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

9:30 am - 5:00 pm EST

Instructors: Saber Soleymani, Dr. 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.

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 early-career researchers 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. Software required for this event are described 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. We will be providing closed captioning for the Zoom portion of the workshop, and will record and distribute the lectures to applicants that are unable to attend the workshop.

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. We will work with applicants to correctly install these software the week before the workshop.
  2. Download these data from Tenaillon et al. (2016).
  3. Install and update a 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 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 primarily use Slack and Zoom to collaborate during the workshop. There are dedicated Slack channels for applicants to network and collaborate. There is a collaborative notes document here, however we do encourage all participants to take their own notes as well.


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


Before July 27th, 2020

Any time Pre-workshop survey

July 27th, 2020

9:30-11:00 Project Organization and Management Dr. Wendy Wong
11:15-12:30 Introduction to the Command Line Saber Soleymani
12:30-1:30 Lunch
1:30-5:00 Introduction to the Command Line Saber Soleymani

July 28th, 2020

9:30-12:30 Data Wrangling and Processing Dr. Wendy Wong
12:30-1:30 Lunch
1:30-2:30 Introduction to Cloud Computing for Genomics Dr. Wendy Wong
2:30-5:00 TBD
5:00 Post-workshop survey