Exploring CellWalk - Tim Davison

0:00My PhD was kind of about like bringing these cellular environments to life. And it was like using these virtual reality headsets, like HTC Vive, and like painting these cellular scenes, like David Goodsell was creating. So we created like the spatial environment, more like you're inside of a VR headset, and you can actually do David's paintings. And then you press a button and it comes to life. Hi, you're listening to What the Tech, a podcast powered by the computer science department of UCalgary and CJSW 90.9 FM broadcasting in Calgary, Alberta. We're here to deconstruct complex computer science concepts bit by bit and explain what the tech is going on. In today's episode, we chat with Tim Davison about his path into computer science and biology, his experience with spatial computing and real-time simulation, and the story and inspiration behind the cell walk app. Hello listeners, and welcome back to What the Tech. My name is Anisha, and I'm here with my co-host, Harim.

1:02Today we have the pleasure of chatting with Tim Davison, who is a University of Calgary alumni. Tim has experience and background in spatial computing, real-time simulation, AI, app development, and computer graphics. Welcome Tim, we are so excited to chat with you. Yeah, thank you for having me on the show. It's a pleasure to be here and nice to meet you. Yeah, awesome. So for our first question, how's it going? And is this a busy time of year for you? It's always busy, but I found that the recent busyness comes in the lead up to fall in September, because that's kind of Apple's development cycle. All the new operating systems come out in September, so you've got to be ready for that. So it's actually pretty chill now. OK, that's good. You have time to enjoy fall. Yeah, absolutely. All right, so you're an alumni of UFC, and you have your PhD in computer graphics and both a bachelor's and master's in computer science.

2:05Can you outline your academic journey for us? What made you choose computer science in the first place? Yeah, I learned to program when I was a kid. So I was always really into computers and programming, but I wanted to be a physicist and make a warp drive and go to other planets and stars. So I was actually going to do a physics degree in university. And I was still programming at the time, too. So I also had a signed up for computer science. And computer science was just so much fun. I love working on the assignments and just everything about it, learning things you don't learn when you're just doing programming like all the theory. So yeah, I second semester, I dropped my physics courses and just focused on computer science. So that was kind of like what got me into programming and computer science specifically. But I was also attracted to the game design program at UFC. I thought that was pretty cool. It was like, I love games. I love trying to program my own games, that kind of thing.

3:06So that was a distinctive thing about UFC over other schools at the time was that they had this program. So yeah. That's very cool. I did not know that we had that program. Oh, I don't know if it's still running, but yeah, back then we had a game design program. That's awesome. Would you say you're a gamer? Or are you just more interested in the game design aspect? Well, computer science ruined games for me. Because you know, it's like Wizard of Oz and you see behind the curtain, right? You see how everything works. And it's like when I see a really cool video game, that's really beautiful. I'm just like breaking down the graphics. So the magic is gone. But I love playing like Dota with my friends, like that kind of stuff, real-time strategy, yeah. Nice. Awesome. I am a gamer, but I am lucky enough that I'm not in computer science, so it hasn't been ruined for me yet. Awesome. Now, the elephant in the room, and you kind of already touched on Apple and hinted towards that. But your platform for immersive biology education,

4:08Cellwalk was a finalist in this year's Apple Design Awards. Many congratulations on that. Do you want to start by explaining to our listeners what exactly Cellwalk is? Yeah, OK, so Cellwalk helps users or students or learners learn biology by replacing static textbooks and learning resources with interactive and immersive spatial experiences. So it's kind of a really cool moment with what we've done with Cellwalk. So when Google Earth first came out, he had this view of the entire planet. And when it first came out, everyone was just looking at the planet and then trying to find where they live. And then zoom in, zoom in, zoom in, all the way down to street level. And that was a big deal. We take it for granted now. We can just go wherever we want. I don't think I could go anywhere without Google anymore. But back then, that was a big thing. But now, with Cellwalk and the technology we developed, we can do the same thing for biology. So it's a Google Earth moment for biology.

5:10You can have this cell floating in front of you. And you can zoom in and zoom in all the way down to the individual atoms of DNA. So it's bringing biology to life. That's what Cellwalk is. And I think that's going to be pretty special for education. It's like, if we lived in the Harry Potter universe and magic was real, then how would Harry Potter learn about biology? You probably won't be reading this static textbook or doing YouTube videos. This cell would appear in front of him, right? And he'd explore it. Proteins would come to life and the space around him. And he would explore their structure that way. But now he can do that. Was spatial computing technology and the technology we developed in Cellwalk? We can do that Harry Potter moment. We can do magic and bring biology to life. Yeah, no, that's awesome. I love the analogy between the Harry Potter and the actual app because who wouldn't want to learn like that, right? Yeah. So you mentioned that you were a programmer with no biology background.

6:12And it was a whole new world and a new thing to discover. What were the biggest challenges you faced in that transition from computer science into biology and biomedical visualization? And how did you overcome them? Yeah, I could answer this maybe with a story. So what even started that was I was starting my PhD, finished my master's and was starting my PhD and that was with Christian actually. And we were working on the Lindsey virtual human project, this 3D anatomy and human physiology database and app. So naturally that's biology. But then Christian let me a copy of this really cool book it's called The Machinery of Life by David Goodsell. And I'm like, whatever, it's just like another textbook. And then I put off checking it out. But then eventually a couple of days later, I actually opened this up and I was like flipping through and I'm like, what is this thing? It was this book and it's filled with these beautiful watercolor illustrations that David created by hand. And it was nothing like the biology textbook,

7:14which is like a cell is this like blob and it has some blobs inside. And like somewhere there's proteins. What is a protein? I have no idea. Where does DNA has these little string things, right? But like you look at a David Goodsell painting and the cell is just like dense and packed with molecules, proteins, DNA fibers and RNA, right? Like all of that is super dense, right? Like I did all that biology in high school and like did AP biology and it's like, I had no idea, right? So it really opened up my mind to what biology was. And I was like, I need to make this like an app. It needs to be like something real. I need to bring it to life and that became my PhD. So that was the start of the path to biology and to actually like gain all of that biology experience is like just like how I learn programming is like I want to do something. So just pick it up as you go, like read a lot of stuff, read a lot of papers, read a lot of books, especially like journal articles and that kind of thing and get into the protein data bank, learn about like

8:16all the protein structures. Yeah, so that was kind of the experience. Yeah, that's really cool. Thank you for sharing that. And you did mention the book, The Machinery of Life and how you drew inspiration from the watercolor illustrations of cellular interiors. How has this artistic inspiration that you apart from other app designers? Yeah, so I think David's illustrations and his paintings are unique in that they convey like real scientific data. It's like actually a state of the art best picture that we have of what biology actually looks like at this level. But at the same time, they're also really beautiful. His work inspired me to learn about biology and study biology. And that's also kind of become my mission is to inspire the next generation of biologists. So how does this tie back to app development? Creating that beautiful aesthetic showing biology, how beautiful it is, the biology itself

9:16can just do all the work for you, right? I do like some color. I try and make it like beautiful, do some graphic design, but at the center of everything is biology. That's kind of what sets us apart from other apps. It's like we're doing real scientific data, real visualization is like the same type of visualization tools and technology that the biologists themselves use. But like now we can bring that into the classroom and that's gonna inspire students the way that David's book inspired me. That's awesome. Yeah, and I love how you use that connection between art and science to build something so amazing. And this was a really big project for you. So how did it feel to see how the different stages of your academic journey and life led you to this project and this big moment? Yeah, that is actually a really big transition going from academia into industry and especially to become like an entrepreneur and build a startup like we're doing. It's a total shift. And I think it's really exciting

10:18because in academia, you have a lot of freedom. You can work on just like this really interesting problem. You can go really deep and there's a lot of support for doing that. But then like once you do it, who is your audience? You're in a really small niche, usually, especially like if you're doing something like a PhD, it's like you just become an expert in this tiny little like drop in the ocean and then there's all these other like experts, right? There are all these other little drops in the ocean. So the reach is important. That's like how science moves forward but you don't have like a big impact. So that's why I want to build a startup around this and reach a big audience. And you know, that experience I had with David's book do that for biology students, right? Because like was the future isn't textbooks anymore, right? Like already like classrooms are using YouTube and other online resources and there's still textbooks, right? But we have these incredibly powerful computers

11:19in our hands like the iPhones and the iPads and they're not being like utilized. Like what do we use them for? We like browse the internet, social media, reading email, sending text messages but like these things have really powerful processors you can play games on them. But man, what is it going to do for education if we could really bring the tools that scientists are using onto our phones, bring it into students' hands and into the classrooms? Yeah, that's a transition from academia to industry. Yeah, that's amazing. And as a bio major myself, it's really exciting to me to hear about this project. And I'm excited for future generations to learn science in a more interactive and exciting way. Like just thinking about myself and going back to like first year courses and just looking at these pictures. And yeah, you get the YouTube video here and there. But when you think of like even computer science, you guys are coding. I feel like you're doing something

12:20that is like applicable right away or you think of medicine and they're practicing doing sutures or things like that. You want something interactive to keep you engaged in the subject that you love. So I feel like this is a really awesome way to do that. So I'm super excited by it. Yeah, absolutely. Like in biology, like maybe there's like lab work and that kind of thing, like what lab stuff? But that is like still really abstract. Like you're doing experiments and then interpreting things, but like you don't get to really see it. And that's like what computer science can do. It can bring it to life. Yeah, exactly. You don't see the mechanisms of the protein. You just, you do the lab. And then next week there's bacteria cultures that have grown under your peachy dish. But what does that mean? How does that happen? So yeah, that's super awesome. So you know, you talked about wanting to inspire the next wave of biologists with cell lock. How important do you think it is to have something like a digital education platform such as cell walk for subjects like life sciences,

13:22like biology? Yeah, absolutely. Talked about it a little bit, but textbooks and even YouTube videos, they're fundamentally like static, right? They don't change, like they're just there. And especially for textbooks, I think the power of a textbook is how much resources and effort goes into creating like even a single chapter, like super thoroughly researched that chapter evolves over like decades, right? Updated with new information, but still fundamentally static. And when do new additions come out? Like every two, maybe five years, that kind of thing. So it's not up to date with the latest. And just by its nature, it's static. And you have to do like beautiful illustrations to kind of explain the science, but like imagine if it could come to life. And those figures were actually interactive. I think that's super promising. And we can do it now, right? Like we have the computer hardware,

14:23it's capable of it, like even an iPhone that we're carrying around, battery powered device, especially like the Vision Pro and spatial computing. Now we can actually bring these things into your space, like it's amazing. So yeah, that's the power of building a platform for biology education. Yeah, one thing that you brought up was textbooks. They update every two to five years with an app or a platform like this. Would you say it's more able to be updated like almost instantly, like as new research is coming out, as we're having new findings? Yeah, absolutely, that's the goal. Because new proteins are published to the protein data bank like every day. And there's new scientific discoveries being made every day. So that's where we're moving towards. So it'd be really amazing if there's like a new article published in, like, Nature. And I don't know, bring those results into cell lock. So kind of what I'm excited to do is bring some of the scientific discoveries

15:24of the last couple of years into cell lock. And yeah. Yeah, that's awesome. And I can see this being a more fun way to conduct literature review as well for research. New articles are being published, and you can see how these new proteins that are coming about are actually working in real time. Yeah, absolutely. Yeah. One of my favorite ones is that flagellar motor complex, like Ecoli and bacteria have, yeah, might be working on something. That's awesome. Have you had people use a platform so far? And if you have what feedback have you gotten from the people that have used the platform? Yeah. So like last year, I actually conducted a couple of weeks of interviews. So I just like, my own social media is like, hey, help me out. I want to interview a bunch of people who've used cell lock. And I wasn't expecting to really get that many back, but I ended up with like a totally full schedule and I was just like doing these for a couple of weeks.

16:24And it was really interesting to talk to the users. I was kind of struck by the diversity of them. There were a few students. There was even a computer science student, but there were a lot of adult learners who were just like interested in this and biology. And I had no idea that this is actually what a cell looks like. I thought it was just that blob with blobs inside of it, right? So that was really cool. And another experience was at WWDC, the World Wide Development Conference, Apple's annual thing where they invite developers from around the world and show off their new technology and give them up to speed on that new technology. I went there and I got to meet like lots of other developers and it was so weird like talking to them. I was like, what do you do? And it's like, oh yeah, I make this like weather app or whatever and it's like, what do you do Tim? And it's like, I make this biology app and I like pull out my phone. It's like, oh, I know cell lock, right? I'm like, that's cool, right? We're reaching a big audience is not just biology students.

17:26We're kind of doing a science communication mission and everyone is trying out cell walk and learning biology and seeing it in a new way. So that's really motivating. It gives me a lot of energy to do what I do. Yeah, that's amazing. That's actually really cool to go to these places and be like, wow, so what I'm doing is really, it's making an impact and it's getting out there and people know about it. That's awesome. Yeah, that's the best feeling. Being a developer, like building this thing like on your laptop and then actually finding out someone's using it, feels so good. That's so cool. And how big is your support team? Because I know you were working with Dr. Christian Jacobs with on this and this is your PhD project. Is there anyone else that's kind of supporting you as you work on this project? Yeah, my PhD was kind of about bringing these cellular environments to life and it was like using these virtual reality headsets, the HTC Vive and like painting these cellular scenes,

18:28like David Goodsell was creating. So we created the spatial environment more like you're inside of a VR headset and you can actually do David's paintings and then you press a button and it comes to life. So that was my PhD. But then I finished it and pandemic started. David Goodsell's lab, Arthur Olson's lab actually invited me to scripts just before pandemic started. So I was there for two weeks and that kind of kicked off the next phase of everything. I was kind of like figuring out why I wanted to do. I knew I wanted to make cellwalk. I didn't know it was going to be called cellwalk. And so I went down to San Diego, work with them, start building like a relationship with them and you know meeting your heroes is amazing, right? And I got everything started and then from there it was about how can we reach a big audience, right? Because the VR headsets still kind of niche but how can we like reach a lot of students in particular? So I was like, I want to build like an iPad app

19:30and an iPhone app. How do we do that? How can we kind of create those experiences that David has inside of his books? How can we bring that to life? And it's like actually that was a really difficult technical challenge because he has some of his illustrations or of like almost an entire cell like an E. coli cell. So like how do you have like hundreds of thousands of individual proteins and then visualize it on an iPhone like in fully 3D? Like we don't have an E. coli model yet. But they were working on some cool models like they have an HIV model and a single protein inside of there has atomic detail, the DNA or rather the RNA is like fully modeled inside of it. It's super highly detailed but like again, how do you put that on an iPhone? And they were also working on another model which was a microplasma bacteria. So actually an entire cell. And this one has something like off the top of my head I think is about 40,000 proteins or thereabouts

20:31but it's about 300 million atoms give or take once you fully visualize this. And again, like how do you like put that on an iPhone? So actually that became my mission over those next couple of years, almost like five years was to develop visualization technology where we could visualize entire cells with hundreds of millions of atoms and now billions of atoms. We have some like neurons now and it's like billions of atoms. It's amazing. How do you do that on an iPhone in real time and make it totally seamless and continuous level of detail? So yeah, some major technology and research development made that happen. And then the support team I work with scripts research they're like one of my collaborators. They support the science, especially for the microplasma model that we have in the app. And then I have a co-founder and anonymous co-founder but he's joining me full time. And yeah, people want to help. Like you start building something

21:31and people just, I will help you. It's awesome. Yeah, well, especially like such a great project like this. And so, you know, if you look at this like E. coli cell and there's so many parts to it, how do you put that on an iPhone? How do you transform that, right? Were there any other difficult ideas or difficult engineering problems that you had to solve? And what were kind of any specific approaches that you took or tools that you use or maybe support that you got from your team and that helped you to solve these problems or start to solve these problems as you work through? So yeah, scripts again, they like helped with the biology. David wrote one of the stories inside of it but kind of developing the visualization technology for cell walk. I felt kind of like another PhD and that was just me in the middle of the pandemic reading tons of papers and just coming up with this new algorithm and way of doing this continuous level of detail thing. So like the way it works is you can look at an entire cell

22:32and we don't need to draw like a billion atoms when we're doing that. We can actually draw a lot less than a billion atoms if we reduce how much detail the individual proteins have but then when you get closer you can add more and more detail. And if you do it finally enough, you can't even tell that there's this transition from like this kind of like blobby protein in the distance to once it's up close, you can see every single atom inside of there. So that was fun to build. Yeah, that is really cool. So we're gonna switch gears here a little bit and talk about your role as a TA. I wanna know what your experience was like transitioning from being a student to a more professional role because I've heard stories where you're TAing for students that you were classmates with in the year prior. So what's that transition kind of like? Hmm, so it was good first lecture I gave, maybe like a little bit stressed, like really had to prepare because I had some really great TA's

23:32and I want to like match kind of enthusiasm that they had and like how they were inspiring me. So I put a lot of work into those first courses but when I was in undergrad I knew programming before I came into computer science. So a lot of my friends were also taking computer science and they were like struggling. So I was helping them out a lot and doing a lot of just like tutoring. So it was kind of a natural transition. Yeah. So you kind of had that experience being a teacher before you got into the TA role already? Yeah, it was fun, yeah, it's a lot of fun. That's awesome. So adding on to that, you worked with Dr. Christian Jacob as you mentioned before to develop an iOS programming course at UFC. What was that like with once being a student to now having a say in creating a course that you could have taken if it was around during your undergrad? Yeah, that was really cool. So yeah, at the time I was really into iOS programming. Like it was part of the Lindsay project. We were all like Apple platform.

24:32So back then it was like objective C. It was just like, oh my gosh, I get to like teach people about objective C and like cocoa programming or app kit and UI kit at the time. Yeah, so it was just a lot of fun. Christian, he's like a really inspiring teacher and he has a lot of experience and he has kind of a different approach to teaching. I remember taking his classes before the iOS programming class and I was, he would give some lectures but kind of his unique thing is he would invite students to give a lot of presentations and that's what we ended up doing in the class. It was like, we gave a lot of lectures but the students were also giving lectures on topics and I think that's kind of a pretty cool way to teach these courses. And that's how you get students involved because they're teaching other students and the best way to learn is when you have to teach it. Yeah, definitely for sure. It's funny because on our episode with Christian, he mentioned the exact same thing.

25:32Teaching is the best way to learn. So that's very cool. So do you think it's important for students to have a say in the process of course development and do you have any ideas of what that would look like? Yeah, absolutely. So they were a part of it because they were giving lectures. So that just kind of happened organically. I think that format just like works. And as for what courses to develop or where to take that next, I think well like AI, right? Like so agent-based programming for like creative minds, something like that, right? Take the iOS programming formula and do the same sort of thing and just like get students making apps that use LLM connect to chat GPT or like open AI or anthropic or Google APIs and you know, just start building the next generation of apps. And it's kind of like the perfect format for it because like this stuff is changing weekly now major discoveries

26:34or major advancements are being announced like every month. There's like no way you can keep up with it. So do the distributed thing of the students keeping up with one topic and giving lectures, I think that could be pretty cool. Yeah, no, that's really cool. And I mean, now that you're bringing up AI, I'm just thinking, he said, cell walk, you kind of started around like COVID when we're at all stuck at home. And I feel like, I mean, from my experience, AI kind of boomed after a bit recently with chat GPT and things like that. How did that kind of big boom in AI affect your project and like did that help or did you find like new resources you could use or new ways you could research for helping make cell walk? Yeah, absolutely. It's had many impacts on cell walk but particularly like that literature review

27:35and doing research. I remember like trying to do that from my PhD and my computer graphics research and that was just like, you have to read so many papers, right? And a lot of those papers like suck and you just throw it away and then you just find like a few good ones. So like, I think that process is still important part of the educational journey but for where I am now is like, now I can just move so much faster on research topics. Like, just have these LLMs. Google's really good, chat GPT is really good. Do deep research, read like Andre papers and like just pick out the best one, summarize them. It just gives me this really high level overview of things very quickly. So it accelerates the scientific side of it, development side of it like cloud code, chat GPT codex, you know, all of these things. Really good at writing boilerplate not quite replacing us as programmers yet. These things make me happy. I think they're probably a good thing generally and making me more productive. And AI has also impacted the app itself.

28:36Apple just released iOS 26 and Vision OS 26 and one of the big new things is they have this on device AI model called foundation models and cellwalk plugs into that now. And, you know, we're bringing biology to life with visualization and we can like look at proteins and tire cells. Now the text itself like comes to life the entire app is like interactive and dynamic. It's like Harry Potter, right? It's like a book that writes itself eventually, right? But we need humans in the loop to make sure everything is accurate, make sure it's grounded and you know, create beautiful experiences. So humans are part of it and AI is just a tool to accelerate everything. And one last thing is biology, alpha fold, amazing. It's like there's all of these proteins that people had nailed down the crystal structure for yet. And alpha fold has been able to protect those structures and move things forward. So, very cool. That's very cool, yeah. And I guess another question I had was with cellwalk.

29:39I mean, I know you'd be able to kind of look into the very specific proteins of certain things. But is it catered to more, I guess, a post-secondary level of education or are you hoping to also like it be something that even younger students can use or things like that? Yeah, so our specific target audience is approximately AP biology. But the content does lend itself to younger audiences and general audiences, as I found out in the interviews and just kind of like the people using cellwalk right now. It's a very broad audience. But you know, if we had to pick on it, it would be AP biology. And that's actually where it's moving. But yeah, I want it to appeal to everyone and inspire everyone. It's just kind of an atlas of really cool biology. And you can find your own way through it. You don't have to start at the beginning and work all your way up. And with the founding Apple Intelligence on the device,

30:40we're also catering the descriptions and the content on the fly for like your level. So you can do like beginner descriptions or you can go all the way up to expert. And then we're basically showing you the raw scientific data and descriptions pulled out of papers. That's super cool. I love that. Yeah. And then, yeah, I guess one of our final questions here, you were one of the lead developers on the Lindsey Virtual Human Project. Can you tell us a little bit about that? How it relates to cellwalk or just kind of your experience working on that project. We did have Dr. Christian Jacob on our last episode that we recorded. So I'm happy to have you on this one and kind of continue that discussion a little bit. Yeah, that was really cool. That was a good project to learn on. And probably would have been a game programmer, I think, or maybe gone back to physics or something if it weren't for Christian, but that got me into biology and made me remember like AP bio from high school

31:43and how cool that was. So that was fun. And got to learn anatomy and work on that kind of thing. So yeah, I liked it a lot. But what was that experience? I had just finished my masters with Dr. Denzinger. And there we were doing some artificial intelligence stuff. So we had these agents and we would evolve their behavior. They could learn kind of like on the fly using genetic algorithms. And that was part of a game. So yeah, this like game engine with like physics and these like little characters running around fighting bad guys and like AI kind of like learning on the fly and the human and the loop, it was like cool. But that engine, I built it from scratch and then we took it into the Lindsay project. So the game engine became kind of the foundation for one of the things we were working on in the Lindsay virtual human project. And more people joined. I led the development of this human physiology component on that project and it was a lot of fun.

32:44We turned that thing into a startup and it didn't work out. But that was still a really good experience because I took everything I learned there into cell walk and it's helping me find the right path through my current journey. Awesome, amazing. Yeah, thank you for sharing that. And as our final question to you today, what advice would you give to students who are considering computer science or who may have just started their computer science journey? Hmm, just speaking from my own experience, it's like do computer science or choose it because it's like fun and you're passionate about building something because that energy and motivation just to build something cool and see something appear on the screen or a spatial computing now appear in front of you. That's like the motivation that will guide you

33:44through your whole computer science degree and shape your decision. So at least for me, it was always about doing something that was really interesting and I was excited about and saying no to things that weren't interesting and exciting. And if you can find that thing that you're excited about, then like everything else is easy. Pass your tests, whatever. And yeah, you'll have a lot of fun. Yeah, I agree. I think people have this idea that computer science is it's just all about coding and it's boring. But once you figure out like what you want to do with that and once you pass your exams and stuff, then it can be really cool. Yeah, so we're gonna wrap this up now. Thank you so much for coming on the podcast today and sharing about your academic journey and how you got into computer science and biology about cell walk, your inspiration behind it and how it was affected by AI and how we can use computer science to evolve education. It was a pleasure to meet with you. Yeah, thank you so much for having me on your show.

34:46And it was a lot of fun. Computer science is so cool and biology. They're awesome. Hey listeners, thanks for joining us on today's episode. If you enjoyed this conversation, make sure to check out our Instagram at at UFC underscore CPSC for the latest computer science events and updates at UCalgary and follow this podcast wherever you may be listening.