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• Garage labs and community labs for learning biology and biotech |
• Hacktoberfest contributions and potential rewards |
• Unpopular opinion: open source can be sustainable and has no business difference from closed source software |
• Importance of self-marketing and not relying on others to promote your work |
• Benefits of open-source software, including transparency and community involvement |
• Value of community engagement and word-of-mouth marketing for startups |
• Concept of "the moat" (being the creator and owner of a valuable product) |
• Debate about whether open source is always sustainable |
**Natalie Pistunovich:** Hey, Ian, how are you doing? |
**Ian Lopshire:** I'm doing great. How about you? |
**Natalie Pistunovich:** I am doing well. I'm excited about our episode today. We're gonna talk about Go in biology and medicine. And our guest is Tim Stiles. Hi. |
**Tim Stiles:** Hey, how's it going? |
**Natalie Pistunovich:** Good. We are very excited that you're here to talk with us about something that I personally did not do enough since high school. |
**Tim Stiles:** Hah! This is great. I've taught a lot of people this; this is wonderful. I don't have any slides, I don't have any whiteboards, but I'll try my best. |
**Natalie Pistunovich:** \[laughs\] So Tim, you are doing biology with Go. How did that happen? Why? Tell us everything. |
**Tim Stiles:** So I guess I'll start with the short story, and then you can start asking me "How did you even become a software engineer in biology?" But starting with Go was -- I've been writing biology software for a while, and I'd come up on this new project where essentially it was a version control system for cel... |
So that's sort of how I started with that in biology. And then it spun into something more, because at that time I was getting tired of biotech software... Because it's a hard topic; you have to know how to write software, and you need to know how to do biology, and the intersection is very, very small. And people will... |
And so what happened was I was getting ready to leave for tech, because I was burnt out on this lack of tooling... And a friend of mine who was working for a professor at Stanford, he called me on his drive down from Stanford to LA where his parents lived, because he was quitting his job at Stanford... He was only 20 a... |
\[06:06\] And so there's this really esoteric, designed in 1978, pre even XML format, that's all whitespace-based, and he's like, "Hey, I can't convert this JSON to GenBank, and GenBank to JSON and back. I can't do it." I was like, "You've got to be kidding me. This is the world's most common data interchange format, J... |
**Natalie Pistunovich:** Wait, in any programming language, or in Go? |
**Tim Stiles:** He was trying to do in Python, and the thing that was happening is that he kept getting this fatal error, on several sequences, where instead of going \[unintelligible 00:06:40.29\] like, you know, letting you just to handle the error yourself, it would just kill the whole run... And so the run would ta... |
So it gave me warnings when I tried to click on it in Firefox... Like, "Don't go to this bug-infested site from the government." I was like, "Okay..." I'm like, "I got to it." And that's the only specification I could find for the file format. It took me three weeks to write this parser. It's not like I haven't written... |
**Natalie Pistunovich:** This is really mind-blowing. I had no idea... Wow. |
**Tim Stiles:** It starts with the complexity of this -- I guess you call this legacy data, or legacy code or software... Because bioinformatics has existed since before the web. We've definitely evolved a lot since the internet came about. But scientists had been using the internet before everyone else by at least lik... |
And so a lot of biotech software is limited by the fact that there's these data formats that the government uses, or some repository uses, but everyone else is just sort of like - most people doing this work are scientists, they're not software engineers. And there's a big push right now for scientists to learn a littl... |
So there's this whole discussion right now in the field of like "How do we write better software?" and I've found myself in the center of it, because I wanted to write this to make cool stuff. Like, it does have medical applications, but I'm thinking of stuff like flying seaweed, and \[unintelligible 00:09:44.01\] tree... |
\[10:10\] So for example, DNA synthesis, which is what we use to make new DNA for certain genes that we're trying to engineer, there's only like two companies that have an API for that, out of like the dozens that exist. Most of the time, if you want to send something to them, you have to do like a drag and drop into t... |
**Ian Lopshire:** So that's the tech side of things. How'd you get into the biology side of things? I think before the show you said you had a degree in computer science, but how did the biology come in? |
**Tim Stiles:** That's true. So this is really funny... So back when I was a student, I first started as a mechanical engineering student, and then I switched to as a design student, and then I got really into robotics. I was playing around with 3D printers, and I was doing a lot of computer vision stuff... And that wa... |
So usually, the line of research there is "Can we find a way to mess with that to stymie tumor growth?" And the answer is, "Yeah, a little bit." But cancer is a very complex disease, with lots of different ways of presenting itself, and it's not the end-all there. |
So I got started in that, but at the same time, my spouse, Ren - we were dating them, but now we're married - she was working at a lab at Harvard Med under George Church, who was a famous synthetic biologist. He's like in Wired Magazine... He's a really nice guy. He says yes to everything. So if you have a synthetic bi... |
And so she was working in his lab, doing self-aid programming, which is this concept... Have you ever heard of stem cells? Do you know what stem cells are? |
**Natalie Pistunovich:** Mm-hm. |
**Tim Stiles:** So stem cells - the idea is that they're -- a self-aid program is the idea that you can turn a stem cell into another kind of cell, a blood cell, or a tissue cell, an eye cell... You know, a different cell. And you do this by introducing various chemicals to it, and there's different stages. So you're p... |
\[14:26\] But how I got in biology is that eventually doing this, walking home with my wife, we were in the same area, so I'd walk 50 minutes to her office, and I was on the way home, and we'd walk home together, and she'd be explaining her work to me... And she was mentioning this thing called plasmids, which we're go... |
And so I was having a hard time -- there was some problem with staining, where I couldn't get quite the information I wanted out of the data I had. There was something going on there. It's been so long since I looked at this, but essentially, I was like, "I need to be able to explain what colors I need, and how it work... |
And so eventually, she got tired of explaining things to me, and very gently suggested I go to this garage lab in Somerville, Massachusetts called BOSS Lab, which has been around forever in some various way, shape, or form... And I showed up there, and I was like, "Hey, I need to learn biology for my work", and they're... |
**Natalie Pistunovich:** You have also built Poly, which is a Go package for DNA... |
**Tim Stiles:** Yes, so for engineering DNA, which is very specifically -- it's very different from what a lot of other people do with DNA. A lot of times they're looking for diagnostics, they're looking for variants, they're trying to assemble it into a whole genome for reference... What my package does is it tries to... |
\[18:10\] And so I started from sort of that principle, and it started with just parsers, which every bioinformatician will tell you that's like the first thing they have to do, is they have to write parsers. It's like the bane of our existence, is taking government data and putting it into JSON. I wish I was kidding. ... |
**Ian Lopshire:** So I want to get into the nitty-gritty details of it, but first... |
**Tim Stiles:** Yeah. |
**Ian Lopshire:** ...can we talk about like high-level what it does? What kind of projects could you do with it? Are there projects you've used for it? ...just to kind of get some context here. |
**Tim Stiles:** Okay. The thing is, it's a very vast library, despite how much I've underplayed it so far... So some real things are - I know that a couple of consultants have actually engineered microbes as a potential therapeutic, and I've done that as a consulting gig for a couple of YC companies that I probably sho... |
But there are things that people could be doing with it, that they aren't yet. One is designing primer tests, like the PCR tests, like the ones you've seen for COVID. There's very explicit tooling to be able to do that, for designing primers, and looking at -- I'm currently working on a project where I'm essentially ta... |
So there's a lot of medical applications, there's a lot of biomedical applications, which most people when they talk to me are very interested in, because it's innately human. Everyone's had a medical condition, or knows someone who has a medical condition. And one of the examples that I should have started with - I do... |
\[21:58\] And this is how synthetic biology works, at least at the early stages, for a lot of companies, is they engineer yeast, or E. coli; not the dangerous kind, not the Chipotle \[unintelligible 00:22:04.13\] kind, but like lab-safe, like difference between like a \[unintelligible 00:22:07.18\] and like a domestic ... |
But the thing is that this is a technology that's been around for longer than I've been alive. It's been around for 40 or 50 years, but it's sort of become this new thing in the public eye of, "Oh, I can do it, too." It's not just the realm of Monsanto, and Eli Lilly, and pharmaceutical companies; it's now getting to t... |
**Ian Lopshire:** Sorry, I'm processing for a second there... |
**Tim Stiles:** Yeah, yeah, sorry. |
**Natalie Pistunovich:** Yeah. A lot of inflammation. Super-interesting. |
**Break:** \[23:20\] |
**Ian Lopshire:** So that kind of made sense... \[laughter\] To my limited mind. So what does it do? Are you like running simulations? Is it statistical modeling? Is it like how DNA reproduce? |
**Tim Stiles:** Not statistical modeling, it's more construction. |
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