Healthcare and Life Sciences

This page describes the collection of Healthcare and Life Sciences software on HiperGator. Artificial intelligence (AI), including machine learning (ML), has the potential to revolutionize human health and medical research by enabling software to learn from past examples and make informed decisions in life sciences. Research Computing AI support will assist in developing and refining advanced models for various tasks in healthcare and life science, including medical image analysis, disease detection, and genomic data interpretation, through support requests or consulting.

Deep Learning Frameworks

There are preinstalled and configured environments on HiPerGator for the most frequently used deep learning frameworks including tensorflow, pytorch, and MxNet. The available deep learning frameworks can be queried using

 module spider [pytorch/tensorflow/mxnet] 

Users can also customize their own conda environment following this tutorial: Managing Python environments and Jupyter kernels

Module environments for Healthcare and Life Sciences

Below are a number of module environments or framework that is configured for training or your deep learning models on HiPerGator-AI.

• MONAI core: MONAI Core is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem.
  • Use the command below to list the available versions on HiPerGator-AI. Please see recorded MONAI Core tutorials for details.

  • module spider monai

• MONAI label: MONAI Label is an intelligent open source image labeling and learning tool that enables users to create annotated datasets and build AI annotation models. MONAI Label reduces the time and effort of annotating new datasets and enables the adaptation of AI to the task at hand by continuously learning from user interactions and data.
  • Use the command below to list the available versions on HiPerGator-AI. Please see recorded MONAI Label tutorials for details.

  • module spider ngc-monailabel

• Clara Parabricks: NVIDIA Parabricks is a scalable genomics analysis software suite that leverages full-stack accelerated computing to process data in minutes. Compatible with all leading sequencing instruments, it supports diverse bioinformatics workflows and integrates AI for accuracy and customization.
  • Use the command below to list the available versions on HiPerGator-AI.

  • module spider parabricks

• Bionemo: NVIDIA BioNeMo is a generative AI platform for drug discovery that simplifies and accelerates the training of models using your own data and scaling the deployment of models for drug discovery applications.
  • Use the command below to list the available versions on HiPerGator-AI.

  • module spider bionemo

• AlphaFold: AlphaFold is an AI software developed by DeepMind that predicts protein structures. It uses deep learning algorithms to predict protein structures with remarkable accuracy, down to atomic levels. The software constructs an initial model, iteratively refines it, and produces a 3D model of the protein. The final output includes 3D coordinates for every non-hydrogen atom in the protein, along with confidence levels for each amino acid residue.
  • Use the command below to list the available versions on HiPerGator-AI.

  • module spider bionemo