Do you have a lab full of undergrads this summer? How can you maximize the efficient use of time for these lab newbies? In this post Dr. Lisa Ryno mixes humor with practical advice for making the most of those summer moments in the undergraduate research lab.
You have graded your last exams, entered final grades, and cleared your desk of all the pedagogy-related detritus that accumulates during the semester. As a professor at a research-intensive primarily undergraduate institution, you are more than ready to shift gears and dive into summer research. Whether you have returning students who (should) know what to do during the inevitable downtime between experiments or a bunch of overly eager bright-eyed newcomers, you can put in a few hours of preparatory work ahead of your students’ arrival that will be worth its weight in gold once the July doldrums arrive.
“What should I do now?”
This question can raise the hackles and cause unnecessary anxiety for any PI mentoring undergraduates in their laboratory. I have even felt like I have gone through the five stages of death and dying upon hearing an innocent student proclaim they are without a task:
Pretend you didn’t understand the student and start up the ancient junky centrifuge, gurgling high vacuum or sonicator to discourage further discussion.
Deliberately stomp around and create messes in the lab for the student to clean up. Power move (admittedly, learned from my toddler): make eye contact while creating the mess.
(With your deity of choice or the universe) “If you just give me one day where I don’t have to answer this question, I promise I’ll volunteer to be on that committee.” You know the one.
Stare into the void until the student sheepishly backs away.
Ask the student “Well, what do you think you should do now?” while giving them a coy look that suggests they should certainly know what to do, even though you don’t have the faintest idea of what they should be doing. Nine times out of ten they will figure out your game, and, if they are kind, play along.
How to encourage student independence in the research lab
While I am, of course, only (mostly) kidding about these responses, I have discovered a few ways to make students happily productive over the summer, while requiring a minimal time commitment from the prepared PI. One point I chose not to cover in this article is the pairing of students in lab on projects. I think this is an excellent technique that often results in strong lab camaraderie and useful interactions among a group of students learning to problem solve without the direct assistance of their PI. I chose not to cover student pairing because, while it is helpful during the times when students are working towards experimental design, collecting and analyzing data, I found that if students are in the midst of an experimental lull, having students in pairs simply means you now have two students who are looking for something to do.
1. Create a repository of key articles and protocols for your laboratory
I believe in beginning with the most obvious ideas. You likely have a collection of articles that are critical reading for any student that is working in your laboratory. I found keeping the electronic versions of these articles in a centralized location in the cloud by using something like DropBox or Google Drive has been incredibly helpful. I can easily give students access to the folders, which I organize by project. I also encourage them to add new papers they find to folders for future students.
Additionally, I have a living document of protocols commonly used in my laboratory that students can access via the cloud. Upon joining my lab, students receive a binder with a printed version of the protocols that they will use immediately, which I ask them to familiarize themselves with before beginning any experiments. I have charged students with adding new protocols (with literature citations) to the living document to maintain an up-to-date catalog of our protocols.
“You likely have a collection of articles that are critical reading for any student that is working in your laboratory. I found keeping the electronic versions of these articles in a centralized location …has been incredibly helpful.”
I believe it is worth mentioning here that it is a valuable investment to teach your research students how to read primary literature and review articles. This endeavor does initially take time and effort on your part, and, while I have yet to make one for my lab, I can see the value in creating a brief guide for new students to follow. If you are really crunched for time, you can point your students to the AAAS website, which has an article compiling the methods by which several real scientists read scientific manuscripts (https://www.sciencemag.org/careers/2016/03/how-seriously-read-scientific-paper).
2. Utilize your institution’s librarians
Send your students to the library to explore their projects independent of your direct guidance. They can use review articles you have curated for your lab (see point #1 above) as a springboard to learn more about topics and techniques that they need to be familiar with to grasp a full understanding of their project. If available, use your institution’s librarians to help students (especially first- or second-year students that have less library research experience) learn to use scientific search engines (SciFinder vs. PubMed vs. Web of Science, etc.), as well as browse the library’s catalog for information pertinent to their project.
3. Incorporate brief, new literature discussions into your weekly group meetings
As a way to encourage my research students to read the scientific literature regularly, I dedicate about 15 minutes of a 90-minute weekly group meeting to discuss exciting scientific articles/advancements that have occurred in the last week. The topics need not be directly related to our group’s projects, but instead are of great interest to the student. They can be sourced from popular science websites (e.g., https://www.sciencenews.org/, https://www.sciencedaily.com/, https://www.popsci.com/), twitter feeds (e.g., @nprscience, @NASA, @LiveScience), perspectives from top scientific journals (e.g., Nature, Science), or through the students’ other social media feeds, but I request that the students go beyond the initial social media-level discourse to find and skim the primary literature source. This activity promotes the participation of the whole lab at every group meeting, and I found that both students and I enjoy this ritual by the end of the summer. I have had the most success beginning lab meetings with these discussions, which helps open up the group to talking and, in the case of meetings that include coffee or snacks, allows the group to settle in before the more formal presentations begin.
4. Encourage students to learn molecular modeling, docking and coding
Allow me to preface this section by mentioning that I am by no means well versed in computer science. In graduate school, I took an excellent structural biology class that had a module which focused on the computational docking of small molecules to proteins, taught by Prof. Arthur Olson and his research group (http://mgl.scripps.edu/), which developed the AutoDock software suite. Fast forwarding a bit, during my first year on the tenure-track I welcomed a bright student into my lab who was interested in the intersection of biochemistry and computer science. I had a project idea, the docking of a library of small molecules onto a chaperone protein using AutoDock Vina, that I was waiting for the right student to tackle. Armed with the instructions and notes from my graduate school class, the student began to work towards the goal, first learning the software, then designing sophisticated analyses of our large data sets, which we published in a peer-reviewed journal. There are many types of ligand docking software, but I found the graphical user interface of AutoDock Tools was particularly useful; the software instructions on the website (http://autodock.scripps.edu/) and technical support from the Olson lab were also critical to the success of the project.
The type of computational support you need for your projects can vary widely depending on your area of study and interests. Luckily, there are a host of freeware programs to choose from…
The type of computational support you need for your projects can vary widely depending on your area of study and interests. Luckily, there are a host of freeware programs to choose from for molecular modeling, and wiki pages and tutorials abound. UCSF Chimera (https://www.cgl.ucsf.edu/chimera/) and Avogadro (https://avogadro.cc/) are my favorites for small molecules; we use PyMol (https://pymol.org, the full version is paid, but the educational version is free) and Swiss-Model (https://swissmodel.expasy.org/) for studying proteins. While it is useful for students to spend time familiarizing themselves with the software you choose to use for your analyses, it is also critical for them to have a clear goal in mind so they can direct their understanding of the software towards something useful. For example, you could have your student explore the various homologs of a protein you are studying by examining differences in their three-dimensional structure using Swiss-Model (to model the primary amino acid sequence of a homolog onto a known crystal structure) and PyMol.
You can encourage your students to prepare an outline for their oral presentation or a pen-and-paper sketched outline of their poster.
Knowledge of database navigation and interrogation and writing of scripts is also an excellent skill set for students to build early. Many programs used in computational chemistry and biology, including AutoDock, mentioned above, use Python programming language. The website Codecademy (www.codecademy.com) has free tutorials to get anyone interested in learning Python or other programming languages.
5. Develop a list of laboratory duties that students can do at any time
This idea is, again, a natural and hopefully obvious solution to student downtime in between experiment preparation, execution, and analysis. Maintaining a list of typical lab duties with detailed instructions provides new students autonomy when otherwise they might feel without an immediate purpose or direction. Tasks like refilling pipet tip boxes, washing and properly storing glassware, preparing buffers, autoclaving essential lab items and maintaining consumables and reagent stocks not only help keep your lab organized and clean, but they help students assimilate ownership of the lab and feel like they are working towards the “greater good.”
6. Encourage students to hone their presentation skills by preparing posters or brief oral presentations.
One of my primary goals in training any undergraduate in my laboratory is to prepare them to communicate their research. Weekly group meetings, larger multi-group journal clubs, and formal presentations in front of all research groups in our department all provide public speaking and communication practice. Students have the opportunity to work on oral, PowerPoint-based presentations as well as constructing an end-of-the-summer poster to hang out in the hallway and present in the fall during our campus’ undergraduate research symposium. Having templates and examples of high-quality presentations and posters allows students to work independently and form the narrative of their project in their own words. You can encourage your students to prepare an outline for their oral presentation or a pen-and-paper sketched outline of their poster. You can help your students create presentation-quality versions of their data through an iterative revision process—a task that can pay dividends when you are ready to write up your results into a manuscript. Will you need to help guide them through this process? Of course! Some students will have more familiarity with preparing oral and poster presentations than others, but there is always an opportunity for students to learn the basics of what makes a presentation or a poster both informative and aesthetically pleasing.
Maintaining a list of typical lab duties with detailed instructions provides new students autonomy when otherwise they might feel without an immediate purpose or direction.
I hope these six ideas help you and your students combat the inevitable lulls during the summer and beyond, and lead to productivity and harmony in your laboratory.
Lisa M. Ryno, Ph.D. is an Assistant Professor of Chemistry and Biochemistry at Oberlin College in Ohio. Dr. Ryno’s work with undergraduates utilizes techniques in molecular biology, microbiology, and biochemistry and focuseson exploring new methods to mitigate antibiotic resistance.