2022 PSU Bioinformatics Data Reproducibility Bootcamp
INFORMATION TOP
Welcome to the PSU Bioinformatics Data Reproducibility Bootcamp!
Important resources:
Instructors
Organizer
Funding and Support
The computational resources are provided by The Institute for Computational and Data Sciences (ICDS).
The boot camp was first conceived and supported in Jun 2016 by the Administrative Supplement to NIGMS Predoctoral Training Grants (PA-15-136)
schedule TOP
Friday August 12, 2022
- 09:30 AM - Breakfast
- 10:00 AM - Welcome and overview of the day
- 10:05 AM - Session 1: Introduction to data reproducibility
- 11:45 AM - Break
- 12:00 PM - Session 2: Interactive coding on the ACI-ICS cluster part 1
- 01:00 PM - Lunch
- 02:00 PM - Session 2: Interactive coding on the ACI-ICS cluster part 2
- 03:00 PM - Session 3: Workflow management by Snakemake part 1
- 03:50 PM - Break
- 04:05 PM - Session 3: Workflow management by Snakemake part 2
- 05:00 PM - Done!
session 1 TOP
Session 1: Introduction to data reproducibility
speaker: Ana Victoria
In this session we will discuss the reproducibility crisis in science and we will go over materials that will help us make our research reproducible.
We will have a look at different online note-taking tools, we will learn how to use GitHub and Git for version control, and we will finish this session by going over helpful bioinformatics tools.
session 2 TOP
Session 2: Interactive coding on the ACI-ICS cluster
speaker: Alan Brown
This session will introduce Jupyter notebooks, the computing cluster at PSU and some ways to incorporate both for more organized coding.
session 3 TOP
Session 3: Workflow management by Snakemake
speaker: Jianyu Yang
In this session we will go through Snakemake, a popular workflow management tool. We will talk about what kind of features should be expected from a workflow, and how to realize them by Snakemake.
A toy example workflow will be built step by step during the presentation, and participants will also have the chance to work on small tasks by their own.