Improving the Bioinformatics Curriculum

While bioinformaticians may or may not have teaching roles in any given appointment, they are frequently called upon to teach, and to do so in a wider variety of capacities than the typical lecturer – from informal training for colleagues and collaborators to reaching into the undergraduate curriculum.

We present recent findings by NIBLSE (pronounced “nibbles”), the Network for Integrating Bioinformatics in Life Sciences Education. In 2016, NIBLSE conducted the largest survey to date on undergraduate bioinformatics education in the U.S. The survey revealed that 95% of faculty believe bioinformatics should be taught, but only 40% manage to do so (with clear disparities for faculty at less-resourced institutions). Input from the survey and a NIBLSE working group has also generated a set of bioinformatics competencies for undergraduate bioinformatics (Sayers et.al. 2018). In the graduate arena, a recent PNAS article (Feldon et.al. 2017) suggests informal learning, such as boot camps and workshops, are not effective, but preliminary results from Software and Data Carpentry assessments suggests that in the right context, training can achieve results. Finally, a survey of NSF-funded investigators in the biological sciences (Barone et.al. 2017) conclude that training in several areas of bioinformatics are the most unmet need for established researchers.

Since bioinformatics is usually taught by bioinformaticians rather than biology educators in general, this talk highlights challenges and opportunities surrounding bioinformatics training, and aims to spark conversation on ways bioinformaticians can and should shape the training landscape. As new methods such as machine learning/deep learning become more relevant to biology, we risk widening the intelligibility gap between the training “haves” and “have-nots.” The community has a need for extensive discussion on this topic and support for development of alternatives to classroom training that can bridge gaps between the large numbers of existing researchers who need to understand and apply data science skills, but who are unlikely to return to formal schooling.

Workshop: Introduction to RNA-Seq with the Kallisto and Sleuth workflows

This workshop will serve as an introduction to the latest methods in RNA-Seq using the Kallisto (https://pachterlab.github.io/kallisto ; Bray 2016) and Sleuth (http://pachterlab.github.io/sleuth; Pimentel, 2017) software packages. We will give a short introduction to the methods of this pseudoalignment-based approach, including applications for single-cell RNA-Seq. This workshop will include several-hands-on activities that will get participants started using these packages to analyze their own data.

We will work with provided example datasets. For users wanting to work with their own datasets, we suggest obtaining a CyVerse account and following these instructions to upload their data to CyVerse prior to the workshop (https://cyverse-data-store-guide.readthedocs-hosted.com/en/latest/step1.html).

Pre-requisites: We will be making substantial use of R in this workshop; therefore, participants will benefit most if they have a basic knowledge of R. If you have little or no familiarity with R we believe you will be able to follow along with the example exercises, although you may need additional support post-workshop to apply what you have learned on your own.

Jason Williams

Mr Jason Williams

Assistant Director, External Collaborations,  Cold Spring Harbor Laboratory, DNA Learning Center

Jason is Assistant Director – External Collaborations of Cold Spring Harbor Laboratory’s DNA Learning Center, and is the Education, Outreach, and Training lead for CyVerse (A U.S. national life science cyberinfrastructure project funded by NSF). Jason organizes, instructs, and speaks at a variety of bioinformatics-related workshops, conferences, and meetings annually. He also serves in an advisory capacity on a variety of bioinformatics and open science projects including his service as Chair of the International Science Advisory Board for EMBL-Australian Bioinformatics Resource. He also serves on the External Panel of Consultants to the National Institutes of Health (NIH) Data Commons Initiative and the NIH’s National Heart Lung and Blood Institute’s Data STAGE (Storage, Toolspace, Access and analytics for biG data Empowerment). He is an active Software and Data Carpentry instructor, and a former Chair of the Software Carpentry foundation. Jason also teaches at the Yeshiva University High School for Girls.

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