Mount Sinai Data Warehouse’s (MSDW) self-service Electronic Health Record cohort building tool, Leaf.

 

The Imaging Research Warehouse (IRW) 1.0  contains over 217 million de-identified image slices for over 700,00 MSHS studies from 2017-2021. Image modalities include DX (Digital Radiography), CT (Computed Tomography), CR (Computed Radiography), MR (Magnetic Resonance), MG (Mammography) and NM (Nuclear Medicine). All images are available on the Minerva Supercomputer and ready for computation and analysis.

 

The BioMe, BioBank Program is an electronic medical record-linked blood/serum biobank with over 50,000 enrolled participants. Genetic, epidemiologic and molecular data are available on these participants, including whole exome sequencing data (WES) for a diverse cohort of individuals from over 30,000 with many ancestral and cultural backgrounds. The WES data is available on the Minerva Supercomputer and ready for computation and analysis.

 

The Electronic Health Record (EHR) data on MSDW, the IRW 1.0 images and the WES data are all located on the Minerva Supercomputer. Minerva has over 2,000 applications available along with a team of computational scientists to help you build multi-scale models using genomic, imaging, EHR and other data types.

 

Leaf can help you develop, visualize and export cohorts, using ICD-10 codes and a range of standard healthcare terminologies, and it is available to all Mount Sinai Health System. To get started with your own Leaf account, click here.

 

Scientific Computing and Data is hosting an introductory application training for Leaf on Wednesday, May 4, from 12:00-12:30 pm. To register for the training and to see more details, click here.