American Society of Naturalists Graduate Council: July 27-28, 2020

ECR2: Command-Line Bioinformatics for Beginners Workshop

American Society of Naturalists Graduate Council


July 27-28, 2020

9:00 am - 5:00 pm CST

Instructors: Saber Soleymani, Wendy Wong

Helpers: Mariana Villalba, Cheyenne Yancey Payne, Reilly Cooper, Kevin Amses, Matthew Gibson

Hosts: Emma Lehmberg, Simon Tye

General Information

Bioinformatics is an essential component of modern genomics research. These computer-intensive methods are often difficult to learn for many without guidance from experienced individuals. In turn, graduate students and early-career researchers at institutions with limited bioinformatics resources are at a disadvantage toward the use of these and other emerging tools in evolutionary biology. As part of Evolutionary Community Responses for Early Career Researchers (ECR2) 2020, the American Society of Naturalists' Graduate Council is hosting a Command-Line Bioinformatics for Beginners Workshop on July 27-28th, 2020. This workshop is free for all members of the American Society of Naturalists (ASN), Society for the Study of Evolution (SSE), or Society of Systematic Biologists (SSB). Applicants with no previous experience with bioinformatics tools and/or command-line programming will be prioritized.

To sign up for this workshop, click here.

This workshop is based on exercises from the Data Carpentry Genomics Workshop. Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. For additional information about the Data Carpentry Genomics Workshop, click here.

Who: This workshop is for graduate students and post-doctoral researcherrs with no to minimal experience with bioinformatics tools and/or command-line programming.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: July 27-28, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed listed under (Setup).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email or for more information.


To participate in this workshop, you will need to:

  1. Install all software for the Data Carpentry Genomics workshops.
  2. Download all data required to complete the workshop. These data are located here and placeholder. These datasets are from Tenaillon et al. (2016) and placeholder, respectively.
  3. Install an up-to-date web browser, such as Firefox or Chrome.
  4. Install Zoom and Slack. The workshop will be broadcast via private Zoom and Slack channels. Links to these channels will be emailed to all applicants two weeks before the workshop.
Data Carpentry maintains a list of common issues that occur during installation, which may be helpful for applicants as they install the required software.

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. Simon - I think we can just use GitHub as a repository for the whole workshop. Have both datasets even, maybe, and all the notes, etc.


Data Carpentry is committed to improving their workshops and encourages all workshop participants to complete these short surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey