Lisa Haye, CUNY John Jay College (Economics, B.S.)
The 2023 VR-REU commenced at the Framers Bowling Lounge as a Memorial Day icebreaker, where we all introduced ourselves to one another, as well as to Professor Wole’s research team. The following day, we convened at Hunter College where we were introduced to some of the program mentors, and I began reviewing the work of my 2022 predecessor to think about how I could either expand or pivot last year’s work towards a new direction. Professor Wole also began his lecture on VR, AR, and MR, and we were introduced to the history of the field, as well as its applications across various disciplines.
I met with both Professor Wole, and my research mentor, Professor Courtney Cogburn, to discuss the potential framework of my project. I began exploring both Unity Terrain and potential city and house asset packages in the Unity Asset Store, as these applications will be key to constructing my visualization models for the project. I also began looking at publications centered around both structural racism and how the issue has been visualized in the past.
We ended this week with Professor Wole introducing us to Paraview, a scientific visualization program, for our self-paced lab session. I submitted my project proposal, and began to draft a schedule towards curating a literature review of my topic, as well as experimenting with Unity Terrain.
This week, Professor Wole taught us the preliminary tenets of writing a scientific research paper and introduced us to Overleaf to compose our writing. Professor Wole also held VR lectures on immersive visual and interactive displays, along with 3D geometry.
Meanwhile, this week my time was split between conducting a literature review to create a bibliography, finding databases that correlate with the data visualization aspect of this project, and familiarizing myself with Unity with a test model of different functions that are key to my 3D models. I identified three potential data points for my models (housing valuation, climate, and the access to green space), as well as two neighborhoods within the Bronx to serve as case studies to highlight disparities based on that data. Professor Wole also introduced me to MapBox for Unity, a location data and maps platform that could be integrated into Unity for precise map development; I am considering using a mixture of MapBox and Unity Terrain as my methodology for the project moving forward.
The week ended with all of us attending the CUNY SciCom’s “Communicating Your Science” Symposium at CUNY’s Advanced Science Research Center, where we listened to various CUNY graduate students talk about their research with general and peer audience presentations. It was exciting listening to disciplines such as mathematics to biology to physics come together to talk about their work in a way that was fun, educational, and most importantly, accessible to audiences who may not be familiar with concepts such as the sonification of star rotations , DNA G-Quadruplexes, and properties of shapes!
Here is a screenshot of my test model on Unity from earlier this week:
This week, Professor Wole gave lectures on immersion, presence, and reality, as well as 3D tracking, scanning, and animation. We all had an engaging conversation on the uncanny valley, the theory that humans experience revulsion as they observe a character that is close to human characteristics, but are slightly off in appearance. Professor Wole’s scientific visualization lab this week centered on Visual Molecular Dynamics (VMD), a molecular 3D visualization program.
Here is a screenshot of the ubiquitin protein molecule, visualized in CPK style and color set to ResID. I am not too sure what those acronyms mean, but I am interested in finding out:
As for my project, I was split between creating a first draft for the abstract, introduction, and related works sections and experimenting with MapBox. I think my methodology is going to shift towards a more MapBox-intensive procedure, with creating custom map styles on MapBox Studio, and then deploying it to Unity3D. Thus, I spent a lot of time getting a crash course on MapBox’s functions; I created a demo map of Riverdale, one of the Bronx neighborhoods featured in my project, to get a taste of how these models would look like in Unity. I actually ran into quite a few errors, most importantly, my map object did not play in game mode and it does not appear in the hierarchy unless I manually move it there, and I wonder if modeling the map will be easier with the 2017 version of Unity (the version most compatible with current MapBox software). Nonetheless, I hope to work these errors out with Professor Wole soon. Meanwhile, here is my demo model of a Bronx neighborhood:
Next week, I hope to begin the formal construction of my models!
Roadblock, roadblock, roadblock – my computer refused to open a project with Unity’s 2017 editor so I couldn’t test if that resolved the problems, my maps continued to refuse to display unless I manually enabled their preview separately, they could not be represented together side by side, and it was difficult to display them properly in the game scene, and I honestly became dejected. I began considering whether or not my project had to pivot back to manually visualizing data with Unity Terrain and assets from the Asset store, and Professor Wole’s PhD student, Kwame Agyemang, and I tried to find any 3D models of New York City that could be imported in Unity, in case a pivot was necessary. Nonetheless, I compiled data from Zillow and the New York City Environment and Health Data Portal to be used for housing valuation, climate, and greenspace data; the former was extracted using a Google Chrome extension called Zillow Data Explorer, and then opened as a Google Sheet, and the latter was manually compiled into a Google Sheets on my drive.
My breakthrough occurred just on Friday, when Professor Wole hosted our midterm presentations for our status updates; after disclosing my setback, a fellow REU student revealed they actually had prior experience using Mapbox! Thanks to Richard Yeung, the problem was resolved – if Mapbox is being used with a recent version of Unity (in this case, I am using Unity Editor version 2021.3.19f1), you must download ‘AR Foundation [current version is 4.2.8]’ and ‘AR Core XR [4.2.8]’ from the Unity Package Manager, and when importing Mapbox SDK into Unity, do not import ‘Google AR Core’, ‘Mapbox AR’, and ‘Unity AR Interface’. With that, I was able to have my map display properly and my use of Mapbox for this project can now continue. It was very nice seeing how everyone’s projects are coming together, and my talk with Professor Wole helped me consider how I will fulfill my research question while also considering Professor Cogburn’s reminder to consider my audience when thinking about representing data effectively. Because of this week’s setback, I am a bit pressed for time in terms of creating my models and writing my methodology for my paper, so this weekend requires me to make up for lost time; nonetheless, as I create my models, I am going to consider how I want to construct a user study for this project.
Obstacles are bound to happen in research, but it is important to keep your mind open to change in projects, and to ask your network and your network’s network for help, you never know who can help until you do. Here is a test model for my two Bronx neighborhoods actually displaying side by side!
With the resolution of my Mapbox problems, I spent this week really honing in on the details of my models, both in terms of what data was being visualized and how I want to represent the information on Unity. My housing valuation model, which I originally presumed would be my easiest model to complete, took some thinking as I considered how I wanted to represent redlining and what data point I would be expressing; I decided to focus on highlighting a sample of property values of single-family homes currently on sale as of June 2023 that are above the median value for the Bronx ($442,754, according to Zillow) and condominiums in both neighborhoods. I am still experimenting with how the climate model could be visually represented, and greenspace is going to highlight the environment of both neighborhoods.
I spent some time working on the methodology section of my paper, and lessons this week included Professor Wole’s lecture on interactive 3D graphics, as well as an introduction to Tableau for our lab work. Professor Wole generously took the REU participants on a cruise from Pier 61 for lunch, and we all ate food and chatted on the water as we sailed by downtown Manhattan, Brooklyn, and the Statue of Liberty.
Next week, I hope to complete my models and finish up my writing for the methodology. I haven’t worked on the details for the user study of my project, so I hope to speak to my mentors regarding its structure.
This week, I was able to complete a model for housing valuation, climate, and the environment, but I could not find a way to visualize climate and the environment in a 3D format so the research is solely going to focus on visualizing housing valuation. Professor Wole, Professor Cogburn, and I discussed the various potential dimensions and codes that could be used to visualize the existing data in different ways, and now that I’m scrapping climate and the environment, I will be focusing on as many ways to visualize housing valuation as I can, while reframing my paper, and reframing the script for my user study. Future work could consider visualizing various forms of structural racism either separately or concurrently within various neighborhoods.
With what I’ve learned technically through visualizing the housing valuation data, portions of the current model I have will translate into the various models I have to create, such as a baseline model to be used as a comparison, as well as a color dimension of the redlined versus non-redlined community. I also have to consider focusing solely on representing single-family homes or condominiums in my target neighborhood; finding literature on either type of housing structure will guide my visualization selection. Here is a screenshot of my experimenting with various design choices for the housing valuation model as of late:
This week I’ve spent the majority of my time working on as many housing valuation models as I can, and talked with my mentors about what questions are going to be relevant towards answering our research question in the user study. I struggled a bit with organizing my time this week, but having conversations with Professor Wole and Professor Cogburn helped ground my expectations and steer my project to the final leg of the marathon.
The cohort returned to CUNY’s Advanced Research Center (ASRC) for the IlluminationSpace tour, where we all interacted with models and systems related to the core science fields that ASRC specializes in (nanoscience, structural biology, environmental science, photonics, and neuroscience), and it was a really fun way to expose us to the objectives of these fields and how they overlap with one another. Sabrina took advantage of our touring of ASRC’s facilities by having us demo the application she created for the REU, and Sabrina sat us down to listen to her experiences with academia; I admired her openness, especially since many of her comments on academia resonate with my own experiences.
Professor Wole also managed to host three program officers from the National Science Foundation’s Graduate Research Fellowship Program to come speak to us about the program’s purpose, its eligibility requirements, and opened the floor for questions. Professor Wole made it clear throughout the program that part of his objectives for the REU is to encourage us to consider graduate school, and introducing us to a fellowship dedicated to funding our graduate studies and research interests (which could potentially be a barrier for students who are considered low-income, and therefore may make them skeptical towards going to graduate school) was really honorable of him to do.
We ended the week with Professor Wole talking to us about the importance of statistical analysis in research, and he gave us a crash course on ANOVA. With the symposium next Thursday, I have a lot of work ahead of me, and I’m excited to see what everyone has accomplished!
The final week began with me finally (finally) completing my user study on Google Forms; users were given context to structural racism and redlining, the procedure, and then users had the option of giving their demographic information anonymously before they were exposed to two questions regarding seventeen versions of my models. Users were tasked with answering two questions to measure their perceptions of the models, and the final section asked users to rank their preferences in terms of structural racism visualization. As of today, I have received 29 responses, so for a survey that has been live for three days, that’s pretty good! I will most likely keep my survey live closer to the deadline of one of the conferences I am applying to in August, just in case I can squeeze in more data for the poster. I also met the cohort for dinner downtown, which was a nice break from working on papers and data analysis.
Professor Wole connected with Iowa State University’s SPIRE-EIT 2023 program this week, and we met with SPIRE-EIT’s PI, Professor Stephen Gilbert, and his students and learned about the three projects they are working on, which was really cool to learn about. I also met with Professor Wole to discuss how to statistically analyze my data, and to also discuss a rather interesting comment I received in the feedback section of my survey; the comment reminded me of the kind of controversy of a project like mine elicits, but also just the nature of research in general – criticism will occur, but I plan to address that comment in my discussions. Professor Wole helped me take in the criticism by talking about his own teacher evaluation experiences, which made me feel a lot better. On Thursday, our own VR-REU symposium was hosted at Hunter, and several of the mentors, loved ones, and the SPIRE-EIT program appeared virtually to listen to our work! Below is the title slide for my presentation, and here is a link to my slides: VR-REU 2023 Symposium
This program has been such a tremendous experience to be a part of and so a series of thanks are in order: I want to thank each of the REU participants I met for giving me camaraderie, knowledge, and overall just a fun experience, I think they were an amazing set of people to be grouped with. I want to thank Kwame and Richard Yeung for helping me when my project hit roadblocks, and I want to thank my loved ones for supporting this journey by pushing me to apply to this program, listening to me talk about Unity, roadblocks, and random facts about Riverdale and Soundview, as well as sending out and completing my survey. I want to thank Professor Cogburn for her mentorship and guidance, especially as a Black woman in academia, and most importantly, I want to thank Professor Wole; he was an amazing PI, an insightful professor, and a great mentor, and I want to thank him for giving me a great introduction to research, academia, and for overall taking a shot on an economics major like me.
After today, I’ll still be working on my paper and poster, and whether I get published or not, I am grateful for the valuable tools this program has given me, and I know my work towards research is only getting started.
Olubusayo Oluwagbamila, Rutgers University New Brunswick
Program mentor: Oyewole Oyekoya, Ph.D.
Project mentor: Olorunseun Ogunwobi, M.D Ph.D.
Week 1: June 6 – June 10
This week, I met with Dr. Ogunwobi, studied his work, and drafted my research proposal. I read papers discussing the presence of single-nucleotide polymorphisms (SNPs) on the 8q24 chromosome, the encoding of six miRNAs on the PVT1 loci, as well as the underexpression of miRNA-1205 in prostate cancer. We decided that my role in this project will be to visualize his research findings, and, along with Dr. Oyekoya, concluded that only certain datasets can be visualized on VMD and Paraview.
On Friday, I physically attended the CUNYSciCom Symposium at the CUNY Graduate Center. There, I watched CUNY grad students make two presentations on their research: one for scientists and the other for non-scientists. I was especially intrigued by how most of the presenters were able to simplify their work for audiences from non-scientific backgrounds, without watering it down. They employed analogies to form some connection with their audience, and linked that connection with their research. This method will come in handy for me, so I took some (mental) notes down. I also watched tutorials on Paraview and VMD, and made attempts at visualizing substances on them.
My goal for next week is to collect data from Dr. Ogunwobi and figure out which datasets can be visualized with my tools. In the meantime, I will continue learning visualization on VMD and Paraview.
Week 2: June 13 – June 17
On Monday, I sat in on Dr. Ogunwobi’s weekly lab meeting at the Belfer Research Building. I listened to a few of his undergraduate and graduate students present their progress on the project they were working on. Following that, I was introduced to Fayola, program coordinator at the Hunter College Center for Cancer Health Disparities Research (CCHDR). She was hospitable, giving me a tour of the floor and showing me the different labs and lab equipment used in their research.
The data I needed was under the care of one of Dr. Ogunwobi’s Ph.D. students who had recently graduated, and there had to be some coordination between her and the current lab students. Because of that I was unable to access any data this week. I did however keep working on VMD and learned some cool tricks. Using the lipase 2w22 as a model, I practiced generating a Protein Structure File (PSF) from a Protein Data Bank (PDB) file. I also learnt how to add mutations to a protein, as well as modifying graphical representations of a protein by coloring or drawing method.
During the week, I virtually attended some interesting VR-related presentations. One was a seminar on the Role of Self-Administered VR for On-Demand Chronic Pain Treatment, and the other was a dissertation defense of a Ph.D. nursing candidate. Both presentations contained research on the effects of VR usage on pain, and both research findings demonstrated the positive physical and emotional results VR usage had on patients. This brought to mind the increasing technological advances happening globally, how much the world has changed over the years, and how much the world will change years from now. I find that fascinating, but also ominous. Maybe I watched too many Black Mirror episodes.
My goals for next week are to collect the data from Dr. Ogunwobi’s lab, continue learning VMD, and study other microRNA visualization projects.
Week 3: June 20 – June 24
This week, I got access to the data needed for this project. There were a lot of files available (over 6,000!), so I spent a good amount of time sifting through the data and figuring out which ones would be needed for my project. I was able to select files with compatible file types, but I did face some difficulties. I was unable to open these files on either VMD or Paraview, and only got an error message when I tried. My guess is that the problem lies either with the files I have, or with my knowledge of VMD/Paraview. Next week, I will test both hypotheses by going back to the lab to further examine these files, while also watching more tutorials on VMD and PAraview.
I also got to work on myresearch paper this week – I currently have my background/introduction, bibliography and a portion of my methods section complete. I faced some challenges transferring this to the template on Overleaf, and so another goal for next week would be to watch turotials on using Overleaf.
Week 4: June 27 – July 1
This week, I spoke to Dr. Wole about the issues I had last week, and he siggested I find similar files from public databases. From the Protein Data Bank, I was able to find four proteins (or their look-alikes) associated with my project: Aurora Kinase A, FRYL, Human Neuron-Specific Enolase-2 and Notch Homolog 2 N-Terminal-Like Protein A & B. I visualized them on VMD, mutated them, and compared the mutated structures with the original. I was hoping to be able to visualize microRNA-1205, or at least the locus PVT1 on chromosome 8p24. Unfortunately, because these molecules are non-protein, and because the Proetin Data Bank only contains information about proteins, I could not visualize them. I searched the web for other open-source databases, or other visualization software. I found a Nucleic Acid Database by Rutgers University (shoutout) and an RNA visualization software called RNA Artist. I could not find any MicroRNA file on the NAD. I tried downloading other files (RNA, DNA) from the NAD and opening them up with RNA Artist, but I kept getting error messages. Next week, I will look more into this.
Since this week marked the end of the first half of this program, I and my peers each made our mid-term presentations on Friday. I had fun putting my PowerPoint slides togather and breaking down the context of my project. Dr. Ogunwobi and I are the only ones in the entire program from Biology/Genetics background, so I enjoyed the challenge of explaining gene expression to Computer Science, Engineering and Art professionals. I also found other projects my peers are working on interesting, and I loved how much progress we all have made on our individual projects. I am looking forward to making more strides in the second half of this program.
Week 5: July 4 – July 8
The beginning of this week was a holiday week, so I spent the first couple of days exploring the city. I also spent some time exploring the Nucelic Acid Database and RNA Artist software. Unfortunately, I couldn’t find anything that would be useful for my project, at least not in the next four weeks. They do seem to be interesting visualization tools, however, so I will keep in mind for future projects. This week, I also got a chance to use some VMD extensions. I used the movie maker extension to make both a single-frame movie and a trajectory movie. I did some more digging, and I found a paper that talked about using other VMD extensions for RNA visualization, such as the NetworkVIew extension/plug in. I hope to explore this next week.
Week 6: July 11 – July 15
This week, I checked out the NetworkView extension and, unfortunately, it doesn’t have the features I would have liked for my project. Asides from that, I made more VMD videos using different graphic representations. Here’s a close-up video of the Aurora Kinase A protein, and another one of its mutant. I liked this representation because it shows the missing bonds and molecules in the mutant structure. Also, it’s a visually appealing representation, which would be really interesting to view in VR.
Week 7: July 18 – Jluy 22
This week, I worked on visualizing the other proteins associated with my project, similar to the videos I made on Aurora Kinase A. So far, I am done with the visualization aspect of my project, and the next step is to convert these into VR compatible formats.
Week 8: July 25 – July 29
This was the final stretch of the program. In this week, I concluded my project my refining the visuals I had created and checking out the VR experience. Due to the techincal obscurity of VMD, I was unable to directly export my visuals with the VMD VR extension. I was, however, able to work around this and display my visuals through Google Carboard headsets. While this format was less immersive than I had hoped, it did involve virtual reality. I also completed my research paper and submitted it for publication. On the last day of the progrram, I had the opportunity to present my work spanning all eight weeks of the program. Here are some 2D-versions of the 3D visuals I presented:
My project had its challenges, but it was overall a fulfilling introduction to 3D biological visualization. I am grateful to Dr. Wole for organizaing and enabling this project, and my mentor, Dr. Ogunwobi, for trusting me with his work. VMD appears to be a very useful software with numerous applications. I hope to further explore it independently over the next four weeks.