Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE)

October 10, 2019

Hot Shops, Omaha, Nebraska

Third annual conference: Roadmap to the Future


Opening remarks

  • Intent is to have a working meeting and work toward developing a product (meeting paper) and a plan for the future. (Bill Tapprich)
  • History of NIBLSE. (Mark Pauley)
  • Review of NIBLSE primary objectives, accomplishments, and next steps. (Bill Tapprich)
  • Conference overview (Bill Tapprich)


Bioinformatics Resources including OER (QUBES/CourseSource)

Learning Resource Incubators and Collection (Bill Morgan)

  • Goal: Develop collection of learning resources and supporting materials aligned with NIBLSE Core Competencies
  • Quantitative Undergraduate Biology Education & Synthesis (QUBES) project hosts the NIBLSE learning resources collection. Each resource is linked to relevant Core Competencies.
  • Began by searching for existing resources.
  • Worked with CourseSource.
  • Worked with QUBES to develop an online forum for “incubators,” in which bioinformatics instructors could work with each other via NIBLSE on the QUBES network to develop new/refine existing learning resources and supporting materials to expand the learning resources collection.
  • Incubator process: Select learning resource (aligned with at least one of the 9 core competencies), establish incubator goals, assemble incubator team, refine resource via remote collaboration (with coordination/communication facilitated by QUBES), disseminate final products via QUBES platform. From there, selected resources for submission to peer-reviewed publications (e.g., CourseSource).
  • To date, 2 have been published in CourseSource (3rd in process); one resource has been the foundation of a QUBES Faculty Mentoring Network.
  • Invitation to contribute to learning resource collection, participate in an incubator, and/or serving on the Resource Review Commmittee

Panel discussion that includes Michael Sierk, Sabrina Robertson, Anne Rosenwald and Liz Ryder

  • Jason Williams: Working with the NIBLSE incubator proved very helpful in getting Cold Spring Harbor Laboratory’s educational materials in front of many students in a variety of contexts; that feedback has been extremely helpful.
  • Roughly, what is the commitment level for an incubator? Designed to be conducted over the course of 6-8 weeks, meeting for an hour or so every other week. Biweekly meetings helps create accountability.
  • If the resource is taken to the next level with the intent to publish in CourseSource, then additional time is needed.
  • Anne Rosenwald, from experience as editor at CourseSource: Resources coming out of the incubator were in much better shape than typical CourseSource submissions.
  • Time commitment in between meetings varies based on role within the incubator. Approximately 2-3 hours/week when you have a task to complete.
  • Some of the incubators have included students and graduate students.
  • Incubator experience: helpful to have a managing editor, participants learned a lot from the process and editors provided input needed to turn rough materials into a shareable product.
  • Participants can steer the direction of which issues are addressed in the incubator process.
  • Question: Are there any efforts to use the incubator process to focus on a broader effortlike designing a whole course? Or are the resources mostly modular types of products?
  • Currently, resources focus on active learning and are focused on a relatively short learning experience—anywhere from 20 minutes to a few hours.
  • Faculty Mentoring Network might be a way to expand on the work from the incubators and take on a larger project—possibly developing a whole course.
  • Some have developed modules in GitHub classroom—allows students to help keep modules up to date because of editing capabilities on GitHub.
  • QUBES Hub has versioning functionality.
  • Genomics Educational Alliance is also interested in versioning, so people can use a given exercise and will know its stable—at least over the course of the semester.
  • Question: Have you considered working with a university library? QUBES deals with licensing issues (usually Creative Commons); the idea of getting help with curation is a good one.
  • Modules have the advantage of being adaptable to different contexts.
  • Incubator is a process for taking educational ideas and translating them into useful products.
  • Ideas for the future: The “conference tour” idea—going to conferences and focusing on inviting people to submit resources; alternatively, do workshops at conferences based on “incubated” resources.
  • Have not yet incubated any resources for Core Competencies 6 (modeling) and 9 (ethical considerations). Only have one resource on scripting/command line.
  • Question: Who is vetting the quality of the resources? We are doing so assessment of some of the resources.
  • QUBES does a good job of “versioning” the resources to track where it is being used.
  • CourseSource is also a means of vetting resources at the next level.
  • To get buy in nationally, need to prove that the resources work.

Addressing Barriers

Barriers to Bioinformatics Integration (Anne Rosenwald)

  • Barriers paper accepted for publication by PLOS ONE (confirmation this morning)
  • Overview of findings related to barriers from 2016 NIBLSE survey
  • Possible second survey (“Survey 2.0”) to explore findings further
  • Number 1 barrier, faculty training—What next to address issue of faculty training?
  • Number 2 barrier, student issues—How to address lack of student interest? lack of math skills?

Panel Discussion that includes Jason Williams and Mark Pauley and Anne Rosenwald

  • How do we help mitigate the risk of implementation for new faculty so that there is reasonable assurance that they will have some success in implementation?
  • Suggestion: Perhaps instead of a second survey, do qualitative one-on-one interviews with some of the people who responded to the initial survey.
  • Developing products through a customer development interview process—NSF SBIR process
  • Possible NSF RCN supplement proposal
  • How do we handle defining bioinformatics in a small liberal arts institution? The survey included a definition of bioinformatics.
  • How do we get students excited about bioinformatics?
  • What are your thoughts about going beyond a course and planning for a bioinformatics concentration or minor in a liberal arts setting?
  • What do we expect students to know (esp. quantitative skills) and how do we integrate those skills into undergraduate courses to better prepare students for graduate school?
  • If we can show examples of student success, will get more buy-in from deans, department heads, etc.
  • Bioinformatics as a component of “data science”—promoting data science skills more broadly.
  • Many times, bioinformatics is viewed by faculty as a service industry, rather than as an area of study in its own right. Need to change how people value bioinformatics; pitching it as “data science,” may help.
  • Survey responses were faculty perceptions of student interest; would be nice to ask students directly.
  • Does NIBLSE have published resources about what someone with a bioinformatics skillset would do? Not yet. That would be a valuable addition.
  • If faculty make connection to workforce needs, that will help with selling the need for bioinformatics to department heads, deans; also an angle for applying for grants.
  • —bioinformatics companies
  • Brigham Young University—where do students with bioinformatics training go? Computer Science majors get excited about application of computer science to biology/human health. Extend reach beyond “biology” to ensure breadth of students are informed about bioinformatics. Interdisciplinary interest. Bioengineers, computer scientists, biology.
  • How does bioinformatics get someone to med school? One angle to use with students, because many students go into biology with the intent of going to med school.
  • Two things we are talking about: 1) putting bioinformatics into biology courses and 2) bioinformatics as a stand-alone course.
  • NIBLSE survey was distributed to a mailing list of biologists.
  • We need to educate advisors on campuses to help recruit students to bioinformatics.

Expanding the Community

Faculty Mentoring Networks (Adam Kleinschmit)

  • FMN is a model developed by QUBES, happens over the course of the semester. Faculty meet every other week via Zoom. Interact through the QUBES environment, which includes a discussion forum, Google Docs. Helps faculty establish teaching scholarship by organizing products in one place.
  • NIBLSE FMN: diverse cohort of faculty (different levels of experience) to expand/adapt NIBLSE resources for use in their classrooms; also considered assessment.
  • All faculty implementing the same resource, creating a community for sharing ideas/adaptations.
  • Valuable networking and professional development experience.
  • Focus of NIBLSE FMN: “Sequence similarity” resource.
  • FMN participants implemented one or more modules in classroom (variety of courses among participants); published adaptation(s) on QUBES

Panel Discussion that includes Bill Tapprich, Barbara Murdoch, and Jacob Kerby and Adam Kleinschmit

  • Barbara Murdoch: Developmental Biology course
  • Jacob Kerby: Disease ecology course; found FMN to be very helpful; plan to use it in Introductory Biology. Tool is very useful for teaching; well done.
  • Bill Tapprich: Senior-level virology course. Modules are aimed at mid- to lower-level courses. This semester, sophomore level molecular biology course.
  • Typically, FMN identify resource that already exists (e.g., NIBLSE resource) and FMN coalesces around that resource.
  • Power of the FMN is that faculty are teaching in different contexts and on different timelines, and faculty learn from varied experiences.
  • Faculty participants documented pedagogical experiences—what worked, what didn’t work—at the end of the FMN. Teaching notes are included with the modules.
  • Development and implementation happened in parallel, with adaptation happening along the way.
  • Topic identified for each of the biweekly meetings.
  • The resource already has well defined learning objectives.
  • Benefits of FMN—one of the real strengths is emotional support from fellow faculty.
  • QUBES provides fantastic support for facilitating FMNs. Lots of flexibility.


Assessing Success Part I (Rochelle Tractenberg)

The GEA Assessment Evaluation Rubric: current status and next steps

  • Evaluate assessments being used (in GEA for assessing teaching/learning in CUREs).
  • Document and facilitate the coordinated alignment of these assessments.
  • Dimensions of the rubric: 1) General alignment between assessment and learning goal, and between teaching and assessment (and with external goals, e.g., NIBLSE Core Competencies, Vision and Change); 2) Utility—whether assessment results help make decisions about learning (sufficient?) and teaching (effective?); 3) Complexity—sophistication of cognitive processes required by the learner to answer the questions/complete the assessment; 4) Clarity—refers to instructions to students, as well as interpretability of the assessment summary (test score, pass/fail label, etc.).
  • Questions:

Who will do the assessment evaluation?

  • Will this evaluation be part of (required for?) GEA stamp of approval? Or part of tagging (required to get materials IN)?
  • Do those who provide/withhold the GEA stamp of approval get some kind of qualification badge? (professional development opportunity)
  • How do you get broader community to buy into GEA’s assessment of the assessments?
  • Who will be incentivized and trusted to assess faculty’s assessments and help faculty improve their assessments?

Assessing Success Part II

Assessment Workshop (Neal Grandgenett and Jennifer Drew)

  • Reliability: consistency of repeated assessments
  • Validity: how well assessment measuers what it’s intended to measure
  • Core competencies anchor work of Assessment Validation Committee
  • Developed tips for validating assessments in emerging STEM fields

Panel discussion that includes Liz Dinsdale and Adam Kleinschmit and Neal and Jennifer

  • Would be helpful to have more examples, even if they are context specific.
  • In educational literature, transfer from one context to another is known to be a real challenge.

Sustainability Exemplar I

PULSE Network (Kathryn Miller)

  • Partnership for Undergraduate Life Sciences Education (PULSE)
  • Ambassadors program
  • Regional networks
  • Recognition program—rubric/peer review process about how departments are progressing in efforts to align with Vision & Change; rubrics available on PULSE website
  • PULSE website
  • Grants to fund program development and pilots; grants at different institutions, needed governmental structure to keep initiatives going as a group, not just individual projects
  • Incorporated as an educational nonprofit 501c3
  • Communities of practice have been particularly well received
  • Trying to transition from grant funding to a fee-for-service model to get enough money to pay for logistical support for the fellows
  • To date, has been volunteer-based efforts, with very limited staff support
  • Oversight of dispersed community involved in delivery of programs
  • “Sociocracy” --- form of government informed by Quaker principles, but adapted for use in business; dynamic governance designed to allow all voices to be heard
  • Processes that encourage equal participation
  • Ideas for funding: charging membership fees, either for individuals or departments, is one possible way to bring in income

Sustainability Exemplar II

SABER Network (Mary Pat Wenderoth)

  • Society for the Advancement of Biology Education Research (SABER)
  • Evidenced-based teaching (rather than “active learning) is more palatable for many faculty
  • Society with membership dues and meeting registration fees; fees reduced for faculty from community colleges
  • Keys to success: Common goal; low cost of meeting (location provided at no cost through University of MN); location of meeting (centrally located); core group of people
  • 2017 Created a steering committee, wrote bylaws, created subcommittees, elected officers
  • HHMI Summer Institute
  • National Case Studies
  • Growing pains: diversity and inclusion?
  • Have regional meeting, SABER West
  • Social media: use it to get the word out
  • Had ASCBE-LSE journal as outlet for publications
  • Bill: UNO Library has established open-access fund
  • Mentor ladder, training new members of the network to conduct workshops
  • NIBLSE could hold a national meeting
  • SABER’s current membership fee is $50

Paper Manuscript: Any volunteers?

  • CBE meeting report
    • Eric Triplett (University of Florida)
    • Jason Williams (Cold Spring Harbor Laboratories)
    • Inimary Toby (University of Dallas)
    • Liz Ryder (Worcester Polytechnic Institute)
    • Guoqing Lu (UNO)
  • Eric will arrange first Zoom meeting

Small Group Sustainability Idea Generation Workshop

  1. What is the focus and scope of NIBLSE going forward?
    • Should we be limited to bioinformatics? or expand to “data science”—data acumen, data literacy?
    • Which of the original four objectives do we still need to address? What components of original objectives are unfinished and need work?
    • What new components have developed as we’ve moved forward that still need attention —e.g., how do we go forward with Core Competencies, Barriers, Bioinformatics master rubric?
  2. What are the next steps for securing funding/resources?
    • What parts of examples (PULSE, SABER) would fit NIBLSE?
    • What committees might be needed moving forward? (e.g., focus on funding)
    • How do we ensure sustainability—regarding resources and organization?
  3. Who do we need to partner with in the short, medium, and long term?
    • Industry partners, professional societies, national meetings, international colleagues (e.g., GOBLET)? Bioethicists? Legal scholars?
    • What would it take to develop a national meeting for NIBLSE? What are the future directions in the field that could generate new directions for NIBLSE? Or should we take advantage of an infrastructure (or infrastructure) that is (are) already there — International Society of Computational Biology?
  4. How do we address faculty barriers?
    • What professional development strategies can we develop to address top barrier related to faculty training?          
    • Clearinghouse of faculty training opportunities?
  5. How do we address student barriers?
    • How do we get students more interested in bioinformatics?
    • Biology-wide or life-science-wide survey of students? How can we evaluate students’ interest in and exposure to bioinformatics to address student barriers?
  6. How do we build community and broaden participation and inclusion?
    • Is there a big project/resource that could be used to help build community? (Great Florida Spitting Contest)
    • Should we expand use of one of our resources more broadly?
    • How do we increase communication/develop our communication networks to share what NIBLSE has done/is doing? (social media presence, other communication strategies)
  7. What’s the next direction for NIBLSE and assessment?
    • Test bank?
    • Broad assessment