Lab Meeting Workshops
Interested in having a workshop given directly to your lab? Contact Bryce at bdgrier@stanford.edu.
Scheduled Workshops
100 - Bash and the Unix Shell March 21, 2025
200 - Data Transfer and Storage March 28, 2025
300 - Containerized Analysis Notebooks April 04, 2025
210 - Efficient Data Storage and Retrieval with HDF5 Late March/April 2025
110 - Git and Version Control Late April 2025
Current Offerings
100 - Bash and the Unix Shell (periodically offered in collaboration with Christina Gancayco from Stanford Research Computing)
introduction to Unix shells
essential Bash commands
developing and executing a Bash script
110 - Git and Version Control
coming soon!
200 - Data Transfer and Storage
Stanford-specific and external resources for data management
command line data transfer tools:
rsync (needed for FarmShare/Sherlock/OAK)
rclone (useful for cloud services)
210 - Efficient Data Storage and Retrieval with HDF5
coming soon!
220 - LLMs as Tools in Research
history, development, and current state of large language models (LLMs)
building a retrieval-augmented model that allows for management and querying of scientific knowledge
300 - Containerized Analysis Notebooks
promoting reproducibility through using containerized analysis
interactive, containerized, brower-based analysis using HPC resources:
FarmShare/Sherlock OnDemand
hosting python kernels on FarmShare/Sherlock
310 - Parallel Processing I
introduction to embarrassingly parallel problems
methods of parallelization at large scales:
GNU Parallel (powerful, shell-based tool that allows for easy parallization of tasks on a local machine)
Pub/Sub (cloud-based service that allows for scalable, aynchronous analysis pipelines)
Future Offerings
311 - Parallel Processing II
320 - Efficient Analysis of Time Series Data
400 - CI/CD Pipelines for Scientific Computing
401 - Scientific Computing Clusters in the Cloud
500 - Integrating HDF5 with Parallel Processing