An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy

• Published in: Gigascience Vol. 12
• Main Authors: Kumar, Anup, Cuccuru, Gianmauro, Grüning, Björn, Backofen, Rolf
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 2023
• Subjects: Accessibility; Algorithms; Amino Acid Sequence; Artificial Intelligence; Astronomical models; Bioinformatics; Central processing units; Computed tomography; Computer science; Containers; COVID-19; CPUs; Datasets; Editors; Galaxies; Gene expression; Graphics processing units; Humans; Infrastructure; Medical imaging; Neural networks; Neural Networks, Computer; Personal computers; Pipelining (computers); Programming languages; Protein structure; Python; Software; Technical Note; Tomography; Version control; Visualization; Europe; CUDA; Galaxy Europe; remote model training; Elyra AI; ONNX; JupyterLab; GPU; artificial intelligence
• ISSN: 2047-217X; 2047-217X
• DOI: 10.1093/gigascience/giad028

Abstract Background Artificial intelligence (AI) programs that train on large datasets require powerful compute infrastructure consisting of several CPU cores and GPUs. JupyterLab provides an excellent framework for developing AI programs, but it needs to be hosted on such an infrastructure to enable faster training of AI programs using parallel computing. Findings An open-source, docker-based, and GPU-enabled JupyterLab infrastructure is developed that runs on the public compute infrastructure of Galaxy Europe consisting of thousands of CPU cores, many GPUs, and several petabytes of storage to rapidly prototype and develop end-to-end AI projects. Using a JupyterLab notebook, long-running AI model training programs can also be executed remotely to create trained models, represented in open neural network exchange (ONNX) format, and other output datasets in Galaxy. Other features include Git integration for version control, the option of creating and executing pipelines of notebooks, and multiple dashboards and packages for monitoring compute resources and visualization, respectively. Conclusions These features make JupyterLab in Galaxy Europe highly suitable for creating and managing AI projects. A recent scientific publication that predicts infected regions in COVID-19 computed tomography scan images is reproduced using various features of JupyterLab on Galaxy Europe. In addition, ColabFold, a faster implementation of AlphaFold2, is accessed in JupyterLab to predict the 3-dimensional structure of protein sequences. JupyterLab is accessible in 2 ways—one as an interactive Galaxy tool and the other by running the underlying Docker container. In both ways, long-running training can be executed on Galaxy’s compute infrastructure. Scripts to create the Docker container are available under MIT license at https://github.com/usegalaxy-eu/gpu-jupyterlab-docker.