Are you running out of resources on your local machine? While Jupyter Notebooks has become the de facto software environment for interactive data analysis, visualization, and machine learning, running notebooks on an HPC system is challenging. We demonstrate the Galyleo command-line tool and the Expanse Portal to run Jupyter Notebooks on Expanse. The Expanse portal provides an integrated and easy-to-use web interface to access Expanse HPC resources. We also cover setting up reproducible and transferable software environments from your local machine to Expanse using Conda. We demonstrate scaling up calculations to large datasets and parallel computing on Expanse, as well as running Jupyter Notebooks in batch mode.
Director for Structural Bioinformatics Laboratory
Dr. Rose is Director of the Structural Bioinformatics Lab and Lead for Bioinformatics and Biomedical Applications at the San Diego Supercomputer Center (SDSC), UC San Diego. He has previously led bioinformatics and scientific computing departments at Pfizer and Agouron Pharmaceuticals. He led the RCSB Protein Data Bank team at UC San Diego, one of the largest open access databases in biology. In his current position at SDSC, he is involved in projects to integrate cross-disciplinary data for novel COVID-19 diagnostic and surveillance methods, and the application of knowledge graphs to COVID-19 and precision medicine datasets. His research interests include the development of interactive and scalable platforms for data integration and machine learning in biomedicine and structural biology. He is an advocate for open-source software development and reproducible computational research.