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[1932.60 --> 1937.20] a c program running in the browser yeah except maybe asmjs but that was kind of a precursor |
[1937.20 --> 1944.84] it lets you do things like simd that's also impossible with just javascript but once you leave the browser |
[1944.84 --> 1952.22] you can do whatever you want so web assembly is one extra alternative to the other hundred you have |
[1952.22 --> 1959.36] so from that angle like there's a few use cases that i think are pretty valuable for web assembly on the |
[1959.36 --> 1966.04] server maybe you want to extend your application let's say with plugins and you want to let users |
[1966.04 --> 1971.76] write whatever code they want and you want to execute that securely web assembly is a good sandbox for that |
[1971.76 --> 1976.18] but then again you're not going to reimplement that yourself you're going to use some other tool |
[1976.18 --> 1982.98] that may be under the hood uses web assembly to solve that problem okay what kind of stuff are you doing |
[1982.98 --> 1993.36] so i'm doing mostly web stuff so bringing bioinformatics tools to the web for either building applications that |
[1993.36 --> 1999.18] analyze data in the browser so that you don't have to figure out bioinformatics dependencies which |
[1999.18 --> 2007.68] are kind of a mess if you want to keep your data private it's kind of a local only type workflow |
[2007.68 --> 2014.94] the other thing i'm really interested in is something i'm talking about tomorrow is using web assembly to |
[2014.94 --> 2022.92] power interactive tutorials for command line tools so that you can you know instead of when a student logs |
[2022.92 --> 2029.04] into your website you spin up a container for them that's super expensive you can run these tools in |
[2029.04 --> 2037.40] the browser give them a similar experience and much much cheaper for you to host what should we know |
[2037.40 --> 2043.52] about bioinformatics that makes sense to us what exactly is bioinformatics oh that's a good place |
[2043.52 --> 2048.54] say that three times fast bioinformatics bioinformatics bioinformatics that was not fast enough that was |
[2048.54 --> 2057.44] there's a pause in there i'll say it three times slowly please explain so bioinformatics is using |
[2057.44 --> 2064.78] computer science and software engineering to analyze biological data okay like dna yes exactly so for |
[2064.78 --> 2070.48] example if you're interested in knowing i don't know which diseases you might be at risk for you could |
[2070.48 --> 2080.08] take a blood draw isolate the dna sequence it figure out what all the letters are and compare those to a reference |
[2080.08 --> 2086.62] and you know figure out what's different there and it has that been associated in the past with some disease |
[2086.62 --> 2093.94] or something like that right and so the the process of figuring that out the algorithms and the the software |
[2093.94 --> 2099.52] around that is basically bioinformatics so what does it take to take these kind of applications that are like |
[2099.52 --> 2104.32] probably behind a desktop application right they're probably written in c or for a desktop environment |
[2104.32 --> 2110.68] and you want to take those kind of applications to the web yeah to to essentially open it up where |
[2110.68 --> 2116.64] you can just go to any platform linux mac windows is that the is that the reason why yeah yeah and so |
[2116.64 --> 2124.30] like one example is uh i have this website called fastq.bio so it takes in some data that you get out of an |
[2124.30 --> 2130.58] instrument and run some really quick data analysis to tell you how good of a quality the data is |
[2130.58 --> 2136.60] and you know it runs in the browser because that's just super convenient people drag and drop their files |
[2136.60 --> 2141.66] and they're done they don't have to figure out install it how to set it up and all that stuff so that's one |
[2141.66 --> 2149.58] use case you wouldn't necessarily do super heavy duty analysis it's still the browser you're kind of |
[2149.58 --> 2155.60] limited by what the user has but it's a nice way to cover a ton of use cases that previously were |
[2155.60 --> 2162.96] not covered and you specialize in the wasm world in bioinformatics in particular like that's where |
[2162.96 --> 2169.62] your usage of wasm is in that silo yeah that's that's right okay so i have a tool called bio wasm |
[2169.62 --> 2178.02] bio wasm yes that's pretty cool can you say bio wasm three times much easier yeah that's true |
[2178.02 --> 2187.32] speaking of how do you guys pronounce wasm is it wasm or wasm well i call it wasm okay but |
[2187.32 --> 2192.64] i'm open to either direction i don't even understand why i call it wasm but i do call it wasm |
[2192.64 --> 2199.60] it's web assembly assembly wasn't yeah it's a wasm i mean if you should have it called it wasm |
[2199.60 --> 2204.10] because i wanted to write me with awesome but that was just a means to an end right right |
[2204.10 --> 2209.00] but i do call it wasm i'm not sure why i don't know either i think we may have been on a podcast |
[2209.00 --> 2212.98] with somebody who seemed to be more knowledgeable than we were and called it wasm and so we kept |
[2212.98 --> 2216.88] going there with him that's true although i think since then it didn't work for richard hip i mean |
[2216.88 --> 2221.50] i still call it sequel light that's cool he's definitely more more knowledgeable than i am |
[2221.50 --> 2228.90] about the project yeah so yeah i'll stick with wasm until i'm convinced otherwise sounds good to me |
[2228.90 --> 2235.08] yeah now what do you call it i call it wasm and so why do you call it wasm because we don't know |
[2235.08 --> 2240.02] i don't nobody knows well that's the thing sometimes just the first way you hear it is just how you do it |
[2240.02 --> 2246.68] right what's a weird phenomenon in computer science and podcasting or real life |
[2246.68 --> 2251.96] conversing is yeah a lot of times with a with a term or an acronym or whatever it is you've |
[2251.96 --> 2257.28] never pronounced we'll read it for years guys we'll read it to ourselves for years and we've never |
[2257.28 --> 2261.72] actually had to say it to somebody else and then you have that moment of how do i say this i've been |
[2261.72 --> 2266.26] reading it for years writing it for years it's a weird moment that we all experienced so maybe we |
[2266.26 --> 2271.58] just had that with wasm okay but i'm glad that we're all on the same page that is good we have |
[2271.58 --> 2276.52] consensus although on our show recently christina warren did say yes i call it |
[2276.52 --> 2280.80] jiff and then she just continued to talk as if we shouldn't stop the world and discuss |
[2280.80 --> 2284.70] do you remember that well she's here we can get her on the mice again christina's here i saw her |
[2284.70 --> 2289.68] downstairs all right want to get her on we'll have to get her hey listen our listeners aka jared |
[2289.68 --> 2293.78] listened to this part of the show and was upset because we didn't get the beef about jiff versus |
[2293.78 --> 2299.04] gif i was upset in the moment i was but she talks too fast so i just let it go i thought it was you |
[2299.04 --> 2305.24] know an appropriate amount of speaking cadence but uh i will agree all right i missed that argument |
[2305.24 --> 2308.82] let's get back we had better things to cover though we did let's get back to robert we also |
[2308.82 --> 2313.96] have better things to cover right now yeah we do we're sidetracked okay so bioinformatics taking |
[2313.96 --> 2319.00] applications that are for the desktop to the web what kind of applications make the most sense you |
[2319.00 --> 2323.92] mentioned this one where it sort of does like data analysis yeah you know what what does the web need |
[2323.92 --> 2328.74] what is a user base need of the web that can use these kind of tools in specific to what you know |
[2328.74 --> 2334.66] and then just in general for what wasm can actually do yeah so i think for it's pretty similar |
[2334.66 --> 2341.18] across the board i think for bio you know tools that do some sort of preview of an analysis are |
[2341.18 --> 2348.54] really useful some analyses are just really small too like if you're analyzing let's say the genome of |
[2348.54 --> 2353.90] viruses they're pretty tiny so you could actually just run the whole thing in the browser and so that |
[2353.90 --> 2361.82] gives you both the advantages not having to install the tools and to do it in a privacy conscious way |
[2361.82 --> 2369.52] in terms of you know more broadly outside bio because you have audiences that aren't a biologist |
[2369.52 --> 2375.76] is that right that are what that are not biologists um we haven't surveyed them recently but i think |
[2375.76 --> 2384.70] that's fair okay i would say we got at least one okay that's good um i guess there's a few categories |
[2384.70 --> 2390.48] if you have a tool that you already have in another language and you really want to bring it to the web |
[2390.48 --> 2397.62] and you don't want to rewrite it all in javascript i think that's a great use case yeah if you have a |
[2397.62 --> 2405.84] slow application that has portions of it that are really heavy javascript compute in some cases this is |
[2405.84 --> 2410.68] something that's also tends to be overplayed this not always happens but you can get performance |
[2410.68 --> 2416.58] improvements by switching it off with web assembly but you can also get worse performance um |
[2416.58 --> 2422.72] and yeah that's kind of the couple of applications i think are pretty relevant describe worse performance |
[2422.72 --> 2428.96] is it like because sometimes access is enough and i'll wait because maybe the web is easier and i can't |
[2428.96 --> 2433.60] install it on my system or i can't because literally i literally can't install the application but i can |
[2433.60 --> 2440.18] browse the web and i can authenticate on the web yeah so one big thing that i've noticed |
[2440.18 --> 2446.58] is that when you have a web assembly module and it needs to communicate a lot back and forth with |
[2446.58 --> 2454.66] the javascript world that is super expensive so if ideally your module takes in a little amount of data |
[2454.66 --> 2460.58] does a bunch of stuff and returns small amounts of data but if you're constantly returning large trunks |
[2460.58 --> 2467.88] and that's because um web assembly only understands numbers so like if you pass in strings converts to a |
[2467.88 --> 2473.18] number pass in an object convert to a number do you know the conversion by any by any chance like if |
[2473.18 --> 2480.16] i said the word the what what number is that to wasm oh of course it's 86 comma 112 no i'm kidding |
[2480.16 --> 2486.28] it that'd be cool if you knew it would it would you could have kept going we totally bought it i would |
[2486.28 --> 2492.76] have been spooked i would have been like oh my gosh well that's cool numbers only numbers only so |
[2492.76 --> 2497.64] the translation layer in between is expensive yeah and so that's actually one way in which you can |
[2497.64 --> 2504.28] try to optimize the performance is that if you switch off you know some javascript with web assembly |
[2504.28 --> 2511.24] you can try to trim that down uh in order to speed it up yeah makes sense back to your |
[2511.24 --> 2518.56] current interest of cli tutorials in the browser yeah are you giving people full-fledged linux environments |
[2518.56 --> 2526.80] in the browser or how does it work not yet so so right now in the v1 um every tool i have to compile |
[2526.80 --> 2535.44] to web assembly and then i have this sort of you know extern js it simulates a console and i kind of |
[2535.44 --> 2542.00] hook those up together in the future what i'm going to do is actually switch that up with a full-blown linux |
[2542.00 --> 2550.16] os in the browser that's going to be a little slower but it's going to be worth it for some of |
[2550.16 --> 2556.24] you know getting some things on there that are otherwise hard to do just by directly compiling |
[2556.88 --> 2563.44] and the way this this is using an open source project called v86 so they they wrote essentially |
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