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. Currently members of the David Corey lab (Neurobiology), Stephen Blacklow lab (BCMP), Karen Adelman lab (BCMP), and members of the Wyss Institute are assisting in product evaluations.

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

     

    Status:

    Planning:

    • Currently undertaking a Proof of Concept review to evaluate functionality, usability, compliance, and technical features of the two most highly rated products, eLabJournal and RSpace, with several labs.  Outcomes will inform selection of a platform for production pilots with research data.
  • 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.

    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 is working in support of the Biodata Catalyst project for 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
    • Evaluate pilot project lessons for HMS wide reproducibility, scalability, and service model evaluation

     

    Stakeholders:

    This project is a collaboration with Paul Avillach (DBMI) and the areas of HMS IT Research Computing, Infrastructure, and Security and Compliance.

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

     

    Status:

    Implementing:

    • Successfully began an obligatory 90-day operational window on June 1 required for formal 3rd party assessment of the environment with the aim of receiving an Authority To Operate (ATO) in October, 2020.
  • 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 Deborah 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:

    Planning:

    • Following listening tour feedback from faculty, HMS-IT has submitted a survey to collect specific information to determine GPU specifications for purchase, and to assist faculty to purchase GPUs for their labs or cores.
  • 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 for the OMERO system with upgraded applications and up to date operating system

     

    Objectives:

    • 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
    • Enhance capabilities with improved systems functions as well as new features on a development environment before push to production
    • 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, and with faculty advisory.

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

     

    Status:

    Planning:

    • The project team is planning to complete the new system architectural design and stand up a development environment with testing completed by mid-summer 2020. The goal is to move to a production environment by the end of summer 2020.
  • 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:

    Planning:

    • Specification of a Pilot OOD implementation is underway. This Pilot will be tested by IT and early adopters. Implementation of Pilot system is pending a long overdue operating system upgrade to O2 planned for July 7, 2020.
  • 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

    Implementing:

    • Proof of concept for general ledger (GL) integration for internal billing and accounts receivable (AR) integration for external billing underway. Pilot cores and school finance teams have been engaged to review workflows and pricing models.
  • 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:

    Planning:

    • A development instance is under evaluation and.  A security review of the system and procedures to ensure containers are appropriately secure is underway.  Implementation is pending due to a long overdue operating system upgrade to O2 planned for July 7, 2020.