Nibbling away at bioinformatics education with NIBLSE

Todd Smith
Wed Dec 04, 2019
Google image results from a search with "bioinformatics"

This October (9-11, 2019), I attended the 3rd NIBLSE conference entitled: "Integration of Bioinformatics into Life Science Education: Roadmap for the Future." It was held at "Hot Shops" in Omaha Nebraska, a space for artists to work, sell, and meet. 

You might ask what is NIBLSE and why are they making a roadmap for the future?

NIBLSE - Network for Integrating Bioinformatics into Life Sciences Education, is five-year NSF funded Research Collaboration Network (RCN [1]) that formed to address the question, with bioinformatics being so important to biology, how come it is not widely used in, or taught as part of, biology education?

The NIBLSE community is hosted by QUEBS Hub [2], and its sated mission is as follows:

The Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE; pronounced "nibbles") is a National Science Foundation (NSF) Research Coordination Network for Undergraduate Biology Education (RCN-UBE). NIBLSE was formed in 2014. The long-term goal of NIBLSE is to establish bioinformatics as an essential component of undergraduate life sciences education by creating a permanent network of investigators to articulate a shared vision of the extent to which, and how best to, integrate bioinformatics into life sciences curricula. Specific objectives of the Network include identification of best practices for (1) preparation of students for bioinformatics instruction; (2) integration of bioinformatics into life science curriculum at all levels; (3) assessment of outcomes; and (4) preparation of faculty trained in life sciences to deliver curriculum in bioinformatics.

NIBLSE formed in 2012, and received their RCN grant in 2014. Since then they have had three meetings. The initial work focused on developing a survey to validate the group's [NIBLSE] assumption - that bioinformatics is not included in routine biology teaching. And learn why not. The survey request went out approximately 12,000 instructors. Over 1200 instructors participated, and their answers and comments were compiled, analyzed, and summarized in two papers:

  1. Bioinformatics core competencies for undergraduate life sciences education [3];

  2. Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction [4].

A key finding from this work was that 95% of the participants agreed that bioinformatics should be more widely taught, but there are many barriers. The most common barrier identified was was lack of faculty expertise and training. The next barriers included lack of student interest, overly-full curricula, and lack of student preparation. Other barriers listed issues related to resources (computers, software) and rapidly changing technology. In terms of student interest, one issue identified was career prospects, students are unaware that knowledge of, and experience with, bioinformatics will help them get good jobs (our Biotech-Careers website can help with that).

The October 2019 meeting

A summary [5] and details [6] of the meeting are provided on QUBES.

In the first four years of the RCN, the NIBLSE group has identified bioinformatics competencies and learned many of the reasons why bioinformatics is not taught. The next question is where does the group go from here?  Hence the title of the meeting, "Integration of Bioinformatics into Life Science Education: Roadmap for the Future," was apropos. 50 individuals, largely from universities and liberal arts colleges participated.   

The format was 1.5 days of presentations, a working session, and discussions. The "main event" was preceded with an evening kickoff of dinner nosh and posters [8]. I presented on our Immunobioinformatics work with Shoreline Community College [7].

In the opening session we reviewed the NIBLSE primary objectives, accomplishments and next steps, and agreed on two actions: 1. Write a paper on the conference, and 2. Form committees to explore future options. 

Resources: In Session 1 current resources such as OER (Open Education Resources, like open source but class materials), QUBES, and CourseSource were presented.  We learned that QUBES is development environment whereas CourseSource is a peer reviewed repository. Both are places where individuals contribute and share materials for others to use, but differ in dissemination philosophies.

Barriers: Session 2 focused on addressing barriers. The "barriers" paper [4] was presented.  The presentation led to a discussion about a whether it would be worthwhile to perform a follow on survey or would it be better to talk to folks who self identified in the survey and learn more from them. While surveys have larger reach, they are extremely limited in their discovery potential. That is when people talk, they interact and explore questions more deeply. In some cases invalid assumptions are exposed. Surveys are limited by the questions and biased toward specific thinking.

Expanding the Community: The theme of Session 3 was expanding the community. Participants presented on faculty networks and the QUBES process for developing a classroom ready products from raw materials. This process includes a managing editor, volunteer testers, and takes about eight weeks over which, between four and five one hour meetings are conducted. The eight-week calendar time can be shorter or longer depending on participant availability. Not sure the presentations addressed the theme, but it was interesting to learn about the process.

Assessment: Session 4 got into the difficult topic of assessment. Good assessment is so difficult that we had a Part I and Part II (below). This session was motivated by a possible NIBLSE goal of developing and (or) providing assessments to accompany learning materials. To support this goal, we need to be up on the latest in assessments, so we had an introductory lecture on how to develop high quality assessments. Assessments are harder than they sound as illustrated by the example of the simple weighted problem test. In this example, a test has a 100 points made up of easy (low points) and hard (high points) problems. Bob and Mary both get a 70. Mary answered only hard problems; she was bored by the easy ones and skipped those. Bob's impatient and only answered the easy ones. Are the 70s equivalent? Who learned more? A good assessment needs to distinguish between the scenarios and measure learning.

Assessments part II, in session 5, explored the current state of NIBLSE assessments. Thus far, 150 assessments have been contributed by various instructors. The challenge being is that they are all very specific to topics being covered by their respective bioinformatics exercises and are not generalizable.  Another challenge is bioinformatics is still emerging (some, like myself, might disagree), is technically focused, and subject to rapid changes. A larger challenge, which came up as a common question throughout the meeting was, is the goal of NIBLSE to teach bioinformatics or to integrate bioinformatics into biology teaching? Answering this question will be key to defining, or at least sorting, assessments. Assessments are hard.   

Sustainability: The last presentation orientated session, session 6, explored sustainability with two exemplars. Kathryn Miller, a Washington University emeritus faculty, shared experiences from PULSE (Partnership in Undergraduate Life Science Education), which is an effort to get Vision and Change adopted in universities at the department level. As PULSE approaches the end of grant support, the organization needs to become self sustaining. Dr. Miller shared how the group is developing a fee for service model and is exploring seed funding. The process has been exciting, challenging, and, many times discomforting.

Next, Mary Pat Wenderoth, from the University of Washington, talked about SABER (The Society for the Advancement of Biology Education Research). She shared how much of her early career time was spent going to meetings simply to attend the one or two sessions on educational research (her passion). This led to a realization that a concentrated meeting and association would have more focus and impact.  Dr. Wenderoth then explained the process of developing SABER and how they grew a meeting from just a few individuals to over 450 (last meeting). When asked about challenges, Wenderoth, said the next stage of growth will have the greatest challenges, because they are outgrowing their current meeting venue, which means new costs and choices.  

Next Steps: The last sessions were interactive. In session 7 we formed small groups to brainstorm questions for the next phase. Then, we broke into new groups to discuss those questions and formulate answers.  The groups reported on their work in a discussion format. We closed the meeting with arm twisting volunteers for the next phase. This included organizing a primary writing team to draft a meeting report and forming other committees.

While many questions were raised during the last sessions. Some questions were even answered with potential action plans, but the most important question, as to whether NIBLSE should be about teaching bioinformatics, or whether NIBLSE should be about integrating bioinformatics into life science education, remains open.  

As noted meeting details are in the links below [5,6]

 References / Notes;

1. NIBLSE is supported by the National Science Foundation under Grant Number 1539900, "RCN-UBE: Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE)."

2. QUBES hub - from The QUBES organization was launched in 2014 to address challenges in quantitative biology education and now provides logistical, intellectual, and community support for innovative quantitative biology education projects and the extended community of instructors seeking resources.

3. Bioinformatics core competencies for undergraduate life sciences education, Wilson Sayres MA, Hauser C, Sierk M, Robic S, Rosenwald AG, et al. (2018) Bioinformatics core competencies for undergraduate life sciences education. PLOS ONE 13(6): e0196878.

4. Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction, Williams JJ, Drew JC, Galindo-Gonzalez S, Robic S, Dinsdale E, et al. (2019) Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. PLOS ONE 14(11): e0224288.

5. Meeting summary:

6. Complete meeting notes:

7. Immuno-biotechnology and Bioinformatics in Community Colleges.

8. Posters 10 of 12 or so titles - some were not in the "book"

  • Molecular phylogeny implemented in an introductory plant classification course 
  • Bioinformatics for Biologists: Have a BLAST and beyond! 
  • Faculty Mentoring Networks Facilitate the Infusion of Bioinformatics into a Developmental Biology Course
  • Hemoglobin – connecting DNA sequence to structure and function 
  • Yeti or Not – Do They Exist? 
  • Immuno-biotechnology and bioinformatics in Community Colleges 
  • HITS: A network to create inquiry-based case studies that make high-throughput 
  • approaches and discovery accessible 
  • Gotta Catch ‘Em All - Using Pokémon to Introduce Students to Phylogenetics and Bioinformatics

  • The Genomics Education Alliance (GEA) 
  • Genome Solver: Student Learning in Bioinformatics After Faculty Training 

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