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 email us at rchelp@hms.harvard.edu
In recent years, Research Computing (RC) has implemented a Pilot ELN service utilizing eLabNext technology. Presently, we are engaged in a Transition to Operation Project aimed at fully establishing and supporting the ELN service. The primary objective of this service remains to assist principal investigators in setting electronic documentation standards for their laboratories, in accordance with the findable, accessible, interoperable, and reusable (FAIR) resource guidelines set forth by the NIH. Additionally, the service provides a platform for labs to effectively track samples and seamlessly integrate them with experiment documentation.
This project, led by Research Computing under the guidance of Linsdsey Sudbury, is advised by the HMS ELN Advisory committee which includes individuals drawn from the HMS community: Steve Blacklow, David Corey, Lucas Farnung, Kristen Buttinger, Katherine Stebbins, Dan Wainstock, Elain Martin, Johanna Gutlerner, Linsdsey Sudbury, Caroline Shamu, Jim Gould, Kelly Arnett, Paula Montero Llopis, Marie Bao, Jeremy Muhlich, Alon Oyler-Yaniv, and David Heitmeyer.
If you are interested in more details please contact: Lindsey Sudbury (lindsey.sudbury@hms.harvard.edu)
Implementation:
In Phase II of the Research Data Visualization Platform (RDVP) project, a Pilot platform was implemented and delivered; 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.
Phase III of the project will deliver a production Research Data Visualization Service that meets the needs of the majority of identified HMS use cases. It will also define policies for use of the platform, and develop improved processes ensure a secure and stable service.
Phase II: Complete. Pilot System Delivered
The team has developed a re-usable cloud-based architecture and are currently supporting Posit Connect servers for 12 different HMS groups who are publishing their own apps. In addition, they are collaborating closely with the CCB to support an on-premises Posit Connect server, enabling the CCB to support other groups while developing their new apps.
Phase III : Implementation:
As of June 27, 2024, there are currently 21 Posit Connect instances in operation to support the RDVP service. Operational procedures, which include monthly updates and user notifications, are operating seamlessly and effectively. The team has successfully met many newly identified user requirements, such as handling large data volumes and providing database access. Recently, a cost-effective method for collecting costs from AWS/EKS Connect instances has been discovered, and the team are analyzing those data.
The O2 Containerization Production Service project aims to create a production quality system for managing and deploying high-performance computing workloads in a containerized environment. The goal is to provide a scalable, flexible, and efficient way of running HPC workloads, reducing the complexity of deployment, and making it easier to manage software dependencies while leveraging the existing cluster scheduling system.
This project builds on earlier work done as part of the Containerization Pilot project.
This Research Computing project will be assisted by HMS community members. They list of key community steakholders will be amended and published prior to the commencement of the project.
If you are interested in more details please contact: Amir Karger (Amir_Karger@hms.harvard.edu)
On Hold:
HMS IT is upgrading to a new storage system designed to efficiently manage large amounts of data quickly. The Research Data Migration project aims to streamline the storage architecture to a centralized, stable, and secure infrastructure.
O2 Home folders and scratch have already been migrated to the new storage successfully, with several benefits and efficiencies already achieved:
This Research Computing project will be assisted by HMS community members.
If you are interested in more details, contact rchelp@hms.harvard.edu.
In progress: Review the current progress on the Research Data Migration page.
The goal of this project is to create an IT service that supports long-term storage and data management workflows for the HMS research community. The initial step in this initiative will create a solution for the storage of inactive data that will focus on preservation and low cost over accessibility, using the term ‘Cold Storage’ to describe this storage tier.
This project is executed by Research Computing in collaboration with IT Infrastructure along with seven labs that participated in pilot testing
Completed: Cold Storage is now available for use.
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.
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)
Completed:
The 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.
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.
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)
Completed:
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
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)
Completed:
This project designed and implemented an Open On Demand (OOD) Web-based environment (https://openondemand.org/) as a production Research Computing service on the O2 cluster. It lowered the barrier for non-expert O2 users to access tools and software. Open on Demand 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.
The resultant service offering has been named the “O2 Portal”.
This project was initiated by the Research Computing group to fill a gap that was recognized in RC’s service offerings rather than to meet the requirements of specific HMS labs. In order to assess OOD requirements, RC reached out to members of the following labs: the Churchman lab, the Seidman lab, the Reich lab, and the Farhat lab.
Complete:
If you are interested in more details please contact: Amir Karger (Amir_Karger@hms.harvard.edu)
April 2020- May 2022
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).
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)
Completed
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).
Production system delivered
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.
By optimizing storage usage reporting, the HMS IT Research Data Management team and other stakeholders can more effectively:
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)
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.
© 2025 by the President and Fellows of Harvard College