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Lab Meeting Workshops

Interested in having a workshop given directly to your lab? Contact Bryce at bdgrier@stanford.edu.

Current Offerings

100 - Bash and the Unix Shell

• introduction to Unix shells

• essential Bash commands

• developing and executing a Bash script

110 - Git and Version Control

• Introduction to version control concepts

• Common git commands and workflows

• Getting started with Stanford GitLab

120 - Python For Scientific Computing I

• Basic syntax, data types, and core libraries

• Jupyter

• NumPy

• Pandas

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)

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

301 - Containerizing Analyses and Workflows

• modifying existing containers

• building custom containers from scratch

• making custom containers available to your lab or to the public

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)

400 - Reproducible Scientific Data Pipelines

• Fundamentals of continuous integration and pipelines

• GitLab CI