HMS IT invests in several projects, driven by research needs and informed by research priorities, to support the research enterprise at Harvard Medical School. 

This page provides a summary listing of those projects and their scope and timeline. We hope this will be informative and seek participation – advice and testing — from interested research community members. 

If you have questions, contact the Research Computing Lead for each project or the Senior Director of Research Computing, Bill Barnett at wbarnett@hms.harvard.edu.

Active Projects

  • Electronic Lab Notebooks

    Description

    The Pilot ELN project seeks to address the increasingly important issues of efficient and collaborative research, improving research data capture and quality, research reproducibility, and sharing of data and results. The goal is to support principal investigators' need to establish electronic documentation standards for their labs, such as aligning with the principles of findable, accessible, interoperable, and reusable (FAIR) resources as recommended by NIH. Outcomes from an extensive collaborative discovery effort between Research Computing (RC) and interested members of the HMS research community led RC to select eLABNext for a 3-year on-premises pilot. 

    Objectives

    •  Pilot Electronic Lab Notebook (ELN) products in collaboration with at least 3 representative user groups
    • Integrate eLABNext with HMS IT Systems for authentication and storage
    • Develop a production ELN service model, to include training, support, and user documentation
    • Determine the next steps for providing a fully supported ELN service to the HMS community

    Stakeholders

    This project, led by Research Computing, is advised by a steering committee of the following individuals drawn from the HMS community: Caroline Shamu, William Barnett, Rachel Cahoon, Jeremy Muhlich, David Corey, Elaine Martin, Stephen Blacklow, Johanna Gutlerner, and David Smallwood.
    If you are interested in more details or would like to express interest in being a future pilot lab please contact: Bill Barnett (wbarnett@hms.harvard.edu)

    Status

    Implementation:

    • As of September 2022, participants in the eLabNext Pilot include members of the David Corey lab (Neurobiology), the George Church lab (Genetics),  the MiCroN Imaging core facility, the Center for Macromolecular Interactions, and the Neurobiology Imaging Facility.
    • The platform has been integrated with HMS IT security, authenticating using HMS federated sign-on.
    • The ELN service model has been developed, including processes for quarterly software updates, user onboarding and off-boarding, training, and support
    • At the request of faculty members, the team is currently investigating the addition of a second ELN platform to the HMS ELN service.
  • FISMA Moderate Secure Enclave

    Description

    HMS IT will establish a FISMA Moderate certified institutional secure enclave for use by HMS researchers for studies that require FISMA certified environments for sensitive data such as large protected health information data sets. Ultimately this environment will achieve FedRAMP certification which will support multiple FISMA Moderate research projects, and CMS and other regulated data sets.

    DBMI is seeking FISMA Moderate certification for an IT platform, BioData Catalyst, funded by the NIH National Heart Lung and Blood Institute (NHLBI) as part of an extensive national collaborative research program increasing access to NHLBI datasets and innovative data analysis capabilities. NHLBI has required HMS IT to managed this FISMA environment. HMS IT will use the Biodata Catalyst project as the initial FISMA Moderate pilot, which will establish a model for other HMS research projects.

     

    Objectives

    • Implement a FISMA Moderate IT environment in AWS as a pilot in coordination with Paul Avillach (DBMI and the NHLBI/NIH)
    • Identify organization gaps needed to support ongoing FISMA Moderation operations
    • Assess reproducibility, scalability, and service model to achieve FedRAMP certification.

     

    Stakeholders

    This project is a collaboration with Paul Avillach (DBMI) and the areas of HMS IT Research Computing, Infrastructure, and Security and Compliance.  Other stakeholders include the Center for Computational Biomedicine and the Departments of Health Care Policy, Global health, and Biomedical Informatics

    If you are interested in more details please contact: Bill Barnett (wbarnett@hms.harvard.edu)

     

    Status

    Implementation:

    • The Pilot BioData Catalyst FISMA Moderate environment is in production. Third party assessment of the environment completed successfully and a formal, 3 year, Authority to Operate (ATO) was granted by the National Heart, Lung, and Blood Institute in March, 2021.

     

  • Open On Demand for O2

    Description

    This project will design and implement an Open On Demand (OOD) Web-based environment (https://openondemand.org/) as a production Research Computing service on the O2 cluster. It will lower the barrier for non-expert O2 users to access tools and software. It provides a single point of entry to O2 services through a web portal, it has a job composing, submission, and monitoring features, it supports file management and editing, it supports interactive login shells and remote desktops. It will also support the use of Jupyter computational notebooks, R Studio, MATLAB and other applications in the O2 environment.

     

    Objectives

    • Identify Research Needs
    • Develop Implementation Specifications to meet research needs.
    • Implement and operate an Open On Demand service

     

    Stakeholders

    If you are interested in more details please contact: Amir Karger (Amir_Karger@hms.harvard.edu)

     

    Status

    Implementation:

    • A Pilot Open OnDemand System has been made available to 11 individual early adopters who have volunteered to test the system and provide feedback. This feedback, along with usage metrics and any technical issues discovered during the Pilot will be used to inform the design of a production Open OnDemand service.

     

  • Research Cores Facilities Management System

    Description

    HMS is implementing a single robust and flexible core facility management system that lessens the burden and cost of managing services on staff, HMS administrators, and researchers and provides improved financial integration and reporting. This system implementation will aid in the billing, scheduling, and administration of Core services. In 2019, HMS executed a community-driven RFP process and selected a vendor and solution (Stratocore's PPMS system).

     

    Objectives

    • Implement a new, centralized, scalable instance of PPMS for HMS Cores
    • Integration with Harvard's Identity Access Management to enable single sign-on for Harvard IT account owners
    • Integration with Harvard's Oracle Financials to automate the invoicing of internal or external Core customers
    • Roll-out of PPMS and onboarding of all HMS Cores over a multi-year timeline, including training of Core staff

     

    Stakeholders

    There are currently 35 HMS-sponsored Cores that play a crucial role in enhancing research competitiveness, securing research funding, and supporting collaboration for HMS researchers and beyond. This project is a collaboration with the HMS Cores, Research Operations, and the areas of HMS IT Information Systems and Research Computing.

    If you are interested in more details, please contact: Bill Barnett (wbarnett@hms.harvard.edu)

     

    Status

    Implementation:

    • As of October 2022, 20 HMS cores have been on-boarded since November 2020.  

     

  • Research Data Visualization Service

    Description

    In Phase II of the Research Data Visualization Platform (RDVP) project, the platform will be architected to use cloud infrastructure, providing a redundant and expandable design and a highly available environment. Making the application accessible to collaborators when they need access to the data.

    Objectives

    • Provide an interactive application environment to enable HMS quad departments to easily display and share their research data.
    • Provision a sandbox environment utilizing R and Python technologies for a PoC deployment and testing.
    • Replicate a fully tested platform for a pilot service and onboarding of users.

    Status

    Pilot System Delivered:

    The team has developed a re-usable cloud-based architecture, and are currently supporting RStudio Connect servers for 11 different HMS groups who are publishing their own apps. In addition, they are collaborating closely with the CCB to support an on-premises RStudio Connect server, enabling the CCB to support other groups while developing their new apps. Also in close collaboration with the CCB, the team is testing the RStudio Connect Package Manager.

    Operational processes have been deployed for regular monthly upgrades, user onboarding and off-boarding, and spinning up new cloud-based servers on the request of on-quad labs.

    The team is currently orchestrating the migration of all apps from non-standard sandbox environments to new standard architecture servers. Once all apps have been migrated, the sandbox servers will be decommissioned. This effort will ensure that these non-standard servers do not cause maintenance and security issues in the future.

  • Software Containerization

    Description

    The goal of this project is to understand how software containers could enable HMS researchers to more effectively undertake research and support research reproducibility.

    The purpose of the HMS-IT Software Containerization pilot is to evaluate Singularity as a container management solution, specifically examining the feasibility of supporting a number of different research use cases across multiple computing environments. Containers have the advantage of assembling software with all of its dependencies as a single package so it can be run in many environments conveniently, in standardized methods and in a replicable fashion. This approach will allow researchers to use software as containers; simplify installation; and allow some labs to use containers to simplify distributing their own software and dependencies. It can make workflows more portable among workstations, the O2 compute cluster, and cloud computing environments. It will enhance research reproducibility by saving an accurate record of which software was used in research computations.

     

    Objectives:

    • Evaluate operational, organizational, and security considerations of Singularity as a container management solution for research at HMS
    • Pilot use cases for containers downloaded from public sources, for containers HMS researchers create, and for containers created by IT groups (e.g., HMS-IT and BioGrids)
    • Evaluate the opportunity for Singularity containers to run on O2, Cloud environments, and workstations
    • Plan for a containerization production service

     

    Stakeholders

    This Research Computing project is being assisted by HMS community members such as Jeremy Muhlich and Artem Sokolov of the Laboratory of Systems Pharmacology (LSP), Alon Galor of the Peter Park lab, Jim Vincent of Biogrids, as well as input from Shannon Ho Sui of the Chan Bioinformatics Core.

    If you are interested in more details please contact: Amir Karger (Amir_Karger@hms.harvard.edu)

     

    Status

    Implementation:

    • A limited pilot instance is currently underway. Research IT continues to expand features and address issues as identified by pilot users. Expanded access to the pilot is expected to occur as stability and flexibility improve into the fall of 2022.

     

Completed Projects

  • GPU Investments

    Description

    Adding new GPUs & storage to support cutting edge research.

    This project will design and implement new GPU (graphical processing unit) and related data storage architectures to support research at HMS. It is driven by the identification of new research needs coming from image analysis and data science (e.g., machine learning) applications both generally across the Quad as well as Blavatnik Institute needs including from the Center for Computational Biomedicine and Foundry awards. It is building on a current project to assess the performance of new Nvidia RTX 6000 single precision GPU card, which has determined that the RTX 6000 performs very well when tested by HMS-IT and a number of different research labs.

     

    Objectives

    • Identify Research Needs
    • Develop Technical Specifications to meet Research Needs
    • Implement and operate new GPU environments

     

    Stakeholders

    This Research Computing project is benefiting from participation of HMS community members including Wei-Chung Lee, the Peter Sorger lab, and SBGrid who contributed their RTX 6000 test results and will provide advice. We also would like to thank the many members of the HMS research community, including the Debora Marks lab, for their responses to our GPU needs survey. Data from both these sources is helping to inform the design and specification of additional GPU purchases for the HMS research community.

    If you are interested in more details please contact: Amir Karger (Amir_Karger@hms.harvard.edu)

     

    Status

    Completed: 

    • HMS IT has expanded the O2 cluster's GPU capacity with funding from the Blavatnik Institute. The addition of 71 new NVIDIA GPUs, including 44 RTX8000 and 21 Telsa V100s cards, significantly increases O2's GPU computing capabilities to support HMS research. At this time, the additional GPUs are available only for labs with a primary or secondary appointment in a pre-clinical HMS department. 
    • Further details can be found on the O2 GPU Wiki page 

     

    Project Dates

    • April 29, 2020 to March 30, 2021
  • OMERO System Refresh

    Description

    The current OMERO server hardware is outdated and needs to be refreshed. Our goal is to set up a virtual infrastructure with up-to-date operating system and migrate OMERO application and data to a platform which will improve its performance and reliability as well as replace the aging infrastructure  

    • Design and approval of new production and development system architecture 

    • Replace the existing hardware with scalable infrastructure with the capability to run all OMERO microservices and can be fully supported on an ongoing basis 

    • Establish a change control process to ensure regular planned system maintenance 

    • Monitoring and infrastructure visibility 

     

    Stakeholders

    This project is led by Research Computing with guidance from HMS constituents in the Laboratory of Systems Pharmacology, MicRoN Core, Nikon Imaging Center, and Neurobiology Imaging Facility, faculty advisory, and a collaborative implementation with Glencoe. 

    If you are interested in more details please contact: Neil Coplan (Neil_Coplan@hms.harvard.edu

     

    Status

    Completed: 

    • The project team has completed architectural design of the new system, deployed to a development environment, and tested extensively. Cutover to the new system was successfully completed on March 11th, 2021.  

     

  • Research Data Visualization Platform - Phase I

    Description

    In Phase I, the deployment of on-premise infrastructure and RStudio Connect software has been completed and the system is being used by the Center for Computational Biomedicine (CCB)​.

    Objective

    • Provided RStudio Connect Servers for the Center for Computational Biomedicine (CCB).

    Status

    Production system delivered

  • Storage Usage Reporting and Visualization (SURV)

    Description

    The project's goal was to provide accurate, interactive reports and visualizations of storage usage for stakeholders across HMS to proactively manage short and long-term data management needs. The previous reporting solution was highly manual, slow, labor-intensive, and error-prone. 

     

    Objectives

    By optimizing storage usage reporting, the HMS IT Research Data Management team and other stakeholders can more effectively:  

    • Help researchers better locate and manage their data. 

    • Reduce time and cost to produce storage reports and improve quality of storage reporting. 

    • Identify which departments, labs, and individuals utilizing HMS storage resources are driving storage growth in order to improve accountability, manage expansion and IT spending, and to balance immediate and long-term research data management needs. 

     

    Stakeholders

    The project focused on gathering requirements, validating the storage reporting needs, and building solutions for labs, departments, cores, administrators, and HMS IT teams and leadership. 

    If you are interested in more details please contact: Jessica Pierce (rdmhelp@hms.harvard.edu

     

    Status

    Completed: 

    Lab and departmental dashboards of the Storage Usage Monitor have been developed and tested by stakeholders. Underlying infrastructure upgrades to allow access without VPN are complete.

     

    Project Dates

    • July 2019 to August 2022