As a new faculty member at a PUI, the switch from a rigid and packed academic year schedule to the completely unstructured summer schedule can be daunting and challenging. I ended up being very productive this summer, possibly too productive at the expense of not giving myself enough time to recharge. I wanted to reflect on my summer to identify what worked and what could be improved with the hope that my thoughts may be useful to other new faculty.

My First Summer in a Nutshell

I defined seven goals for the summer and accomplished all of them. I describe these accomplishments below.

1. Wrote and Submitted My First Grant Proposal

I entered the summer with a one-page summary of my objectives (similar to the specific aims page of an NIH proposal). By the end of June, I had a complete first draft of my project description. In July, I wrote my RUI impact statement, revised my project description, and produced the other associated pieces (e.g., the budget, a description of the facilities, list of collaborators). The final proposal was submitted to NSF on August 6.

2. Wrote and Submitted a Manuscript to a Journal

During the academic year, I applied my inversion detection method on additional data sets. I began to draft a paper in Winter. The paper proved to be challenging to write and I ultimately had iterative through multiple narratives until I found the “one” that worked. I completed the manuscript in early August, posted it as a pre-print on BioRxiv, and submitted it to a journal.

3. Mentored Two Students

I mentored two students for the summer. Krystal was a BioMolecular Engineering major who did research with me during her last quarter. Despite graduating in May, Krystal continued working with me over the summer. Krystal finished her comparison of inversion detection methods and presented a poster at AGS and IEEE COMPSAC. For the last-half of summer, Krystal implemented a variant-calling pipeline for Anopheles data from my collaborator.

Matt finished his first-year as a Computer Science major. My goal for Matt was to expand his horizons and introduce him to bioinformatics and population genetics. Matt attended AGS and then spent June implementing a population genetics simulator to study the impact of effects such as mutation, recombination, and repression of recombination on nucleotide diversity and PCA of SNPs. Matt presented his work as a poster at IEEE COMPSAC.

4. Attended AGS with My Students

The Arthropod Genomics Symposium is one of my favorite conferences. AGS attracts the same folks year after year, is small enough (150-200 people) to get to know everyone, is frequently held in the Midwest (reducing travel costs), and provides opportunities to learn biology.

This year, I brought Krystal and Matt. We flew to Kansas City, MO, rented a car, and drove to Manhattan, KS. Krystal had opportunities to present her work as a poster, explore options for graduate school, and learn about potential staff bioinformatics positions. Matt was exposed to biology and research. In both cases, students were exposed to research and the academic world beyond our small, engineering-focused university.

5. Grew and Nurtured a Collaboration

Last October, I started collaborating with a colleague at the Medical College of Wisconsin. I reached out after citing one of her papers. She has been nice enough to share her time with me. Over the summer, I performed some statistical analyses for her and she co-mentored Krystal. By working together, we began to better understand each others’ work and identify projects of mutual interest. Since starting her M.S. in Bioinformatics, Krystal effectively became my collaborator’s student; Krystal’s work on the variant-calling pipeline laid a foundation for a potential M.S. thesis project.

6. Updated My Materials for the Data Science class

As I described in an earlier blog post, I was constantly operating under recurring deadlines my first year. Most of my materials were minimal and essentially “placeholders.” I spent the month of August substantially updating my materials for the Data Science class. I significantly edited and expanded existing lectures and labs, created new lectures, tutorials, and labs, and updated the materials to a new textbook. This work will pay off significantly in the Fall when I teach the class for the second time.

7. Identified a Research Topic for the Academic Year

At the end of the summer, I identified a research problem that dovetails with my collaborator’s work on enhancer maps for Anopheles genomes. Over the next academic year, I’ll work with a new MSOE student to explore the problem and prior work. My goal for next summer is to be able to write either a grant proposal or paper.

Lessons Learned

By reflecting on my summer, I identified several factors that helped me.

1. Optimizing the types of efforts for the academic year and summer

The summer provides big blocks of time for focused work. The academic year provides smaller blocks of time that are interspaced with classes and other responsibilities. I would describe research time during the summer as “highly concentrated”, while the available research time during the academic year is “lowly concentrated” and spread out. One of my main challenges is to identify which times of year are best suited for each part of the research process (e.g., background reading, planning, experiments, and writing).

In retrospect, I realized my summer accomplishments were seeded by efforts during the academic year. For my grant proposal, I spent the academic year reading background literature, thinking about potential research problems, and working on my one-page specific aims document. For my paper, I did most of the data analysis and thinking about the narrative during the academic year. In both cases, the most productive writing was done entirely during the summer.

The same pattern applies to Matt’s project: I spent the academic year reading about modeling and simulation for population genetics and writing prototypes. When it came time to mentor Matt, I was able to guide him in his own effort in a step-by-step fashion because I already had a detailed plan laid out.

I think part of this is that certain parts of the research process can’t be rushed. Background reading, project planning, and experiments are not necessarily sped up by having larger chunks of time as long as I have enough time to make consistent progress. After reading a paper or executing an experiment, I need a few days to think deeply about how to interpret the information and understand the implications. In that situation, additional work hours generate diminishing returns.

In contrast, I find that writing productively requires keeping large chunks of contextual information in my head. The dense schedule of research time during summer, which requires less multi-tasking, is well-suited for writing.

2. Organizing My Work

  1. I limited my goals to what I could complete. The summer will go quickly. At first I thought I wouldn’t know how to fill / use that time productivity. But then I quickly found that I didn’t have enough time. If I spread myself too thin, I wouldn’t be able to finish anything. I limited the number of goals to what I can finish.
  2. I chose “big” goals which needed time and attention I couldn’t provide during the academic year.
  3. I prioritized one or two goals over the rest. These are what I “needed” to accomplish; everything else is what I “wanted” to accomplish. In this case, I needed to submit my grant proposal.
  4. I staggered the timelines for my goals. Trying to make progress on 5 fronts at once wasn’t conducive to getting anything done. Instead, I focused on two goals at a time.
  5. I tracked my work. I used a Trello board with a list for each week. I used colored cards for each day. Every day that I worked on something, I added a card for the appropriate goal. At the end of each week, each month, and the summer, I could review how my time was spent and use it to improve my time organization.

3. Working Productively

  1. I limited other distractions (commitments, meetings, etc.). The academic year has a rigid schedule with a lot of context switching. Summer was my time to focus on one thing at a time (less mult-tasking!). To avoid losing productivity, I consistently worked to reduce and weed out distractions. I made an effort to say “no” where I could and limit the number of meetings and commitments in any given week. This was hard to do, however, and required continuous effort and re-assessment.
  2. I found my most productive time and guarded it. I was more productive in the morning than in the afternoon. If I had a meeting in the morning, I struggled to focus and be productive later in the day. Likewise, I found that I needed large blocks of time. Therefore, I reserved mornings for focused work and scheduled meetings for the afternoons.
  3. I found my most productive environment. I find it difficult to concentrate and focus in my office. I’m able to focus more easily when working at a local coffee shop or in my living room. I used this to my advantage by avoiding campus over the summer.
  4. I started a local grant writing group. Through one of my colleagues, I met several other faculty who were also working to submit grants and do summer research. Through regular meetings, this group provided support as well as practical feedback and advice that helped me achieve my goals.

4. Taking Care of Myself

  1. I built and relied on a support network. Outside of the grant writing group, I had several friends and colleagues I turned to when I needed to vent. I found that helped me substantially this summer, especially when I was feeling overwhelmed, intimidated, or stressed out by writing my first grant proposal.
  2. I kept up with my self care. I kept a regular schedule with my personal trainer. Exercise has been and continues to be an important part of my mental health; workouts do as much for my mental health as they do my physical health. I could have done a better job of getting out on my bike (that fell by the wayside) and spending time with friends.
  3. I (should have) scheduled a vacation or two. I took a few days off during the summer (e.g., a trip to a local botanical garden) but nothing that counted as real vacation. My wife and I did technically schedule a long weekend vacation over Labor Day but had to cancel it. In retrospect, I should have made more time for downtime.


My summer was very productive. I can’t complain about the outcome: I accomplished every goal I set. I am particularly proud about (and grateful for) submitting my first grant proposal. With the proposal completed and submitted, I now have a better sense of what a proposal entails and feel confident that I can write more. Overcoming that hurdle along with developing the skills and knowledge for writing grant proposals will pay off significant dividends over the rest of my career.

Growing my relationship with my collaborator will also pay off. My hope is that the collaboration will be long-term, providing opportunities and benefits on all sides.

As I prepare to start classes on Monday, I am grateful for the time I spent improving my materials for the Data Science class. I feel the class is planned to the point that I have very little to do. In contrast, I am spending a lot of time remembering the content for the Introduction to Software Engineering course. Over the quarter, I will need to re-organize and polishing my materials.

I find two resources particularly helpful this summer. The book How to Write a Lot by Paul J. Silvia is short but packed with great advice on how to be productive. Secondly, my Ph.D. advisor Scott Emrich emailed me a handy overview of approaches for organizing writing time that he’s observed in academia.

All of that said, my summer was very intense. I was very stressed through large chunks of the summer. And this did affect those around me.

Next year, I want to be a little less ambitious and enjoy more of my summer time. I want to do a better job of riding my bike consistently, taking my dogs to the dog park, and enjoy a vacation or two with my spouse.