Category: Empower the Future of Research

UFIT Awarded Contract with USDA

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UFIT was recently awarded a multi-year contract to collaborate with the USDA’s Agricultural Research Service (ARS) to deliver AI training. UFIT Research Computing staff will offer sessions using established AI Practicum training modules as as develop new modules in consult with ARS staff. This contract will enhance existing Practicum AI content and allow UFIT to more rapidly build online content for the UF community and beyond. The new modules developed with the USDA will also be available to UF faculty, staff and students, with particular benefit to the IFAS community.

Part of the contract’s funding will be used to hire a new AI training staff member, who will develop the new training modules, deliver in-person sessions, and produce online content for UF’s Professional Workforce Development site.

Eight new, four-hour, beginner and intermediate courses are planned. As well, and in consult with ARS and IFAS, some advanced AI topics are under consideration including areal image analysis, agriculture-specific computer vision, genomics, and agriculture-specific reinforcement learning for robotics.

Production of online content is underway. The in-person content already available to the UF community will be offered to ARS staff starting in Spring 2023. Anyone with questions about UFIT’s contract with the USDA is welcome to email Training and Biocomputing Specialist Dr. Matt Gitzendanner.

Supporting Women in High Performance Computing and AI

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To celebrate and promote women’s participation in high performance computing and artificial intelligence, UF Information Technology is hosting a Women in HPC & AI panel discussion and luncheon event on Thursday, December 1, from 12:00 to 1:30 p.m. This in-person panel will be held in the UF Informatics Institute (CSE Room E252) and is free, but pre-registration is required. Lunch is included with your registration. The panelists are:

• Dr. Bonnie Dorr, Professor, Department of Computer & Information Science Engineering
• Dr. Mei He, Assistant Professor, Department of Pharmaceutics
• Dr. Heidi Boisvert, Assistant Professor, School of Theatre+Dance
• Dr. Sarah Moeller, Assistant Professor, Department of Linguistics

Space for the event is limited. Women in High Performance Computing (WHPC) is an international organization working to build a diverse and inclusive workforce by promoting the role of women in computing. UF’s Women in HPC & AI is the local chapter of WHPC. Its aim is to offer mentoring opportunities and resources for female students, faculty, and staff while building a strong cross-disciplinary professional network across UF. Anyone with questions is welcome to email Applications Specialist and AI Support Team Lead Ying Zhang.

Expanding External Usage of HiPerGator

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Federated identity access allows only authorized users secure access to multiple services and domains via a single set of verified credentials. To support federated access to HiPerGator, on Monday, Sept. 19, 2022, the following websites will be updated to use the InCommon Discovery Service:

• jupyterhub.rc.ufl.edu and jhub.rc.ufl.edu
• support.rc.ufl.edu
• galaxy.rc.ufl.edu
• ondemand.rc.ufl.edu and ood.rc.ufl.edu

InCommon is an integrated service enabling single sign-on, access to cloud and local services, and global collaboration. UF faculty with collaborators at other InCommon federated institutions will benefit by not having to arrange GatorLink IDs for them. State university system and SEC institution faculty will also benefit, because they will now be able to use their institutional account credentials; a boon for those institutions’ instructors teaching large classes using HiPerGator AI.

Users will be directed to the InCommon Federation Discovery website after the update is complete. Be sure the ‘Remember selection for this web browser session’ checkbox is selected to skip this step in the future on the same computer. Then, select ‘University of Florida’ from the dropdown. After selecting University of Florida, users will be directed to the GatorLink login page (https://login.ufl.edu/).

UFIT wants all HiPerGator ecosystem users to be aware of this impending change. Anyone with questions about these InCommon federated access additions may contact Training and Biocomputing Specialist Dr. Matt Gitzendanner.

Fall 2022 HiPerGator Training

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Registration for the fall 2022 Research Computing training schedule is now open. The training sessions will be held on Thursdays from 10:40 a.m. to 12:00 p.m. And for the first time, this semester UFIT is offering both in-person registration and Zoom attendance options for each training.

The in-person location is the
UF Informatics Institute Seminar Room. All sessions are open to faculty, lab staff, and undergraduate and graduate students. Please register by 9:00 a.m. on the day of the training to ensure you receive the Zoom link. Sessions will be recorded and posted on Research Computing’s pre-recorded training page. To learn more about any of the training options and to register, visit https://rc.ufl.edu/calendar/.

Sep. 08: 10:40 a.m.-12:00 p.m. │ Intro to Research Computing and HiPerGator
Sep. 22: 10:40 a.m.-12:00 p.m. │ Intro to the Linux Command Line
Sep. 29: 10:40 a.m.-12:00 p.m. │ HiPerGator SLURM Submission Scripts
Oct. 06: 10:40 a.m.-12:00 p.m. │ HiPerGator SLURM Scripts for MPI Jobs
Oct. 20: 10:40 a.m.-12:00 p.m. │ Running Graphical Applications on HiPerGator
Nov. 03: 10:40 a.m.-12:00 p.m. │ Jupyter Notebook and Managing Conda Environments
Nov. 10: 10:40 a.m.-12:00 p.m. │ Git and github.com

Fall 2022 HiPerGator Symposium

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The fifth annual Fall HiPerGator Symposium will take place from 9:00 a.m. to 1:00 p.m. on Tuesday, November 1. The symposium will be held virtually via Zoom and consist of three parts: a keynote presentation, 10-minute ‘lightning’ talks, and poster sessions. Dr. Bala Balachandar, Newton C. Ebaugh Distinguished Professor in the Department of Mechanical and Aeronautical Engineering, will deliver the keynote presentation. The full Symposium agenda is available online.

The symposium is open to everyone in the UF community and to research faculty in the state university system and Southeastern Conference member institutions. Register to attend here.

All postdocs, undergraduates, and graduate students can submit to present a lightning talk or a poster. The fall symposium focuses on high-performance and high-throughput computing, leveraging HiPerGator 3.0 and its storage systems. While AI applications may be considered, the spring symposium focuses specifically on AI. Visit the event registration page to submit a proposal for a lightning talk or a poster. → Applications to be a presenter must be received by October 14.

Anyone with questions about the Fall HiPerGator Symposium may contact UFIT Applications Specialist Ying Zhang.

Supporting UF’s $1Billion Research Portfolio

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UF’s research portfolio exceeded $1 billion for the first time in the fiscal year ending June 30, 2022. UFIT supports two applications– UFIRST and myinvestiGator–that enable researchers to manage their sponsored funding. Numerous financial analysts, developers, and data engineering staff are involved each week with the maintenance of these applications.

“A world-class research institution requires world-class administrative tools. Keeping our faculty and research support teams empowered through easily accessed, up-to-date information is key,” wrote Stephanie Gray, assistant vice president & director, Division of Sponsored Programs. “UFIT helps keep UF Research running with their excellent support of UFIRST and myinvestiGator.”

UFIRST Numbers
4,244 active users in FY22
14,677 new projects added to UFIRST in FY22

myinvestiGator Numbers
2,000 faculty and staff users in FY22
Approximately 17,000+ system logins in FY22

Assistance getting started on both applications is available through UF Research. Training materials and helpful companion docs for UFIRST and myinvestiGator are online:
https://learn-and-grow.hr.ufl.edu/toolkits-resource-center/financial-toolkits/grants/.

Full Service Video Production For UF

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UFIT Video Productions offers in-studio and location production services for faculty and staff.  The production studio facility, located on the second floor of the Hub, features a variety of video recording tools to enhance your academic and outreach videos, and a team with multimedia expertise to assist you. Whether you need to record lectures for a course or create a department video for recruiting faculty or students, consider UFIT your one-stop shop for all things digital and video production!

Faculty and staff can request full-service studio production services or utilize the On-Demand Studio to self-record. UFIT can also film anywhere on campus to make your welcome video, alumni spotlight, interview feature, and department tour videos really stand out. A recent addition to our services is 360 video capabilities. Some examples of recent work are available on the Video Production Sizzle page.

Please submit the CITT’s https://citt.ufl.edu/request-assistance/ form to get started with a video project.  On behalf of UFIT, we look forward to working with you!

Introduction to Data Analysis and Graphics

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UF Information Technology is again offering its extremely popular R Programming course this fall. This online, self-paced training is offered free for faculty, postdocs, staff, and graduate students.

The fall 2022 course dates are August 29 to October 29. To register, visit UFIT Training’s R Programming page. Pre-registration is required by August 26.

The eight modules in the course are: Introduction to R, Data Preparation, Exploratory Data Analysis, Mean and Median Comparison, ANOVA, Correlation, and Linear Regression, Multiple Linear Regression, Proportion Comparison, and Logistic Regression. A detailed syllabus is available on the R Programming page. Enrollees must have successfully completed at least one graduate-level course in statistics prior to the start of the training.

Anyone with questions about UFIT’s R Programming training is welcome to reach out to instructor Dr. Jose Silva-Lugo.

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.