Office of Undergraduate Research

• Students defending theses/graduating this year are mainly working on video coding (of animal behavior), survey analysis, data analysis and writing. We have team zoom meetings focused on related projects to facilitate support and discussion on related research topics- trying to keep the zoom meetings to under 10 people instead of our typical larger lab meetings, at least for now while everyone adjusts. We have always had a shared online lab document to track project progress, some students have created sub-pages to further outline the progress of their individual projects and to keep everyone on the same page.
• Other student RAs are assisting with ongoing projects, helping with video coding, data analysis and literature searches. Basically focusing on all aspects of work that can be done remotely. Students have been encouraged to share experiences and help one another within our group team meetings and also across teams to provide extra support to each other during this time, this has facilitated new peer mentoring opportunities that seem to be working well. This is in addition to feedback from me and postdocs/grad students who also attend the meetings and help set up peer-peer connections.  We have taken on some new students this term, so working through training them online via zoom.
• We have had some discussions about data we may still be able to collect via other means (e.g. zoom, online surveys), and also what we might learn about human-animal relationships and animal welfare during this time that would not be relevant/possible to study at other times. Students have been excited to think about this and have generally been positive and resilient about adjusting to new approaches to participating in research efforts during this time.

This term I have 1 URSA and 2 other undergraduate students working in my lab. My lab is focused on bioinformatics analysis and building databases for plant pathways in silico.  Fortunately, I had one month to directly work with the students and was able to introduce them to tools and protocols we use for collecting information and analyzing genomic data. The students now work remotely and I review their work weekly and have one-to-one meetings with them every week.

Student 1 

• Project: Diets of trout and salamander in a stream network
• Working remotely: Data analysis and writing; google docs and google spreadsheets (Zoom meetings and email correspondence to check progress – weekly or biweekly based on need)

Student 2

• Project: Symmetry of Chinook Salmon otoliths under different rearing conditions
• Working remotely: Data imaging using a dissecting scope (at the student’s home); image processing using MS Excel and R (Zoom meetings and email correspondence to check progress – daily, weekly or biweekly based on need)

Student 3

• Project: Extracting size information of salamander and fish using digital photography
• Working remotely: Image processing using ImageJ; data storage in google spreadsheets (email correspondence to check progress – biweekly)

Student 4

• Project: Literature review of prey-consumer relationships on aquatic invertebrates and fish
• Working remotely: Instructions were provided using Kaltura; data storage using google spreadsheets in a shared drive (email correspondence to check progress – weekly)

• One student: doing a literature review on sifaka species' conservation status and population threats.
• One student: designing a research proposal for a masters' level project, but on her same critter (barn owl) of interest.
• One student: doing fieldwork, but she's voice-recording her sightings of diurnal raptors over various field types as she walks on her 2-mile dog walk path. 
• One student: designing a masters' level research proposal to test potential efficacy of various cover crops in reducing vole damage (either under vines or hazelnuts - still a work in progress).

• REU undergraduate student from the University of Wisconsin
• Project involved:
  • collecting archived data from various sources (National Oceanic and Atmospheric Administration, US Geological Survey, Center for Coastal Margin Observation and Prediction.  Data included a long (>10 year) time series of temperature and salinity in the Columbia River estuary as well as other variables that impact temperature in the estuary (e.g., river discharge, air temperature, temperature and salinity of the adjacent ocean).
  • Learning and performing time series and statistical analyses on the data to understand how temperature varies on different time scales (inter-annual, seasonal, weather-band, tidal) as well as correlation analyses between temperature and other ‘forcing’ variables.
  • The undergraduate is a physics major.  This project provided an opportunity to learn and apply programming skills (with Matlab) and statistical analysis methods and apply them to data with environmental and ecological relevance.
  • As part of the CEOAS REU program (led by Kaplan Yalcin), the student wrote a brief research plan and gave a brief oral (remote) presentation on this plan.  In addition, the student wrote a project report and gave a seminar (remote) to my research lab.
• Interaction with the student mainly involved:
  • Weekly remote meetings and science related seminars set up as part of the REU program by Kaplan Yalcin
  • Weekly (or twice per week) remote meetings with me to discuss the research project, processing and analysis methods, and related underlying science (e.g., estuarine physics).
  • Every other week remote meetings with the combined labs of myself and Melanie Fewings (CEOAS) that includes four graduate students and one post-doc.  Discussions during the meetings often centered on the research of members, but also included discussions on how we are all coping and managing life and work during the pandemic, etc.

Summer student working from U. Puerto Rico (Physics) in the CEOAS REU program led by Kaplan Yalcin.  What was supposed to be a summer field experiment instead became a remote-work numerical modeling project on nearshore ocean hydrodynamics, which turned out very well.  See J. Lerczak's notes on the CEOAS REU remote program, whose structure helped a lot.

• Project involved model simulations of surf zone rip currents, including analysis of their hydrodynamics and comparison to remote sensing field data.  The student will present his results at AGU (American Geophysical Union meeting) this Fall.
• It was helpful that the numerical model had been mostly set up in advance.  Otherwise, having to troubleshoot model setup and technical issues might have been time-consuming, without the ability to bounce questions off myself and grad students in person.  We just set a boundary where the student's role was to interpret the hydrodynamics, not to edit Fortran code.
• Remote connectivity: The REU student ran simulations on our local servers by logging in through ssh/Putty, then downloaded (ftp) the outputs for Matlab analysis on his home computer.  This worked OK.  Other students in my group have converged on a combination of sshfs in Linux/Mac for accessing files, and MobaXTerm for working directly on OSU machines.  sshfs in particular can make it seem almost like you are working in the office.
• Interactions with the student:
  • 1-1 check-ins via Zoom MWF, with e-mail contact in between.  We initially created a Slack channel, but the student seemed to prefer quick e-mails.  This worked fine.
  • We read one key paper per week together, convening on Mondays to discuss the previous paper and choose the next one.
  • Bi-weekly lab group meetings with my grad students.  In these meetings one person leads a discussion each week on a topic related to their work.  The student seemed to get a lot out of this and felt part of the group.
  • Reused several recorded Zoom class lectures from Spring term, to help fill in some theoretical knowledge.

• Only 1 student is hoping to continue URSA research, doing genome analysis online in relation to a GWAS in the lab…..Henson Tran.  Project specifics still TBA. 
• The others will wait until summer or fall or beyond (including one STEM Leader)
• All of us are meeting every other week via Zoom for discussions/lectures on the general topic of CRISPR in plants and related biotech

We have 1 URSA student working to “fill gaps” in Wikipedia about women in STEM. Please, have students edit Wikipedia - articles need improving. Have them take their topic and make a list of articles in Wikipedia that relate to their topic. Then  identify the weaknesses in those articles and fix/add. If you have questions, please contact me, I’m happy to help. [email protected]

I am currently working with three students on various projects. I meet with each student at least once a week over Zoom and also had each of them make a Trello board so I could monitor their progress throughout the week. Their projects are as follows:

• Student 1: Assisting me in writing a paper on some research we had done the past year. We share a Google doc and make modifications together as we discuss the content.
• Student 2: He is writing a script our lab can use and I am using Zoom’s “remote control” feature to work with him on the project. It has worked out great so far.
• Student 3: He is helping us analyze data that we have generated. Most of the data analysis is either done in Excel or R so he shares his screen and we discuss the results

We are taking advantage of this time to analyze and organize data, write down protocols and catch up with the literature. The students are compiling all of their results in a PowerPoint document to present later on, analyzing all of the data they have put together, making figures with that data, and reading assigned papers. They are also writing down their protocols and uploading everything into our Box Lab shared folder. We have lab meeting and individual meetings once a week, and one of the students presents a paper of their choice related to their project during the lab meeting. Four of them are taking advantage of this time to write whatever they can for their honors thesis.

The lab has several students who are doing remote projects for URSA this spring. The students meet with project supervisors over zoom weekly and are encouraged to attend weekly lab meetings on zoom. 

• Student 1: Assessment of mussel cover at sites in OR and CA. Visual analysis of photos collected during the summer at each site. 
• Student 2: Helping a Postdoc in the lab coordinate a marine disease response network (PRIMED). In charge of organizing membership information and keeping the website and live map of collaborators up to date.
• Student 3: Working on data entry for her URSA project during Spring term. Once entered, will put the project on hold until next Fall when she can finish sample processing in the lab. Her project is on whether there is a relationship between larval mussel settlement and turfy algae. 
• Student 4: Working on data entry for samples already processed for his project; will be transitioning to remote photo analysis once entry is complete. Photos are complementary to biomass sample processing in the lab and involve similar skills, including functional group/species ID.

My students do computational research, so it’s pretty easy to work online.  We meet using Zoom and  students either ssh into my group computers or just run simulations on their own computer.