Eilbeck Lab

It has been a while since I last updated – but this time, it has been a combination of teaching load, COVID, budget season, grant writing, white coats for black lives, and teetering on the verge of burnout. DBMI has been working at home since March. In BMI we have all become adept at zoom – even having our weekly coffee break virtually. We have taught, collaborated, and attended conferences virtually. We have all worked hard these last few months. It has been a work-life without a lot of punctuation. The days all merge together, the kids are at home and we are always in zoom calls. I could go on about the impact of this on women in particular, but that would be a long post.  I will mention that summer camp was canceled and we eagerly await news from the school district about the fall. Here are some updates from the blur that has been the last 4 months:

Education:

• In March, a week into our 9-week intensive med school Host and Defense course, Paloma Cariello and I had to switch to online teaching because the campus closed due to COVID-19. Needless to say, we were disappointed not to be able to connect in person with our students. But we learned a lot about how to manage 125 students online. Our students were resilient and were very forgiving of the little things. I am grateful to the students who called into my office ours and buoyed my spirits. I am grateful to the faculty who did their best under the circumstances to provide the best education possible. Most of our faculty are involved in infectious disease, so the pandemic took a lot of their time. Our support staff did a great job of getting the material on YouTube. After the course ended – this photo ended up in my inbox. This means so much to me. This is why I teach.

• In DBMI, my Foundations of Bioinformatics course is going to be offered with an upper-level undergraduate option. This is quite exciting.

• We held a 2-hour virtual retreat on Education for DBMI. This is part of our continual improvement. We looked at the following issues –
  • Academic Progress
  • Behavior and Emotional Issues
  • Mentoring Norms

We held breakout sessions, sending people to zoom rooms to discuss the different cases we had developed. It was a really successful experience.

Grants:

• Simon Fisher and I submitted a renewal T32 proposal for Computational approaches to Diabetes and Metabolism Research to the NIDDK.  I am so grateful to Bridgit Todd Hughes for keeping us on target during the lockdown.
• We put a proposal together for the AMA’s  Accelerating Change in Medical Education Innovation Grant Program, titled:  Better than Broccoli: Turning health system science education into a fun and healthy treat. This grant has been accepted and now the hard work begins. Damian Borbolla in BMI and I worked with Sara Lamb (Med School Curriculum). Health System Science contains a clinical informatics component for med students. This is a great way for our department to integrate more with our medical students throughout all four years. Damian and I are joint core educators in the med school bringing informatics expertise.

Research:

We have been conducting community-based studios where we focus on the delivery of NBS results. It has been a humbling experience to meet so many parents and listen to their shared experiences. This is part of the requirements gathering for a project we have with the Utah Department of Health.  The results are fascinating and I am certain we can improve the overall experience and workflow. My colleague Mike Conway is helping with the analysis and the team that leads the discussion is from the CCTS. Many thanks to Brieanne for her professionalism.

 

Service:

Since I became interim chair I had to step back from some of my service, but I had the opportunity to co-lead a GA4GH working group on Genome Annotation and I have accepted with enthusiasm. Genome annotation is close to my heart and this group will help with the requirements and the API that link together variant representation and variant annotation as well as groups that perform expression analysis. The Co-lead is Sean Upchurch. Watch this space.

Conferences:

• My favorite conference of all time was postponed before COVID. The AMIA Educators Forum did not happen this year, and Anne Turner is leading the efforts to brainstorm how to bring it back. I miss this conference. I miss the workshops the most. One of the themes has been that the organizers bring in educators from the city that hosts the conference and there is a wonderful exchange of ideas. So that didn’t happen.

• Then I was signed up for IPHIE Master class in Seattle. That didn’t happen either.

• Bill Hersh and his team did manage to turn the NLM training conference into an online extravaganza. Three days of talks with me glued to the screen, reading the comments, and the tweets while listening to the students. It was the most intense multitasking I have ever done. Our students did a great job and the T15 cohort just shines.

Upcoming papers:

A collaborative paper detailing the sequence features of bacterial gene regulation has been accepted. The Sequence Ontology has updated terms related to these features and we look forward to seeing the paper in print. More about this when it goes public.

Full-text papers available:

• Watkins M, Eilbeck K. FHIR Lab Reports: using SMART on FHIR and CDS Hooks to

increase the clinical utility of pharmacogenomic laboratory test results. AMIA

Jt Summits Transl Sci Proc. 2020 May 30;2020:683-692. PMID: 32477691; PMCID:

PMC7233102.

• Watkins M, Rynearson S, Henrie A, Eilbeck K. Implementing the VMC

Specification to Reduce Ambiguity in Genomic Variant Representation. AMIA Annu

Symp Proc. 2020 Mar 4;2019:1226-1235. PMID: 32308920; PMCID: PMC7153148.

Students:

Andrew Miller has completed his MS degree and presented his capstone in June. We will miss him.

New intake – we have a bumper crop of Ph.D. and MS students starting in the fall and I am excited to have them all get started.