Dec 27, 2022 | Status Update
There will be scheduled maintenance to MSDW2 PROD SQL Server on Wednesday, January 11th, from 5:00-7:00 PM. Leaf, ATLAS, and the Mount Sinai Data Warehouse will be down for maintenance so that Scientific Computing and Data engineers can upgrade the SQL Server from CU 12 to CU 16, which will fix security vulnerabilities and apply some bug fixes in critical systems software.
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. Thank you.
Sep 20, 2022 | Status Update
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.
Aug 26, 2022 | Status Update
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:
- BioMe Biobank
- BioMe Biobank Global Diversity Array (Sema4)
- BioMe Biobank Global Screening Array (Regeneron)
- BioMe Biobank Whole Exome Sequencing (Regeneron)
- Cancer Patient Cohort
- Cancer Institute Biorepository
- 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
Aug 24, 2022 | Status Update
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:
- Cancer Patient Cohort
- BioMe BioBank
- Cancer Institute Biorepository
- 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.
Jul 26, 2022 | Status Update
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.
Jun 22, 2022 | Status Update
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.
