I am here at beautiful Red Canyon, located in Fremont County, which has long been recognized as an area of high significance for rare and endemic plant species. Red Canyon is an extremely unique place in its biology, geology, and physical characteristics. Because of this unique habitat, there are species endemic to only red canyon. During the early and mid 1980s, four rare plant species were discovered in the canyon, an adjacent limestone mountain area. One of these species is Barnaby's clover. The Red Canyon area is the only place in the world where Barnaby's clover is found. Barnaby's clover is a matte forming clover that is restricted to ledges, crevices, and seams of reddish cream colored Nugget sandstone. Additional survey work in the area resulted in the discovery of three more rare species, including two candidate species for federal protection. In a world where fitting in is so often emphasized, Red Canyon's rare plants fit right into their unique environment. From the University of Wyoming Cooperative Extension Service, I'm Rachel Miller, Exploring the Nature of Wyoming.


Suitable for children under 13 years of age viewer discretion is advised What's going on guys picture prime here once again with another episode of the script rapper It has been quite some time I was just mentioning to John Thomas that I haven't done a sit-rep in over a month So we'll take these off again with a brand new youtuber that some of you may not be familiar with John Thomas prime 84 John Thomas, how are you doing tonight? Oh? I'm doing pretty good Well, what welcome to the channel sir. I know you've been a long time subscriber of mine. I've always seen you in my chance Yeah So don't tell my people a little bit about you Well, uh, let's see here Some people call me John. Miss prime 84 or just John a miss or try to say my name As best John to miss a prime But I also go known as shaggy because when I do gaming with my friends I do shaggy impersonations, but you could just call me John Johnny Johnny Bravo Johnny five Whatever you like. It's no big deal. Um, I'm a transformer fan from G1 to Sound up today stuff Nice, do you do a collect a lot of third-party or you primarily hasbro? Not third-party. This is a wheezing SkySaurus and I do have I think a few others Just not a lot third-party have been really get into it because money costs on some I could get, you know, mainline stuff with About the price, but lately right now. I just switched forward to the third party That's me. I've always been more of a hasbro guy because it's more affordable But I hang out with a bunch of guys that collect third party in friggin legends class and I'm starting to get more of those in I love that Marvel Megatron. I just recently got Yeah, the way the third party is like legend skill size the engineering on those things It's like oh my god. I wish I was like a bigger figure because I would just blow hasbro out of the water Well, it's like that Megatron. I mean it looks exactly in robot mode as MP 36 But the transformation is so much more simpler. Oh, there's Larkin's boom right off the bat with a super chat Johnny five cause you two mobile Thank you so much Larkin. We'll just start this one off with a Bert. Everybody loves a good Bert Bert is always with us in spirit. That's still one of my favorite ones really. You should have been there when it happened live Well, let's go ahead and get rolling with this set rep for those of you who don't know The set rep is my show where I interview another transformers youtuber And I have 10 questions I think you might have your speakers up too loud. I can hear me talking after I talk Could be my phone, let me check see if I turn down Dear jeez So anyway, yes it rep I have 10 questions for my guest Five questions regarding him as a transformer collector and five questions regarding him as a youtuber and slow DK Just hit us with a super chat out the gate too. And I know which one he wants. He didn't even need to tell me Where is it? Where is it? And I've been smoking since I was born man. I could smoke anything man You better light it in here, man, right these gas fumes, man I Need to upload the other one I mentioned before that my first video I switched Bert and I and you couldn't tell the difference between us So when I change it that way you can kind of make us out a little bit more But I have to see if I have the other one. All right. Well, let's go ahead and get started with question number one Is what's the appeal of transformers for you? well Really the appeal of transformers to me is just playability and you basically are buying One toy, but it has multiple purpose. It's a robot or it's a beast a vehicle and it's multiple change Just fun to play with and I've always loved that and everything and you know, just kind of Rune and stuff. That's why I liked about transformers You just have just a giant robot and next, you know, it turns to another creature or vehicle or Whatever so playability Just I love it Now you said you collected from g1. Are you a g1er? Were you around when they first came out? Well, I was born in any four. So that's the year they came out and everything so I grew up The g2 Area, but I'll rewatch all the g1 episodes and everything. I've even got them on discs and everything so Uh, just to show how much of a g1 fan I am. I am a g1 fan begatron Complete I need getting a sticker and they're all faded I know the perfect place you can get some stickers too. Well, they're in my cart All right, well aside from g1, which is always the number one answer What's your favorite transformers fiction? They have to be these wars Hey That's the show I grew up as a kid, you know, it was my generation of what you had was g1 cartoons and everything and I just like it they it's That they tied in with g1, but it was like another new spin On characters a new like idea and everything that like bringing back all characters and and still um Respecting the g1s really Did you have you heard the story of how g1 got tied into beast wars? it was accidental In the very first beast wars episode primals talking about the great war And the great war was just they were mentioning the great war something that had the two warring factions together And the internet right then is during its infancy, right? So all these transformer Pages uh chat rooms whatever just went nuts all the great war. They're talking about the autobot decepticon war So when they started seeing that online, that's when the writers of the show started researching g1 more And decided well, what the hell let's just tie it in together And I think it was like a couple episodes later You see star scream fly by in cheetor's dream with the decepticon logo on him and everything So it was just kind of a fluke is how it became part of g1 And that's I've heard about that too and that's why I like about beast wars because The fans is what helped make you know, tie that into it as well. So You know, it's they were listening to the fans and you know, what reading their stories and stuff and all the online and stuff That's why I liked about it It's like what the fans did to save the sonic movie Yes, exactly Even my kids when they first saw the trailer with the oh Sony they're like No But he made a comeback. Have you seen chip and deal yet? No, I haven't oh my I've already seen the images and all this stuff from it I highly recommend it. Yeah, people waste of no time spoiling the cameos, but even though it's still a good movie All right back to the questions. Do you have a favorite figure? Or grail a figure you will never let go of you're looking behind you right there Your house is on fire or something's going on. You can only save one What is it? They're only 30s rhinos They're only 30s. That's a good figure. Yeah, especially after you got the kingdom when you're like, what in the hell and it's I was disappointed and it was just it's not fun to transform from my opinion A lot of people are not having issues, but I have issues with it That's part of the fun if I'm sitting here cussing and parts are popping off while I'm trying to transform a figure I'm not enjoying it Like I I can understand some parts have like a little bit tight tolerance, but that one that just There's no tight tolerances would have been easier just harder to get it lined up and tab into them all that stuff Hey, thank you so much for the super chat Really appreciate that's another one of our toy hacks winners right there. Let me uh Find Chauncey something worthwhile here When I see ones I do like that. I'm like, you know, I will not look good if I ever get really skinny That's like this one I made the other day for friday the 13th That's what I look like in high school That was nowhere near that in high school That was the fashion when I was in high school I Make a mean emo guy Hey deluxe is in the chat. I got a lot of people in the chat tonight 26 people for a wednesday. That's not too bad Skinny ppr's first All right, so we got to the did we answer? Yeah, thrilling 30 round ox So now what figure is your white whale? What's your most wanted toy? Oh man, that's Been really hard. I've been I've had my friends ask me that too um I think it's well, it's not really one it's Majority I need I want I'm a big combiner fan. I love the combiner transformer. It's a whole shelf. It's nothing but combiners But I don't really have a lot of g1 combiners So I think those are my only griles of getting all g1 combiners Do you have any of them any of the g1s? Uh Not g1, but I have like you know the r.i.d Furticus style one and the desert camel that came out with the r.i.d in the early 2000s I got those are the closest g1s that uh that bruticus right there was my stand in for a g1 for years And I had I had the gold one that you do I can see right there And then I had the one that came out with the kb toys. I guess it was the regular release It was gray and then they think they re-release so many different versions of those Oh, Jason. Hey, welcome to the chat my friend Pick me up. What decals did I miss out on none yet? I got like a ton of decals in today. Let's see Where's one of jason's favorites? Here we are leverage eject No reaction quiet on that one All right, so Which combiner would you like to get first? What's your number one g1 combiner you'd like to get a hold of? The secons that don't have any secons. I've got I've got different variations of Uh superior defense or all the other ones, but I don't have any of the secons not even the new hasbro ones because I can never Find them in a good price out and I wouldn't I didn't get those because they were ridiculously priced For generation selects figures you were paying 34.99 for a deluxe and I forget what snap trap was it was just like 70 bucks. Maybe I think it was like 59 or something.  I'd love to have them, but no That's what kind of kicked off my g1 buying back in the day was when big bad toy store Did their re-release of the piranha con gift set? And I got that and I was like, oh my god. I forgot how fun g1s are Yeah, I I remember that said and I missed out on it.  So it's no big deal There we go. I would save my zing zing megatron. It was a gift from a wife probably the largest non-combining figure right now That's me and mp01 my wife bought mp01 for me while I was in Iraq So that that actually was part of that. He was the uh mascot of my channel until I got my official logo for a longest time I just we can still see him up there on the wild point and you can't see me point mode and screen You can see him up there on my shelf holding the flag Yeah So Let's say my wife asked me how much it would cost to buy all the main line tf releases each year I don't even want to think about it I I forget I think fire talks the other day was talking about go box because they're rock lords He's become rock lord obsessed lately And he says man, I hate to think how many rock lords that I bought recently And I just said you never want to add up your expenses on these toys All right, well, what's your favorite transformer character? any fiction any media Oh, I've been the guy I use my for my logos rhinox rhinox. I was wondering Yeah, I just grown up the show, you know, I Always thought that rhinox was like the backbone of the whole maximal team.  So I just like how they built this character and everything in the show and so It was almost a slap in the face in beast machines when you found out he was tank or Don't remind me I was so upset when I first when beast machines first came out I was like what happened to rhinox and then they go like oh it's tanker. I like no done And I didn't finish that series until like I think last year. I finally actually sit down and watch the whole thing I got it all on dvd and I haven't watched it in years But I liked the finale other than the whole Cybertron turning into earth with all the biological plants and stuff. I did like the final battle between megatron and optimists Yeah, I like that too. I just you know, just kind of weird off that all these Cybertronius now are just skipping and merely into the fields and stuff. I was like Yeah The nineties was weird man All right, so now we are rolling into youtube questions and youtube territory What possessed you a grown man to do toy reviews on youtube? Mmm, I would probably have to say my friends finally convinced me to do it We uh, I have a group of friends that also like transformers. They all collect different figures We're all different collectors of transformers and stuff and we Usually we'll get together once a month and just have a meet greet at a coffee shop Show what new stuff we got talk about stuff. What's coming up and everything and I always You know voiced my opinions on The figures they got or I got kind of like as a little review and stuff just for just, you know Fun and everything and they're like you should do a youtube and I was like I don't have the equipment to do that because this is back in like mid 2000s and everything because Didn't have really have a good pc computer Internet was crappy didn't have a camera. So I was like, I'm not built to do this stuff and everything and so I just Hold up, you know, put off the whole thing Idea till they find it, you know what my friends finally like, you know, it's like you just do it just for fun You know and I I was like, well Technology is more affordable now. I can do everything on my phone I'm literally still doing everything on my phone And just slowly doing it And everything so so learning I don't know the whole algorithm Nobody knows the algorithm. Um, yeah There's stuff that I will rush to put out and in my mind. I'm like this will do great and barely any views And then something that you would never expect would be popular Just blew up like in my latest I think I did The one that surprised me It was a legacy figure that I thought for sure. Everybody wanted to take a look at No hits whatsoever. I mean just very low for what I normally do Yet might be reissue cyber shark Figure from beast wars, which is not even a well-known figure. Just shut up so And my title wave reviews doing really good I knew that one was going to do good because I've had people ask you need to do armada reviews And I'll have like two armada figures. So once I got that title wave. I was like, I've got to get that one reviewed out quick Legacy skids. I think that was it elites Yeah, digital says even the algorithm doesn't know the algorithm I think they did in japan I think Because that was the first one I bought. I mean, it was I think I got off ebay It was the gold one that you have up there on your shelf That one's technically all the gold on him is actually the desert camo gold I just want it so I can look like the japan one or the Show accurate version really from a distance. You didn't even have to correct me and everybody will thought oh cool. He's got the japan one Yeah, no, I'm gonna. I'm gonna tell what it is All right, buddy. What keeps inspiring you to get in front of the camera Um Just basically try and get behind the camera and just you know If I always have like the one thought I always try to get you know try to do the reviews is I'm going to throw my opinion if somebody's having difficulty of trying to decide a figure I've always thought, you know, it's like you don't really have to buy every figure in every line You don't have to buy if you want to buy a certain character and he's in multiple lines buy that certain one and and if you've been on like The edge of buying a figure and everything I'm kind of I'm trying I'm still learning It's trying to help voice my opinion see if that'll help make your decisions Like well this figure does you know does really well articulations if you like doing display dramas Posing for your figures or if you collect certain characters or you're just this particular line and everything I'm just trying to help out Try try to help out people make their decision. That's why I always trying to want to do And that's a one thing I learned real quick doing this. Don't buy figures just to review No, there there are people that why didn't you review this figure that why didn't we review that? I was like, well, I've seen reviews on it. I didn't like it So I'm not going to buy it to review it for you guys to say I didn't like it So if you see me not review something that means hey, patriot prime didn't buy that So he must not liked it because that gets expensive just to buy figures to review Because I did that uh a lot throughout the siege line because there was a lot that Like a lot of the exclusives that I ended up reselling later on. I just had no interest in them I just bought them just to review and so I've really reeled that back Gotta see if there's anything here in the chat Let's see Speaking of title wave I was a little disappointed there wasn't a comparison shot it with him and a titan But I'll forgive you all what it been was that you'd see a calf I forget which figure I compared a titan to I think it was scorpionock or one of them I did Maybe a metroplex What was it? I want to get all the god speed to you craig I think that's why burton he's focused only on optimus primes. I think he's almost got them all except I know he passed on that 700 dollar one. Oh, yeah I'm gonna get the Yeah, I'd like to get the 40 dollar one the way I looked at it is okay, and we'll get a 700 dollar Remote control prime that I'll probably play with for an hour It'll go on the shelf And that's it Or maybe every now and then bring it out to show a guest but hell nobody ever comes to my house anymore Um, yeah the jade one that I might get that one The the dad bottom is prime The affordable collector prime All right, there are thousands of toy reviewers on youtube what makes you any different from the rest Other than the shaggy voice um Really, I'm not much different from All the other rests. I mean there's other youtubers are better than me and stuff. I try not to compare Myself with them. Um, you know, I try to My reviews kind of my way and not try to Do the same with it Like how other viewers do because they do it a lot better and everything and I don't want to kind of copy that type of style I want to try to find my own style and my own way to do reviews and stuff but Yeah It's a learning process. I go back and look at some of my old ones and I'm like, yeah I do too, but I They're for like remembering this is like this is how I started and Slowly trying to grow better and see when I first started I did some of my favorite figures first And I've debated on, you know, there's so much out right now Anyway, but I've debated on going back and re-reviewing some of my very first ones This guy here. I never completed reviews I did I think three limbs And I didn't do it because I was just like, uh, this is horrible So I never really finished complete doing this one guy and I'm thinking about redoing it as one thing or Something else see I didn't start reviewing new figures until siege came out because In my mind, I was just getting started. So I was focusing on g1 because nobody was doing g1 at the time And I had somebody in Uh a comment section asked when are you ever going to review some of the new figures? I'm like, well, I'm not everybody's reviewing those And he told me he says man. Nobody watches your reviews for the figure They watch your reviews for you And that just stuck with me Sage advice from patriot brine all right, so question number nine What is the one thing you find the hardest about being a youtuber? Uh, well Lately right now what I was going to been it's just having time to actually sit down Do do the review because I don't do a script.  Do you think I have a lot of time but new really All elites hits me. What's What's the one thing you find the hardest? Well, like uh, jonathan said it's the time I got a full-time job. I got a kid got a wife and just finding the time To come up and for me I've got to be in the right mindset if I'm like feel like I have to do something or if I'm rushed I'm going to sit down here and just screw it up the whole time. I got to be in the mood And to do it of course. I'm kind of double duty and with regular figure reviews and toy hacks reviews And it just I got to be in the mindset. I've got to find the time And what's aggravating here? I live right in the middle of the town I've got the road right here by me. So there's only certain times of day I can film without you hearing cars in the background Now I've got a damn bird's nest right outside my windows through the daytime All you hear is birds chirping in the background of my videos, which is why there's music in my videos now So That's the thing for me. It's all time I've got plenty of stuff to review. Just when am I going to have time to sit down and do it because for me Doing a review, especially the way I do it because a camera faces me Then it goes to the figure them back to me again. Am I editing and everything I do a 10 to 15 minute review can take me two to three hours That's because I'm so damn picky It's gotta be just right No, all right. So last question Do you have any channel goals for yourself and where can our viewers find you? This is your chance to plug your channel Well My goal for being a youtubers. I don't really have a go. I'm just doing this as a hobby for fun and hope to help Other people make a decision on the figure that they've been on the fence about and everything So I yeah, I'm not looking to try to get you know, the thousand subscribers So and all this other stuff.  And if I try to make it into like a business or anything I it won't be fun for me at all And where you can find me is on youtube jonamus prime 84 There is a link to jonamus primes channel in the description of this video And one of the things I thought was funny about jonamus was last week burt Did a scooby and shaggy impersonation like he was talking to each other So jonamus reached out to burt and says hey, man, I do a good shaggy Can I take your scooby and combine it with my shaggy? burt says yes And so jonamus made one and he uploaded it burt's original videos like two to three hundred views jonamus redid it and you have how many now it's over three thousand, right? Yeah, it's like 3.3 k I don't know how At all Really, I guess I just hit the right time zone for upload knit or something I guess or shaggy must have been trending or something Like man, he was sure hungry That is a good one. Thank you Well We forgive you That's all right Well, that is pretty much it. That's all of my questions. I'll leave that open to the chat right now We'll stay on for a few more minutes. Does anybody in the chat got anything you want to talk about want to bring up Want to ask questions about What's gas prices like in your area? Uh, we're still under four dollars Under four dollars. Mm-hmm. It's so like three Some places are 389 or 399 But it's we're we're 419 That's it and kind of rolling through the Be me and stay at home dad. I don't really have to drive a lot. I just go pick up the kids from school and that's it fire talks I have two And one of my ebay cart dammit I don't have any I got a go-bot. He's my only one in my collection I have three go-bots four four ones at work I've got like a some of my collection at work my desk bots I play with Well, the one I got is a conversation starter and people walk into my office Yeah, the one I got it's a mr. 34 go-bots of forklift because when I used to work, I drove a forklift That's the reason why I got it. Was that scoops? Oh I can't remember exactly Now I was never that familiar with rock lords, but this one that fire talks gave me this is one I remember I think a cousin of mine or somebody had that one So I did do have a little bit of remembering with that one And that's what I'm filming tonight 429 Well, I think that about does it far sit rep tonight. I know it's it's getting late So I've got to hit the hit the sack and get the work in the morning all that fun stuff John, I want to thank you so much for hopping on Talking to me for a while letting my people get to know you. Hopefully you can send some subs your way And they can see your shaggy video where you beat Burt is at his own game I'm so sorry Burt if you're too much that I didn't I don't know why that went up so high Yeah, I thought that was awesome. I was like, what the hell because I thought it was his and I'm like, well, wait a minute So, uh, big shout out to everybody in the chat decide to stop by and see us on this Wednesday night Um once again, John, thank you so much. Make sure you subscribe to him And uh, I guess we'll see you next time. Don't forget to like don't forget to subscribe. This is patriot prime signing out who


introducing myself a little bit and obviously dating myself a little bit as well, but then my background has always been microbial genomic, so this workshop is really near and dear to my heart because this is what I enjoy doing and what I've been doing for the last 10 years or so. So initially I started doing microbial genomic analysis and then did some meta genomic analysis as a postdoc. And after that I joined EC Center for Disease Controls to lead down the petition there and essentially worked on building genomic epidemiology capacities in our public health sector for about eight years. And in 2020 right during the pandemic, I moved to SFU full time as an associate professor there and focus more on research rather than a mixture of research and service, but still very much interested and still very much involved in public health collaborations, especially in working with public health to improve data sharing and also to improve collaborative data analysis and so on and some of that messaging will come across in our series of lectures in this workshop. So that's a bit of introduction of myself and I will begin the introductory lecture of this workshop. The purpose of the introductory lecture really is to provide a bit of a common background and a bit of level playing field for everyone in the workshop so some of you may find a material quite redundant when you've heard about it already, or maybe you're even more of an expert than me in some of the material covered. And if that's the case, do feel free to contribute in Slack and adding to the material about your own experience with your own knowledge. I think we very much welcome, you know, sharing of knowledges for those of you who might have less background in the area. Hopefully the lecture is accessible, but if it's not, again, please do feel free to post any clarification questions on Slack and the TAs and other instructors and myself will attempt to answer any questions you might have. Okay, so as I mentioned already, I'm at Simon Fraser University and I run a group called Center for Infectious Disease Genomic and One Health. I mean, I already talked about the course overview, but I thought I would post the course overview from 2017. This is not in your slide deck, but I just added it sort of as a contrast to the material that we're doing today. And in 2017, this of course was pre-pandemic was when this workshop was first offered. And you can see that a lot of the material still very much in common, but you can also see that we really only focus on bacterial genomic analysis and not much on viruses. And this is, as you'll see later that because pre-pandemics, the most active area of genomic epidemiology was focused on food-borne bacterial pathogen research. So a lot of our collective experience and also our examples were drawn from that area. So we sort of talked about the phylogenetic analysis, molecular subtyping of bacterial virus, bacterial genomes. And then we of course still have an antimicrobial resistant section. But what we changed out a little bit, what we actually add to is the phylogenographic section. Now we sort of rebranded more phylogenomics and more with a viral and more integrated approach to add non-sequence and non-microbial. My non-evolutionary phylogenetic data to the analysis. And then we also incorporate data visualization more as an overarching theme throughout all the modules rather than its own section. This is, as Nya already presented, the updated module with a lot more focuses on viruses and also adding environmental microbiology aspect to the workshop. And we expanded the number of modules and it's a three days, now it's a four day virtual workshop. I should also know that Samira Baraka from Sunnybrook will be our keynote speaker and I was late in asking her for a title. That's why it hasn't been decided, but she'll be talking about her experience during the pandemic. And Samira is actually once a workshop participant as well. So this is nice to have her coming back to give this keynote. Sorry, I forgot to advance my slides. So the general learning objectives for the whole workshop is to understand how genomic epidemiology can improve clinical and public health microbiology. And also to process genomic sequence data using various bioinformatics tools for bacterial and viral genomes and metagenomes as well. And also to interpret genomic data in epidemiological context and to understand the importance of data standardization and sharing. And actually that's another module that we instead of embedding in just in passing, we pulled it out and made it its own module this time around to highlight the importance of that. We also performed several types of genomic epidemiology analysis as part of your lab sessions, and you will hopefully throughout the workshop throughout the interaction recognize the limitations and challenges associated with genomic epidemiology analysis. This is very much still an evolving field with new methods and new techniques being developed. Specifically, the learning objective for this module is to understand why infectious disease research is important and be familiar with some examples of genomic epidemiology studies. I think the importance of infectious disease research probably doesn't need to be highlighted after the collecting collective experience we've been through. But it may also not be surprising that we are as a society quite forgetful and often post pandemic. A lot of the good intentions get drawn out by other priorities. So something to keep in mind that we should leverage the collective efforts have been put into fight this pandemic and then make sure the lesson learned are not forgotten or the efforts are ignored. And so we also will be familiar with some sequence data processing. I'll give a very, very, very high level overview of how we process genomic sequence data. So you know the data that you're receiving how they were generated and then to understand the challenges associated with sharing genomic epidemiology data, which would actually be further expanded upon in module three. Emma's section. So I want to start with some examples of genomic epidemiology studies so as we all we know we all live in an increasing interconnected world with in this case so many of you from different time zones different areas around the world. So the picture here shows the flight path of commercial air travel and we know that pathogen often travels with with with its human or animal or other hosts and can quickly transport throughout the world. So it's also interesting to show these two figures side by side. They're just a month apart showing the. This is the satellite picture of the airplanes in that's actually in the air. And this was not just the flight path anymore and you could see that, you know, after the pandemic was declared the number of international travels and what even domestic travels reduce significantly so the for example, travel between Europe and and North America or between Asia and Europe, you can see that it reduced significantly and not to mention to Australia and even as well. So, case to point about pathogens can travel with with human passengers here is a study. It's quite old from 2015 but I still like it a lot it's a study by the Danish group that look at microbes that I found in the airplane toilets. They so they fill out filter out the microbes from the human way ways that are collected from 18 different flights and that traveled across three different continents and then they looked at what what the microbiome profile looks like in the samples. So they cluster the samples based on the microbiome profile and then they also look at the presence of antimicrobial resistant genes in the samples. So we found that this the samples in the cluster based on geographic locations, as you can see in the the tree on the on the left and see that the North American ones on the left Asia in the middle and so on so again North American on the right so it shows that the microbiome profiles could actually be used to differentiate the origin of the the the flights. Moreover, they also highlighted that there is a higher proportion of antibiotic resistant genes found in flies that originated from Southeast Asia. So that the study highlight that am our genes could spread quickly around the world three global through global travel travelers, and you'll learn more about am are in a MG antimicrobial resistant AR genes or antimicrobial resistant genes in module six and how these can be identified and characterized. Next, I want to highlight the study that look at emerging infectious diseases. So emerging infectious disease events were defined as the detection of newly evolved strains of a pathogen so for example a new variant of coronavirus SARS-CoV-2, but not the reemergence of a known pathogen or known strain in this so that's their definition and I looked at it over the last six decades and they notice that there's an increasing trend over the decades as you can see here on the graph all the on the on the graph here all the number of emerging infectious disease events increase over the decades and then further they looked at different sub categories of EIDs and they for example notice that the number of drug resistant versus non drug resistant cases also increase over the decades. Similar the vector born versus non vector born, which is the vector born's white also increase over the and about two third of the emerging cases are so called zoonotic so these are the white so the basically the non black so why orange or red and highlighting the importance of a one health approach to understand emerging infectious diseases as these events seem to be dominated by zoonotic diseases. Okay, so next we'll look at this is almost a decade ago now the Ebola outbreak in in West Africa in 2014 or 2013. So it highlighted the global interventions using genomic epidemiology approaches to understand the transmission and the spread of this virus. This is the most deadly Ebola outbreak in history resulted in 20 more than 28,000 reported cases and 11,000 more than 11,000 deaths. It has a significant impact on global travel and even though, and at that time I was at BCCC even though there wasn't any case in Canada, all the public health agencies were under high alert and had to conduct training and preparedness tasks in case that the case and uplending in Canada, and I think other countries went through similar exercises, this a precaution. So the Ebola genomes on approximately 5% of the cases were eventually sequenced in from from this outbreak and this result in the wealth of information so this study which highlighted some link down here. Look at the early samples that were sequenced and in the analysis revealed that the outbreak believe to actually start with a single human exposure to a natural reservoir and not a repeat exposure doing this particular outbreak. And also the outbreak was then sustained by human to human transmission from Guinea to Sierra Leone, and it's likely to be from a single event but with two distinct strains transmitted in parallel. So they were able to, as you can see here, identify separate clusters doing using genomic sequence data. And these transmission were likely sustained through, as I mentioned, human to human and the widespread of the transmission was likely results of lack of proper quarantine facilities in the early stages of the outbreak. And the phylogenetic analysis also show that the transmission from Guinea to Sierra Leone, as I mentioned is from likely from a single event so the phylogenetic analysis has the ability to really tease out based on the genetic diversity or genetic variations the likely transmission scenario. But although epidemiological, in other words, contextual evidence is needed to collaborate on the genetic evidence. So the phylogenetic analysis combined with epidemiological investigations helped to unravel the complex transmission dynamics and provide healthcare workers. The knowledge or the information to institute effective policies and interventions. But as I was saying, there's still unfortunately a huge delay at the beginning resulted in an unacceptable mortality in this outbreak. So fast forward to 2018, there was another outbreak in DRC. And because this time around the DRC's, the practitioners are much more prepared than have experienced dealing with outbreaks. And also globally, there's a faster mobilization of resources. And I understand, of course, even though it's incrementally better than previous experience though, I mean, a lot of the mobilization efforts is still challenging, but nevertheless, WHO and World Bank have set up standing emergency fund to deal with these emergencies. And also, there was stockpiling of vaccines to try to stamp the onward transmission of the virus. And of course, drugs were developed during the first, during the last, I should say the Ebola outbreak and were made available for subsequent outbreaks. Just like what we're doing with the vaccine development and drug development in our, in the COVID-19 outbreak. So they also were able to engage globally or outside healthcare workers faster and be able to put the health interventions in earlier. Now, so the next outbreak that I want to highlight is the Zika outbreak. So unlike Ebola, of course, Zika is Zika virus causes much milder symptom for most people and have been endemic in Asia and in Africa for many decades before they cause an outbreak in the more naive population, or naive to the virus population in the Americas. And because the population in the Americas were naive to this virus, it causes a lot more severe cases in the newly exposed populations. So the outbreak resulted in a few thousand micro syphilis cases, syphilis cases, I mean, like, and this is likely, again, due to the populations not being, having immunity to the, to the virus. And because the symptom of Zika infection overlapped with other fluffy viruses, such as dengue and other surveillance efforts based on symptoms alone is not sufficient. So laboratory tests based on serology and molecular tests such as genomics and others were needed to for confirmation. Yes, Andrew. Will, we're still seeing the Ebola slide. Oh, sorry. I kept forgetting to advance slides. Yeah, thanks. Just forgot to advance that one. Yeah, so the depicted slides actually just depicting some of the patterns that was detected using genomics information. So the phylogenetic reconstruction of the case suggests that the viruses has circulated in South America. For at least one years prior to it being noticed in an outbreak, as I mentioned the symptoms of coin mild and overlap with other known viruses. So the data was, the state I was used to reconstruct the transmission route as shown in this diagram in this picture on the right and the gap in surveillance efforts. Because the viruses is not known to the population, or at least not not keenly aware by the population affected the surveillance effort. Right. So genomic based surveillance. On the other hand, go moving into the future will reduce such a gap in and allow potential new viruses to be detected as well because genomic based approaches much more agnostic to the pathogen. Okay, so the, the next case I wanted to highlight is related to avian influenza viruses. And this is a study that in collaboration with BC CDC was the BC animal health center. And the CFIA Canadian food inspection agency and few other partners, we conducted a study to see if we could detect avian foods from environmental samples. So, as many of you know, avian influenza travels with their bird host, and because these migratory birds has a wide range and their flyways often cost with each other. And this resulted in opportunities for different strains of influenza viruses to commingo and to to reassort right we are reassort their genomes and a new variant that could therefore rise from this mixing of virus populations. So in 2014, there was a. Oops. There's there was a North American and that's a global outbreak of H5 and to rain that initially come in as H5 and one I believe and then and in Fraser Valley of BC, a large number of farms were affected result in a quarter million of birds that were destroyed in the process. And as the bird travel from Alaska down to West Coast and into the United States. US actually was also affected by this outbreak and it resulted in about $3 billion of damage in North in United States and about 300 million damages in Canada. So we're engaged to see if we could have a better approach to do avian influenza surveillance. Because that's because the bird based testing was actually quite ineffective.  Sorry, I guess there's a timer on this slide so it keeps working itself. I apologize for that. So the overall positive rate from these existing surveillance is less than 1%. In other words lesson one out of 100 samples tested will be positive. And as a result of that the presence of high pathogenicity avian flows that resulted in the outbreaks evaded the detection process the surveillance process. So we took a different approach we essentially went into the wetlands where these birds were residing or and and then we collected mud from this environment that contains the birds species, which then contain these viruses and then we through rounds of amplification, then attempt to detect the viral RNAs, which then translate or transcribe to DNA and in from there we use sequencing to identify the subtype of viruses present. And this resulted in a much higher positivity rate and roughly 30% of our samples were tested positive of course we tested high in the farm samples or has much more highly positive as expected, but even in the environments we were able to have a fairly high positivity rate. And more importantly, as a tree pointed out here the samples we collected actually then show the virus strains that cluster together with the outbreak strain of the virus, suggesting that our approach does can be used to identify the specific strain of the viruses that cause outbreaks. And last little bit I will last example I'll highlight is that to illustrate why genomic sequencing is important. So many amr genes are encoded in mobile genetic elements and therefore can move independently of the host core genomic material. So through the process called horizontal gene transfer rather than clonal expansion. So detecting the genes by PCR, if you just focus on the subset of genes marker genes or if you focus on this identification genes alone is insufficient to understand and characterize the antimicrobial resistant profile of the organism and to understand the transmission of these ARGs, these genes. So here's a study that showed that the amr profile as shown in the he-map on the right is actually quite different from the phylogenetic tree that's built based on MLST patterns. So you'll learn more about MLST, the corginal MLSTs in Ed's lecture tomorrow. So stay tuned for that. But what I want to point out is that the core phylogeny of this bacteria actually are not consistent with the antimicrobial resistant genes that they carry. So you can see some of the ones that cluster together phylogenetically actually have different ARGs. So you can see the patterns on these he-maps are quite different. Okay. All right. So I will now just, that was some examples of using genomic epidemiology just in various applications. But I will now move more towards the process itself. So the, as I mentioned, whole genome sequencing of foodborne pathogens was the name of the game at the beginning of genomic epidemiology, partly because there's a lot of global efforts to use genomics sequencing to study foodborne pathogens. So, for example, the UK public health England, which is now called something else, have star sequencing all summoner isolates in the UK since 2014. And US FDA and also CDC also created a distributed network of labs to utilize whole genome sequencing for foodborne pathogen tracking and identification. So they call this system genome tracker. This result in a large number of genomes coming available publicly, and that could be useful analysis. So one study I want to highlight is actually one that was done by Jimmy, one of my students and also TA in this workshop. And we really benefit from the availability of these genomes. And so he took all the publicly available genome and compared the serotypes of Salmonella to the phylogenetic tree that were constructed using genomic sequences. And again, you'll learn how to do that later in this workshop. So on the this minimum spending tree with a clustering tree on the watch, this is a neighbor joining tree, but it's shown us a clustering pattern. Essentially, what I want to highlight is that trees are labeled with serotypes, but the tree, the clustering patterns will determine phylogenetic distance. And you can see that in most cases, they do correspond to each other, the serotype, the names, right, new port or interior this do correspond to the sequence based phylogenetic analysis. But there are some exceptions where if when you see the colors mixing in, that means there's two serotypes that are in the same cluster. Well, when you see same colors in different clusters, that means that the same serotype is subdivided into several distinct clusters. But in some cases means that the name and phylogenetic analysis, the serotype and the phylogenetic analysis are inconsistent. And what we were able to just make sure is that indeed most of the, so on the right here, the X axis shows the number, a threshold. So what's the cutoff that we use to cluster these genomes? And on the Y axis, the number of clusters that zero vars, I should say, that either have their, that either fall into one cluster or to multiple clusters. So not monophilic versus non-monophilic. So you can see that when you have a very stringent cutoff, right, so the organisms are more similar to each other, the serial raw information is concordant with the biologic information in the, but as you increase the cutoff used, then you see more and more serial groups fall into the same cluster as you, as you would expect. And then as I mentioned, some of these then correspond to cases where you have polyphylidic structure for the serial vars. Now we end with a bit of the COVID related topics. Of course, COVID is near and dear to all our hearts after a significant effect our life for the last three years. But genomics really have been the hero of COVID-19 pandemics, because this is actually the first time we were able to deploy genomic epidemiology in almost real time to study an infectious disease outbreak. So the sequencing of SARS COVID genomes can tell us how the viruses spread regionally, preventionally, nationally and internationally. In other words, we can track transmission to the viruses. We also can use it for outbreak investigation as I mentioned previously for, by looking at the clustering patterns and by looking at comparing the biogenetic results with the epidemiological evidence. And however, the other advantage of having the sequences is that as the virus is involved, your detection methods such as PCR can fail, right? So many of you might have heard of primer dropout where the old, the primer that would, the primer that would design based on the sequences no longer work on the mutated sequence because it doesn't, you know, as well. And therefore regions of the genomes would not be amplified if there's, if the primer regions contain mutations. It could also allow us to reliably characterize the different variants and systematically look at how the mutations evolve over time. There are many, many studies looking at these type of mutation to functional variations. And the studies, of course, informs effective measures in health care and in public health. So many, there are many national international efforts at the early stage of the pandemic and all throughout the pandemic to try to implement genomic epidemiology to study this outbreak and to, in response to this outbreak, I should say. In Canada, this is highlighted by the Canadian COVID-19 genomics network. And it was established in March 2020 at the early stage of the pandemic was an initial investment of $40 million from the federal government and $20 million went into viral genomic sequencing and $20 million went into human host genome sequencing of the infected individuals. So this is a large consortium driven approach with partners from national, provincial and public health laboratories, hospital laboratories and other research institutions. And there's also large scale genomic sequencing centers involved industry partners and other academic labs and researchers from different institutions. So the goal was to coordinate SARS-CoV-2 and host genomic sequencing efforts. Our initial goal was actually just to sequence 150,000 viral genomes and 10,000 human genomes. And as you'll see later we, at least for the viral genome went way over that. And the integration of sequence data need to then be coupled with the contextual information and because there's large number of groups involved that requires to harmonize the data collected across various agencies. So that was the effort that Emma will describe more later. And also the key here is to work together. So heavy emphasis and facilitating data sharing nationally and internationally. And most important is to, as I mentioned, not to have all these efforts went to waste and have capacity that built in at the right places to prevent future pandemics for future. We cannot prevent pandemics, but we cannot prevent outbreaks, but hopefully at least prevent future pandemics from happening and do better pandemic preparedness. Okay, so this is just to show that this is a global, sorry, a national effort, the KENCOGEN, and to date actually more than half a million viral genomes were sequenced in Canada with both KENCOGEN funding and actually a lot of provincial and federal additional investment in generating the data. And all the data, of course, need to go somewhere to be utilized. So there was a virus seed data portal set up, led by McGill and Ontario Institute Cancer Research to provide the genomic information and the associated metadata to researchers and these are publicly available resources. Okay, now, so genomic epidemiology, you'll hear about this term, you know, many, many times throughout this workshop, and you'll get further sort of refined definition for this term. But for now, I'll just give a very high level definition, and I would characterize it as a combination of whole genome sequencing data from pathogens with epidemiological investigations to track the spread of infectious disease. So the epidemiological information provided the contextual evidence for this genomic data and the genomic data provided diagnostic information to support the epidemiological evidence. And this is a very different from a traditional clinical microbiology laboratory approach where different tests were used with different organisms, and they have different turnaround time they have different equipment needs they have different person now needs to, for example, reading a microscope, not a ton of equipment just reading a microscope is quite to characterize the morphology of a pathogen is quite an expert you need quite a bit of expertise to do that and it's not something you will just be able to do with a few days of training. So, so we want to replace a large number of, well, at least complement a large number of laboratory testing with a more consolidated approach using whole genome sequence based workflow. So the workflow is in a very high level simple view essentially involves collecting of DNA samples and sequencing the set samples and to generate the sequences that in process using boundary tools, which then lead to diagnostic with report prevent preventive measures where even new drugs being developed. This then course provides interventions to particular disease or the benefit of the the approach is that it really simplifies the workflow need and it has much faster turnaround time than some applications. It's also cost saving by reducing the number of platforms and instrument needed and sequencing has become such a commodity that a lot of the know house is available in the community, and the results of, in other words, the sequences are also more comparable insurable than other test result types. So then the, the sequence data can also be useful value added analysis such as pathogen evolution analysis as I shown before MR predictions reception before and transmission and dynamic modeling which you will see more in the subsequent sections. It does have some challenges though this approach that it results in the results are harder to process and to interpret it because the volume of the data involved. And this is, I guess, why we're all here to learn about the process, but also it requires more computational resources to support these type of data processing and analysis and to do this, if you don't have the adequate infrastructure could be quite challenging. It also is a rapidly changing technology, the technologies involved are rapidly changing so it's keeping up with the technology. On itself requires a lot of our R&D work in itself requires a lot of R&D work, and this is why collaboration between practitioners and research can really benefit the process. So the per sample cost is still higher than some of the traditional tests, but this could be is being reduced further as we start batching large number of samples and start streamline some of the operations. So briefly about high throughput sequencing so next gen sequencing and third generation sequencing and collectively calling high throughput sequencing and sequence data have many clinical and public health laboratory utilities. This is some of them here that you will actually learn more about throughout the workshop. The data, as I mentioned, could also be used for understanding pathogen evolution and understanding the characteristics of these pathogens, which you cannot do if you're just looking at the market gene, for example. So there are several sequencing platforms on the market. The most popular ones I would say are the bottom three for now, the Ilumna sequencers, the Nine and Four sequencers are probably by far the dominant technologies. The PacBio and IonTorrent called gene studios are still used by places, especially gene studios seem to find its way into diagnostic facilities given the streamlined workflow used. The costs of for sequencing have decreased drastically over the years and this fairly recent study actually highlights some of the characteristics associated with each of the platforms. And the cost, for example, the cost per million reads or the cost per million, in this case, billion basis and so on. They also highlight the runtime needed and the throughput and so on. So this is a useful reference to have. Last I want to highlight, it also mentioned the read accuracies and the re-lens and the read accuracy of these two columns here, the read accuracy of the different instruments. So just want to briefly mention the shore versus long re-sequencing and you can you'll see some of these mentioned in subsequent lectures. So shore reads, as exemplified by Ilumna sequencing, are much cheaper per base, but the re-lens is only a few hundred base pairs, typically in the low hundreds, so one to three hundred base pairs. Their higher capacity throughput instruments in the in the Ilumna family of sequencers, they're also much more accurate than the long re-sequencing. So the per base error rate is less than, it's less than point one percent. However, the reads are consensus reads, so they're of many molecules rather than a single molecule. The long read technologies, on the other hand, are more expensive per base and their lower capacity throughput machines. And also, because they're typically reading from a single molecule, their accuracy is low, also lower than shore reads. But the typical re-lens is at least a few thousand base pairs to tens of hundreds of thousand base pairs and there's actually competition to see who can get the longest read possible out of the Minaya sequencer. But because of the, well, actually I'll get to that shortly, but we'll first want to characterize the pathogen genomes. So bacterial genomes typically contain a single circular chromosome, some are linear, but mostly circular chromosome, but also only a single copy, so they're haploid genomes. They may contain extra chromosomal DNAs called plasmids, and the genome size typically range from half a megabase to roughly 10 megabases. There's some large ones being discovered more recently, but when we talked about pathogens, the average is actually about three to 500 megabases and roughly correspond to 3,000 to 5,000 genes. Viruses are much more diverse. They can be DNA or RNA. They could be single-stranded, double-stranded, and they're classified into seven high-level families. Their size range from one to two kb's to one to two megabases, again, some large viruses are being discovered, and they depend on host cellular mechanisms to replicate, so that's why their genomes are much smaller. There are also eukaryotic parasites such as fungal, protist, and worms. There are usually a few 100 megabases or a few, I was missing a word there, but basically a few 100 megabases in genome size, and there are usually multiple chromosomes. And these genomes are constantly evolved through different evolutionary forces, so the genomes can undergo deletions, reducing the genomes, often increase the fitness if the organism is in a specialized niche. They can only infect a certain type of host or become an endogenic pathogen for certain hosts. The genomes are also undergo rearrangements, and this could of course affect the expression of genes when the genomes are arranged. And same thing with gene duplications, the genes could duplicate and could lead to selective loss of the copy of the genes, but new functions can also evolve when you have gene duplications. So, very different from the predominant mode of eukaryotic transmission, which is typically sexually reproduction within the species, bacteria through horizontal gene transfer could actually acquire genes from a wide range of non-parental organisms and other species or other strains. And therefore, its ability to rapidly change its genome composition is quite remarkable. So briefly, I would just want to mention a few terms, and I think Fiona will go over this a bit more as well. So homology means similarity due to shared common ancestry. So it's a yes or no characteristics, right? We don't talk about degree of homology, we talk about degrees of similarity. So you either share the same ancestor or you do not. So just keep in mind when you think about homology, it's yes or no, not degrees of differences. And within the homologous genes, in other words, genes that have the same ancestry, you have orthologs that arise due to species. And paralogs that arise due to gene duplication. And xenologs that arise due to horizontal gene transfer. So there is no homology because they don't share the same ancestor. Okay, so now the process involved in Ho Chi Nong's shotgun sequence analysis as follows. So you first have your DNA isolated, and then sequenced in the, sorry, the DNA, if it's from an isolate, you first would culture it, and then you will share the DNA, attract the DNA, share the DNA. You might end up only selecting certain targeted region through PCR amplification for sequencing, and then you put it on the sequencer followed by analysis. From microbiome hyper studies, you of course bypass the cultural step and you go straight to go straight to amplification followed by sequencing. Okay, so the sequence data analysis essentially involves trying to piece together millions of billions of overlapping reads. And and assemble them, we're putting them together for subsequent analysis. Or alternatively, you will process them as reads and then use them for analysis, but not again will be discussed later. So as I mentioned, there's the steps are assemble your reads into contents or back into the genome, and then annotate the sequences to have functional information and location of the genes determined, and then you would then carry out variant analysis, and that should say module five rather than module three. Okay, now the genome assembly process, there's two different flavors. One is the noble assembly where you compute algorithm essentially try to identify overlapping sequence and merge them together. There's also reference assist assembly. Sometimes people refer them as mapping that will map your sequences to existing related genome sequences. So the assemble qualities assembly qualities and therefore affected by the reference genome use if your reference genome is very different from your own genome, then the assembly quality will be lower because the mapping process it will not be as accurate. And there are actually dedicated lecture for this and you can look up if you're interested in. So the main point that I would like to mention out of this discussion is to say why the long reads are beneficial. So why do we in my career genomics sequencing often prefer to have longer reads rather than shorter reads and that's because in the genomes they're often repeat elements in. And if you have short reads, then that does not spend the entire repeat as shown in the blue. So each you can think of each of this as a repeat sequence and if you think the darker blue is the short reads that you could see that they don't spend the entire repeats and the sort of result of that. They don't resolve the repeat properly and often can lead to misassemblies. So for example, only recognizing two distinct repeats as opposed to six up here. On the other hand, if you have long reads as depicted in these long blue reads, then your long reads can be longer than the repeat sequences. I'm hoping you can see my mouse cursor. And as a result, the long reads because it spans the whole repeats will have less trouble putting recognizing that there's this long repeat in the genome and therefore assemble the genome correctly. So the novel assembly of short re sequences that contain often have trouble spanning the repetitive regions is the message that want to highlight here. As I mentioned the different sequencers have different error rate without going to the details just want to say that the third generation, such as me and I on the pack bio usually have a much higher error rate. And that requires extensive error correction or consensus based error correction. The next gen sequencers such as the Luna on the other hand have much lower error rate. And this ability for long reads to close the gaps in the genome or to span regions that otherwise the short read cannot successfully spend usually resulting more more complete genomes with fewer gaps in them. So contact just means contiguous sequences and your complete genomes ideally would be a single contact that's been the entire chromosome of the genome, and a number of extra chromosomal elements such as placements in its own separate contents, but often we don't see that. Okay, so the annotation process is the process of assigning functions and gene locations to the sequences. And again, we won't be covering this in the lecture in the workshop this this time, but it's just for you to familiar with some of these terminology. Okay, so I'll skip over this actually for now. And just so to highlight there are automated systems and because this is process that have been more or less automated. That's why you can just take the results from these automated annotation and carry on with your work. And there are some caveats, but it's not something we will grow on too deeply in this workshop. And for the sake of time, I will just say that a lot of the work that we're doing essentially fall under the umbrella of comparative genomics essentially we're trying to identify variations in the genome and use those variations to link to epidemiology, epidemiological evidence. So the type of variations could be regional, could be gene by gene, or could be single nucleotide, and you will see both the gene by gene method and the single nucleotide method being discussed in the workshop. Okay, skip that. And then I want to introduce the idea of a pan genome so compare the genomics resulted in the pan genome concept being proposed in 2005. And this was the realization that when you look at several strains of within a single species of bacteria. So you can see that some of the genes are shared and these are called the core genome, and they're typically correspond to housekeeping genes that are important for the survival of the organism. And you also will see strength specific accessory genes that correspond to lifestyle or adaptation type of genes. And the genome calculation essentially give you a sense whether a particular species have an open or closed pan genome or closed pan genome means that there's a somewhat limit number of new genes that you expect to see when you sequence more of a given organism, given species, I should say, an open pan genome such as E. coli, on the other hand, the more strains you sequence, the more new genes you're going to discover. Okay. And yes, so the last little bit is actually just touch base on while we will cover more in depth in module three. So this to highlight one of the ongoing efforts called Eric that were integrated rapid infectious disease analysis platform or that was developed by the National Microbiology Laboratory in Gary's group and and this collaboration with Gary Fiona and actually Andrew and almost everyone that's in this and this is actually when we've how we first got together and eventually proposed the workshop. And it's to build the tools to pop the software platforms needed for doing genomic epidemiology analysis by practitioners so it has simple user interface, so on and so forth. And so mention the partnership. Hey, I'll skip all these and just jump to the end. Some of these will be highlighted. So I would want to highlight one thing to end this lecture which is there is a challenge in data sharing in Canada in that Canadian comprised of 14 distinct healthcare systems at the provincial level and there's no universal standard for data collection we're sharing and also there's no legal binding public health data sharing agreement in Canada. And as a result of that during the early days of the pandemic data sharing in Canada was quite delayed. And as you can see here, the analysis time done by our point show that the delay between sample collection and submission to public repository was quite delayed in Canada and also the type of metadata or the contextual information available for these records is also quite limited. And that prompt some of the efforts by us and others to to try to correct course and by and large we were quite successful in that. So some of the reasons outside of the delay include capacity to process sequence data and metadata for public health laboratory within the public health laboratories to be able to release such data. And there's also multiple sign off needed release and of course there's very the German privacy concerns and that's why these protocols were put in place. And the desire to have only release high quality data was another reason that was delayed so mentioned a few studies led by young jolly's group and my group really tried to take a social science angle to understand the problem so one was focusing more on privacy concerns and the second focusing more on Canadians opinion on this on data sharing and just going to the punchline to say that most Canadians are actually in favor of sharing the identified records and the identify sequence records and related contextual information such as symptom vaccine status of the case age so on and so forth. And so the, the onus then now is on public health and on low makers to try to reflect the willingness to share data but also to do data sharing responsibly. So the idea is that data not been collected may result in a subset of data that can be shared this what we call the minimum contextual data, but still a large number of types could be collected in response to health care needs or research needs and so on. And then mechanisms for more responsive data sharing will need to be put in place to allow us to benefit from all the resources going to put into data collection. Okay, with that, I will thank you for your attention and in my lecture.


Hey there, so this video is just going to show you how to make that link an angel that you're looking for So if you go over to the site that you want to get the link from you want to highlight the link Copy it and then come back here into your course you'll go to add content and then you'll select link and You give the link name, you know CNN article and then here where it says link URL We'll just put in the link there and what I strongly encourage is where it says link target You want to do new window in no banner and once you have that you should be all set you've hit save The link will show up and if you click on it What's going to happen is it's going to show up blank and that's okay What you need to do is come over to this little shield, especially if you're using Firefox or if you're using Chrome You'll click on the shield you will disable protection and The article will show up now there is one catch if you're using a YouTube video This is where it gets a little bit more tricky And so if you want to do a YouTube video, you're going to add content You're going to add a page and then you're going to go over to the YouTube video and Scroll down to the share area You click on that little share button and this is the link that you'll want to copy So you copy that link You come back into Angel you give the page a title, you know YouTube link In the text area here, you're going to paste the link You're going to highlight it You're going to click on this icon, which is of a little globe and a chain. It's a web link and You're going to paste it right into here. So right where it says URL That's where you're going to paste it and again with target you're going to go to target tab And then under target put in new window So if you click okay, if we click off here, you see that it's an active link and then you're just going to hit save So here again, you can the student will be able to go to the page And then they'll be able to click on this link and it will bring them to a video So that should hopefully clarify how to do that. If you have any more questions, just let me know


we are now building a stock video library free for you freedom family because you asked us to but this is behind the music also free for you and only free for the freedom family the track you're listening to right now tear it down you can download by clicking the link down there in the description below it's part of the music factory project and then we'll tell you all about this piece music factory is all about free music for you that's a hundred percent owned by freedom which means you have no chance of getting monetization issues or copyright strikes it's a hundred percent safe to use and we can make that claim because we own it outright to learn more about the music factory click that i and to hear about this track and how it was composed listen to ben take it away my friend hello freedom family i am benjamin music composer and coordinator and i want to thank you for joining for another music monday the piece you are hearing called tear it down was written by me for the freedom family featuring traditional orchestra and suspenseful guitar effects and heavy brass this piece is attended for suspenseful action sequences it was inspired heavily by haun zimmer's work on the dark night and various similar works by composers like james newton howard it relies on the simplicity and repetition to give you a sense of suspense and oncoming action or turmoil enjoy the piece and after we will discuss some of the mechanics behind it so as you heard this track relies heavily on the use of brass drums and spiccato strings to give you a sense of pulsing excitement percussive sounds from guitars taiko drums and the osnato strings keep the piece driving very hard and the low dynamic brasses keep the track feeling dark and heavy there really is a whole lot to say about this piece it's pretty straightforward and it's great for use in action sequences and trailers another feature of music monday is that we would like to have you the freedom family ask questions to our composers in our next episode we'd like to feature your comments and questions to myself and others what would you like to know about me or the music that i create ask in the comments below and next week we also hope to feature a music by a new composer who has joined us and also give them a brief interview thank you for watching and listening freedom family remember you can download this and every piece created for the music factory catalog in the link in the description don't forget that using our music offers no penalty to you your every new is never and will not ever be affected by using the music in your videos if you'd like to fill out a simple survey click the link in the description to tell us what kind of music you'd like to see us creating for you also if you're a composer be sure to fill out the composer contact form so we can get in touch with you to join our team click that i to partner with freedom and join the freedom family so we can all grow together you get many perks like position music you also get epidemic sound a lot of other access to royalty free videos sponsorships and many things to help you grow just click the links down there in the description below to get involved in our community our forums our discord chat servers meet our graphics team meet our community team all of that on discord and the forums what are you waiting for get started and we will grow together as a family because this is the freedom family you are part of it we are all part of it and we're all growing together to get more george click that big f that will subscribe you to freedom central home of the george show and pewdiepie gave one of you freedom family a big shout out click that video to see the shout out and to see our new 3d sets for you and click that video to see what youtube recommends you watch next


Okay, this is the first in a series on SED. SED is an application that I use regularly. I think a lot of shell scripters use regularly. SED stands for Stream Editor.  There's a lot that can be done with it. And a lot of us, like myself included, use it for the very basics. But I thought it would look a little more into what we normally do and actually look at it just a little bit more than I've thrown out in the past. Before I get started, I want to mention, because someone will complain about this, the title of this video, at the end I have the word bash. It says Linux shell bash. Someone will complain that this has nothing to do with bash, although you use SED within bash. And I'd put that in the title basically because most people who are going to be looking for this video are probably going to be searching for that. And when people come to my site, I want them to be able to search either shell or bash. And I want this video to show up. So that's why I put that in the title for any of my command line videos, even if it's not bash specific. Anyway, here we go. Real quick, I've already created a little text file here called text. And it just has some random stuff I typed in it just for to have me give me something to work with. We got a line says 10 tiny toes. This is that. Five funny zero, one, two, three, and tree twice. Okay. So we're going to look over very basic substitution. We'll get into more advanced stuff in the future, but this is some basic things you may want to know.  We can cat the file into there. In fact, I'm going to quickly copy. No, no, I'm going to leave that. Okay. You can cat out the text file and pipe it into said like so. And then what we can do for substitution, we're going to say substitute forward slash forward slash forward slash. And we're going to give in between the first and second forward slash what we want to replace what string we want to replace and second one, what we're going to replace it with. So for an example, I can say T here and then here I can put an uppercase T because we're going to be replacing the lowercase T's with uppercase T's. If I hit enter at this point, we'll see the lines from the text file, but we have only modified the first T in each line to be capital. You'll notice that the second T and the third T and the other T on that line. It doesn't. So basically at this point, we haven't modified the original file. We've just displayed a difference. So if I cat out the text file again, you can see that nothing has been changed. So we haven't changed anything yet. We're passing it information. So before we move on to making the other T's uppercase, I commonly do this. I cat things into it. I pipe things into it. I should say, and this is good if you're piping the output of another program, but really that's not necessary because what we could do is just at the end of our command here, say the name of the file, and it does the same thing. So the need for piping is not necessary, but is how I commonly do it, just a habit of mine. So I wanted to point that out. So our command right now is said. And inside our quotations here, we're saying we're going to substitute, that's what the S stands for, lowercase T for uppercase T inside this file. Once again, not modifying the file now, just displaying it on the output different. So to make it so that we can change the other T's on the lines other than the first T on each line, we want to change it by putting after our last forward slash here a G, which stands for global, meaning find all the lowercase T's and transform them. So there we go. That's what we've got now. We've got every T is now an uppercase T on every line. Again, we have not modified the actual file yet. If I cat out that file again, you can see we still have all lowercase T's clear the screen. I'm clearing the screen by hitting Ctrl L or you can type clear. So at this point, how do we actually modify that file? Well, we can create a new file by redirecting into it. So we can take the output of this and put it into new.txt or whatever you want to call it. So now I can cat out new.txt and you can see that it's the old file but with the T's replaced. But if I cat out text, you can see that it still has all the lowercase. So we have not modified the original file. If we wanted to modify the original file, what we can do is forget about piping that. We're going to say said and then we got our command here and the file. Well, we want to edit inline. So we're going to say dash I and that's just saying to edit the original file, modify the original file. So now if I hit enter and there's no going back after this, I mean we can always we will reverse it but there's no undo. So make sure you want to do this. Normally to be safe, I usually pipe in a new file and then maybe rename the old file or something just all depending on what I'm doing. But you see we get no output because it wasn't displaying the changes. It was just making the changes. Now I can cat out that original text file and you can see that we have modified it. Of course, in this particular scenario, we can change it back by changing all capital T's to lowercase T's inline because we have our dash I. I'm pretty sure I means inline. That's what I've always said to myself. I'm not sure if I read that somewhere or made that up. But dash I means change it in place in place. Maybe it stands for it. Let's see. So now if I cat out text, you can see we put it back to how it was because we just went through and took all T's all capital T's and made in lowercase T's. Now if we had a file that originally had uppercase T's and lowercase T's and we changed all them, it'd be kind of hard to go back without a lot of script foo because you'd have to know where all the other ones are and if there was no pattern, then you kind of screwed. So if you are to use this dash I, make sure that you really want to change that file or at least make a backup copy if it's an important file. And of course, I'm just using T's in this beginning tutorial just to keep things simple. And you can replace full strings or full lines. So at this point, I'm going to say this replace this with that. And if I hit enter, I'm going to do it. I'm not going to do it in line. I'm going to do it here. I'm just going to display it. I'm removing the dash I. So we're not modifying the original file. I'm going to hit enter. And there we go. We can see now line two, what you say this twice now, this is that now says that is that. Again, I removed the I so we did not modify the original file. So this is our first tutorial. I know this is very basic. This is stuff that we've done in the past. We're going to get into a little more advanced stuff in coming tutorials. But I just wanted to start off with something simple. I thank you for watching. Please visit filmsbychrist.com. That's Chris Decay. There should be a link in the description. Check that out. And I have plenty of videos out there, and more to come in the coming weeks on said so for the next couple of Mondays, because Mondays is kind of a shell tutorials or operating system tutorials dealing with Linux. And we're going to be looking at said in depth over the next couple of weeks. Again, thank you for watching. Visit my site and I hope that you have a great day.