The IT Department is investing in a number of 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 members of the research community. 

If you have any questions, please reach out to the Research Computing Lead for each project, or the Sr. Director of Research Computing, Bill Barnett (wbarnett@hms.harvard.edu).

Active Projects

  • Electronic Lab Notebooks

    Description:

    The goal of the Electronic Lab Notebook (ELN) discovery project is to provide improved IT infrastructure support for laboratory-based research at HMS. This project will evaluate needs, test solutions for the use of ELNs at HMS, and establish the technical architectures needed to capture, manage, and share research data and metadata. It is part of a greater Research Workflow Infrastructure (RWI) program designed to set HMS on the path to supporting technology-empowered laboratory research workflows for the HMS research community. The 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. It should support PI needs to establish electronic documentation standards for use in their labs, such as aligning with the principles of findable, accessible, interoperable, and reusable (FAIR) resources as recommended by NIH.

     

    Objectives:

    • Facilitate quad discussions about ELNs and RWI across the HMS research community
    • Evaluate Electronic Lab Notebook (ELN) products from potential vendors:
    • Test and Pilot 2-3 promising ELN platforms with representative set of labs/departments
    • Determine the next steps for providing fully supported ELNs to the HMS community
    • Develop reference architecture for capturing experimental data and metadata for research rigor and reproducibility

     

    Stakeholders:

    This project is led by Research Computing with active collaboration from interested community groups to evaluate appropriate software products and gather researcher requirements. Throughout the Winter of 2020 the project conducted a broad call for participation from the HMS community. Members of the David Corey lab (Neurobiology), Stephen Blacklow lab (BCMP), Karen Adelman lab (BCMP), and members of the Wyss Institute assisted in product evaluations.


    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:

    • Outcomes from an extensive Proof of Concept review of eLABJournal and RSpace led Research Computing to select eLABJournal for a 3-year on-premises pilot.
    • As of Jan 2021, members of the David Corey lab (Neurobiology), and the MiCroN core facility will be our initial eLABJournal Pilot users. Under the guidance of the ELN Steering Committee, two additional cores are to be onboarded in the near future. Discussion is underway regarding an additional lab.

     

  • 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:

    • The 6 pilot cores have been live since November 2020. The project team is now working to onboard the next cohort of cores that will include: Mouse Behavior Core, ICCB-Longwood, Single Cell Core, and Research Computing.

     

  • 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 summer of 2021.

     

  • Storage Usage Reporting and Visualization (SURV)

    Description: 

    The goal of this project is 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 current reporting solution is highly manual, slow, labor-intensive, and error prone. 

     

    Objectives: 

    By optimizing storage usage reporting, the HMS IT Research Data Management team and other stakeholders will be able to 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: 

    This project is 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: 

    Implementation: 

    Work is currently focused on building self-service reports and visualizations for research stakeholders, with the appropriate access controls. The data model is being updated to future-proof reporting for when data migrations occur. The launch of researcher dashboards is scheduled for Spring 2021 with other stakeholder engagements to follow. 

     

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 29th, 2020 to March 30th, 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.