SIPS Summer Bioinformatics

Cornell University

May 22 - June 26, 2023

1:00 pm - 5:00 pm ET

Instructors: Travis Wrightsman

Helpers: Mohamed El-Walid, Jack Fabrizio, Zong-Yan Liu

General Information

Who: Pre-registered SIPS students and post-docs. This is not a public workshop.

Where: Stone Classroom (Room 103), Mann Library, Cornell University. Get directions with OpenStreetMap or Google Maps.

When: May 22 - June 26, 2023. Add to your Google Calendar.

Requirements: If you have a Cornell NetID, then none! You can use one of the classroom computers. If you do not have a Cornell NetID, then you will need a laptop with a web browser and internet access.

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Mon, May 22 (Day 1)

Before starting Pre-workshop survey
13:00 Introductions
13:10 Introducing the Shell
13:40 Navigating Files and Directories
14:30 Break
14:35 Working with Files and Directories
15:20 Redirection
16:05 Break
16:10 Writing Scripts and Working with Data
16:50 Feedback
17:00 End

Wed, May 24 (Day 2)

Before starting Pre-workshop survey (if not completed)
13:00 Introductions
13:10 Getting Started with Conda
13:30 Working with Environments
14:45 Break
14:50 Using Packages and Channels
15:20 Sharing Environments
16:05 Break
16:10 Optional: Common Bioinformatics Tools
16:40 Feedback
16:50 End

Fri, May 26 (Day 3)

Before starting Pre-workshop survey (if not completed)
13:00 Introductions
13:10 Automated Version Control
13:15 Setting Up Git
13:20 Creating a Repository
13:30 Tracking Changes
13:50 Exploring History
14:15 Ignoring Things
14:20 Break
14:25 Remotes in GitHub
15:10 Collaborating
15:35 Conflicts
15:50 Open Science
16:00 Break
16:05 Licensing
16:10 Citation
16:15 Hosting
16:25 Feedback
16:35 End

Mon, Jun 12 (Day 1 Alt)

Before starting Pre-workshop survey
13:00 Introductions
13:10 Introducing the Shell
13:40 Navigating Files and Directories
14:30 Break
14:35 Working with Files and Directories
15:20 Redirection
16:05 Break
16:10 Writing Scripts and Working with Data
16:50 Feedback
17:00 End

Thu, Jun 22 (Day 2 Alt)

Before starting Pre-workshop survey (if not completed)
13:00 Introductions
13:10 Getting Started with Conda
13:30 Working with Environments
14:45 Break
14:50 Using Packages and Channels
15:20 Sharing Environments
16:05 Break
16:10 Optional: Common Bioinformatics Tools
16:40 Feedback
16:50 End

Mon, Jun 26 (Day 3 Alt)

Before starting Pre-workshop survey (if not completed)
13:00 Introductions
13:10 Automated Version Control
13:15 Setting Up Git
13:20 Creating a Repository
13:30 Tracking Changes
13:50 Exploring History
14:15 Ignoring Things
14:20 Break
14:25 Remotes in GitHub
15:10 Collaborating
15:35 Conflicts
15:50 Open Science
16:00 Break
16:05 Licensing
16:10 Citation
16:15 Hosting
16:25 Feedback
16:35 End

Setup

To participate in a workshop, you will need access to an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.