Category: Empower the Future of Research

Medical Imaging for AI Research Inquiries

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UFIT is hosting two MONAI-focused tutorials in July. Both tutorials will be held via Zoom:

Tutorial Name: MONAI Core
Date: Tuesday, July 12, 12:00–1:00 p.m.
Registration Link
Description: MONAI Core is a PyTorch based and GPU-accelerated deep learning framework, specifically designed for medical imaging. This tutorial will cover:
• Why MONAI Core: the unique and impactful features of MONAI Core
• MONAI Core on HiPerGator: end-to-end demo on HiPerGator

Tutorial Name: MONAI Label for Medical Imaging with NVIDIA
Date: Tuesday, July 26, 12:00–1:00 p.m.
Registration Link
Description: MONAI Label is an open-source medical-imaging-specific tool for both AI-assisted annotation and building your own AI annotation models. This tutorial has two parts:
• An in-depth MONAI Label introduction
• A step-by-step demo on HiPerGator

MONAI is a freely available, community-supported, PyTorch-based framework for deep learning in healthcare imaging. MONAI provides domain-optimized foundational capabilities for developing healthcare imaging training workflows in a native PyTorch paradigm. Anyone with questions about the MONAI tutorials or other training opportunities offered by UFIT Research Computing may contact Dr. Matt Gitzendanner.

Cancer Patient Dataset Available

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To expedite clinical data delivery, UF Health’s data experts recently introduced ready-for-use, UF Institutional Review Board-approved patient record registries so faculty and staff can advance medical knowledge and the delivery of care.

UF Health Integrated Data Repository Research Services released a new dataset featuring details about more than 300,000 patients diagnosed with or suspected of having cancer at UF Health since Jan. 1, 2012. The dataset is available for anyone within the UF and UF Health community. This follows broad use of the UF Health COVID-19 patient dataset which includes records for 300,000-plus patients who presented with COVID-19-like symptoms, and were tested for COVID-19 at UF Health since Jan. 1, 2020. With pre-approval by the IRB, the protected patient information in these registries is de-identified and delivered quickly, bypassing the customary study-specific review.

For details and examples of how this data can be used, please click here for the full story along with a faculty Q&A.

Remote Computing Assistance Available

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You don’t need to be on campus to receive research computing assistance. Remote support and virtual walk-in hours are available on your terms with UFIT Research Computing.

Using Zoom and Slack, researchers can get the consultation they need, when they need it. UFIT staff have years of experience with the university’s computing resources and are ready to support you and your project. Visit the Remote Support webpage to schedule an appointment.

UFIT’s proposal support service can help you stretch your research budget and save you time. Staff can provide personalized commitment letters and help write data management plans. UFIT also regularly offer virtual NVIDIA workshops and computing trainings to maximize your workflows within UF’s HiPerGator AI supercomputing environment. The
RC Training webpage lists upcoming events.

UFIT is committed to supporting the university’s researchers where they are, in Gainesville or around the globe. Please contact the Research Computing staff for assistance with our research computing portfolio of services.

Optimizing Performance on the NVIDIA Platform

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UFIT is offering a 90-minute tutorial, “Performance Analysis and Optimization on the NVIDIA Platform,” on April 14. The tutorial is free and open to faculty, students, and staff.

Tutorial: Performance Analysis and Optimization on the NVIDIA Platform
Date: Thursday, April 14, 2022
Time: 12:00 PM – 1:30 PM
Pre-registration is required

The tutorial will be lead by an NVIDIA scientist who will present an introduction to performance analysis on accelerated CPU-GPU servers. Attendees will learn how to use NVIDIA Nsight Visual Studio profiling tools to understand the behavior of AI and high-performance applications to determine what optimization steps are appropriate for improving the overall time-to-solution.

Registrants will be sent the secure Zoom link the day before the tutorial. Anyone with questions about this event may contact UFIT’s AI Team Lead and Senior Application Developer Ying Zhang.

Progress Towards the 2020-25 Strategic Plan for IT

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The 2020-2021 Contributions Report is now available online.

“This annual report covers July 2020 through June 2021, an extraordinary period of change and challenge,” said VP and CIO Elias Eldayrie. “I am extremely proud of the way our staff not only contributed to the university’s effort to combat COVID-19, but also that we could still support the campus with more than 300 completed projects and enhancements during this time period.”

UFIT is deeply committed to improving UF’s customer experience. Investing in new and innovative ways of delivering campus support is a primary focus for the work underway to achieve the goals outlined in the University of Florida’s Strategic Plan for IT: 2020-2025. Anyone with comments about the publication may send them to UFIT Communications.

Start Your AI Journey with the GAITOR Club

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As UF’s first AI-focused student organization, the GAITOR Club integrates learning and engineering to help students understand artificial intelligence (AI). The goal of the organization is for members to engineer real-world business and marketing solutions using AI applications.

“There is a starting place for everyone in AI,” said Cole Johnson, president of the GAITOR Club. “AI is often associated with being complicated, but the GAITOR Club wants to simplify that gap with practical applications of AI.”

To help students learn AI concepts, the GAITOR Club hosts Machine Learning Mondays and AI days, open to students across UF. The organization also offers AI training courses. On the engineering side, students can dive into AI concepts each semester in four collaborative teams: art, natural language processing, hardware, and thought-model analysis. Using HiPerGator AI, each team creates products to analyze data and influence business decisions. Patrick Lehman, head of the natural language processing team, focuses on providing valuable applications for a range of clients:

“I recognize the privilege in being able to produce AI-oriented projects with motivated people. Being a member of the GAITOR Club allows me to produce applications to value.”

Students regardless of year or major can begin their AI journey with the GAITOR Club. Follow the GAITOR Club on Instagram for information on their networking events and outreach activities.

Two New UFIT Brochures for Campus

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UFIT has new brochures on two of our most popular services.

2022 UFIT Help Desk Flyer
Besides updating services and support available, the UF Computing Help Desk flyer also sports a new, alternative name: the UFIT Help Desk. Both names are still correct, but the UFIT Help Desk is a modernized nickname that has become a common reference…so we’ve built the nickname into the 2022 flyer graphics.

2022 HiPerGator Trifold Brochure
The 2022 HiPerGator trifold brochure was developed for use inside the UF Data Center (UFDC). Getting a tour of the UFDC and HiPerGator Room has become a significant component of the research faculty recruiting process. The new trifold brochure gives potential faculty hires, along with state government officials and other constituents visiting the data center, an updated accounting of the compute power, number of cores available, storage, and speed of HiPerGator 3.0 and AI.

State Faculty Presenting at Spring HiPerGator Symposium

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Registration is now open for the Spring 2022 HiPerGator Symposium. The symposium will be held virtually (hosted on Zoom) and showcase the research in artificial intelligence being conducted by faculty and students from the University of Florida and researchers utilizing HiPerGator from institutions in the Sunshine State Education & Research Computing Alliance (SSERCA).

The date and time for the symposium is Thursday, Mar. 24, from 9:00 a.m. to 1:00 p.m. There will be more than a dozen presenters, including:

Jayantha Obeysekera, Florida International University [“Understanding, Prediction, and Modeling of Flooding due to Sea Level Variability in Coastal Regions Using Data Mining and AI Methods”]
Sudeep Sarkar, University of South Florida [“Scaling Up Computer Vision Algorithms for Image and Event Recognition”]

The full list of presenters will be available on the spring symposium webpage. Students, faculty, and staff of Florida institutions, as well as Southeastern Conference universities and national constituents, may register to attend. Registrants will receive the Zoom link and sign-in information prior to the symposium. Questions about the Spring 2022 HiPerGator Symposium may be emailed to Dr. Erik Deumens, director, UFIT Research Computing.

Numerous Options for Video and Streaming Services

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UFIT provides software and web applications for faculty to record and stream lectures, discussions, learning material, and special events directly to computers and mobile devices. In addition to services for teaching and learning, a full media services menu is available for campus social, research, and administrative events.

A highlight of academic video recording and streaming options is that Mediasite recording technology is installed in several classrooms. To get started, just schedule your recording time and room and leave it to UFIT. The classroom recording functionality is fully automated, so instructors just put on the lapel mic and begin teaching! (More than 20 classrooms have automated Mediasite recorder capabilities.) A member of UFIT will monitor your recording and send a technician if needed. Your course’s video, audio, and computer feed will be uploaded to the course catalog, ready for your students to learn. Through MyMediasite, tools are available to create and manage your recordings. Recordings can be imported from Zoom or MS Teams, uploaded from your computer, or recorded using the Mediasite Mosaic software. MyMediasite can also be used to add quizzes to recordings and add recordings to Canvas.

UFIT regularly streams, records, and uploads online, face-to-face, and hybrid events for campus. Details for all services, including MyMediasite access and pricing information, is published on the Video Event Services webpage.

UF and Nvidia Co-Hosting Hackathon

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UF and Nvidia, in collaboration with OpenACC, are jointly hosting the UF Hackathon from March 29–April 6, 2022. The deadline for teams to apply is
Feb. 21, with selected teams being notified shortly thereafter.

UFIT’s AI team, along with Nvidia AI staff, will serve as mentors to help teams parallelize and optimize code for GPU acceleration. UFIT is also providing HiPerGator AI as the work platform for the UF Hackathon. Teams from the University of Florida have priority during the application process, but teams from other Florida universities and all SEC universities are also able to apply.

The UF Hackathon is a multi-day, intensive hands-on event designed to help computational scientists and researchers port and optimize their applications using GPUs. It pairs participants with dedicated mentors experienced in GPU programming and development in AI, high performance computing, and data science applications. The event will utilize computing resources from HiPerGator AI, currently ranked as the 2nd most powerful supercomputer in U.S. higher education.

Participating teams will leave the event either with applications running on GPUs or a clear roadmap of next steps to leverage GPUs. Anyone with questions about the UF-Nvidia Hackathon may contact Ms. Ying Zhang, applications specialist and AI team lead for UFIT.