 So welcome everyone if you're watching this on YouTube or if you're watching this directly on Twitch We're just having a discussion about coffee and coffee brands. So Don't read chat. There's a lot of people that are spewing their favorite coffee brands all over chat, but that's okay Good so like I said during the introduction which wasn't recorded or at least during waiting for the stream Is that today? We will be talking about one of the subjects that I like the most So we will be talking about QTL mapping So quantitative trade locus mapping and we will be talking about correlated trade locus mapping No one ever heard about correlated trade locus mapping Because correlated trade locus mapping is a method that I developed during my PhD So I love talking about it, but it's not a very well Used method or a very well known method for that fact because I'm very bad at marketing but Anyway, that doesn't matter. So quantitative trade locus mapping is a very common strategy was developed in like the 1980s And it's the best way to associate phenotypic variation with regions of the genome So let me show you guys the overview for today so the overview for today is first I want to talk a little bit more about phenotypes and phenotypes in relationship to heritability right because we already talked about phenotypes We had a whole lecture about phenotypes But I just wanted to recap some things and then talk about phenotypes and their heritability or their relationship to heritability And then the next part will be quantitative trade locus mapping. So a QTL Which is a region of the genome, which is associated with a phenotype And besides that I want to Introduce to you guys different crosses so different types of experimental crosses that you can make So that you can do QTL mapping. We will talk about effect size likelihood And of course if you talk about QTL mapping, you always have to talk about genome-wide association as well Because it's more or less the same thing But of course there are some differences. So during the lecture I will show you what the overlap between the two methods is and what the differences are and Then of course, we will talk a little bit about fine mapping of QTL There will be a question for you guys in chat So pay attention because there will be an impromptu question where I hope that you guys will answer me And of course after that I put a whole presentation about CTL mapping. Okay, so that is really annoying One drive. Why are you making sounds while I'm streaming that should not happen. Anyway So that's the overview for today. So I'm really excited. So let's just jump into it and by jumping into it I mean the answers to the previous assignments like last week We had the whole our introduction lecture and we didn't have time to do the answers to the previous assignments And since I do want you guys to know what the answers are and how to solve them Let's go to the assignment. So these are not the previous assignments, but the previous previous assignments so the assignments for the Metabolites and pathway lecture Good so With that out of the way, let's jump into question number one So I'm going to read question number one. So question number one is about using the metlin database So I actually scrambled this morning to get my password for the metlin database reset I sent two emails and fortunately people were awake and they answered me back And I actually got access to the database again. Otherwise, I couldn't show you the answers, right? So let's Switch to Firefox so that you guys can see the metlin database. So when you log in then it looks like this, right? So it's you need an account Because it's a kind of well, it's not a private database But it's a database for academic use and use by companies and of course companies need to pay for it But if you're an academic you don't have to pay for it. You can use it for free So the first question is we have measured a compound in negative mode Which is a certain mode of the detector so of the mass spec detector and this compound has a mass overcharge of 565.0518 and it was measured with a 15 ppm mass accuracy Good. So now the question is which Compound was measured. Of course, this is only one of these peaks in a mass spectrum, right? So you have a mass spectrum which goes from zero to all the way up to like a thousand sometimes 1500 depending on how Good your detector is and you get all of these peaks in these spectrums, right? So one of these peaks was found at five. Let me just copy it. So it's 565.0518 And it was measured at 15 ppm accuracy. So let's change 30 to 15. It was measured in negative mode And then you get all of these add-ups. I didn't mention the add-ups or the peptides or stuff So we're just going to keep that on the default and then we're just going to go and say search We have detected a nominal behavior from this IP user ID and have temporary blocked access from some period of time Access to this page will resume shortly Like I said, I scrambled this morning to get my account unblocked and apparently they did allow me now to log in But they did block my IP address Yeah Like big woohoo got blocks from the servers that I wanted you guys to use and wanted you guys to see um Yeah, I know what the general restrictions are All right, I will send them another email vpn If I start my vpn here, um, then Well, it's not so much an unexpected event Because I did reset my password twice this morning and then started emailing them saying that well, you send me a temporary new password, but every time I try to log in it doesn't work And I got a mail back saying that well, if you just copy paste the password that's in the email It actually adds two spaces in the front and I was like Why would you do that? So that was the kind of issue that I had But we figured it out, but apparently I reset my password like one too many times All right, so let's forget about the metlin For now I will try it again and otherwise we Just put it on the schedule for next week. This is so silly All right. So the next question was also about metlin. So we can't do that one Either, um, but the next question is then about the Kyoto encyclopedia of genomes So let's go to keg That's not what I wanted. I did want to get the location of the database Unfortunately on keg, you don't have to log in. So You can still get blocked, of course, right? If you do automatic spidering of these things then Yeah, they generally don't like that But uh, yeah Actually, was anyone able to do the metlin? exercise Because I will put the answers to the assignments online so then you guys can see which compound we were looking for But I was just wondering if anyone was able to Make an account log in Not get their ip address blocked and in the meantime was able to search for peaks in a mass spectrum All right, so keg is more or less structured like a book in a library, right? They use kind of the dewy decimal system in a way. Um, at least when you look at the map pathways So, um, so the first question was what is the keg identifier for photosynthesis pathway? So the easiest way is just to say go to pathways, right? And then here you have the Metabolism overview, but here they have a list of all of them, right? So there's a lot of different pathways that they have. So let's just find on page and photosynthesis photosynthesis, so the photosynthesis pathway is actually called m MAP zero zero one nine five, right? So that's just the number that they assign to the photosynthesis pathway We can click on it. Um, and then we can see the pathway in keg And it looks like this. So let me zoom out a little bit so that it fits on the screen So of course the photosynthesis pathway is taking place in the In the chlorophyll of plant cells. Um, so and of course it has different, uh, different Different protein complexes and these protein complexes together Generate energy from sunlight So if we look at the photosynthesis pathway, we can see the reference pathway How many species will not encode the, uh, however many species will not encode the entire pathway Which proteins are missing in the photosynthesis pathway of arabidopsis pali italiana, right? So this is the whole photosynthesis pathway, right? So we see all of the different genes or different proteins of which these different complexes are made up So now when we want to show the photosynthesis pathway for a certain animal, right, then, um We can go and say Change pathway type which opens up a pop-up Unfortunately that you can't see because it doesn't capture the pop-up But when you click the button here, right, um, change pathway type It says open a new window. Um, so it opens up a little window And then you just get a list of all of the different species that are in cag, right? So if we look at the list, the first one is the reference pathway Um, and then the second one on the list is actually arabidopsis paliana that we're interested in So when I click arabidopsis paliana, it, um, reloads the pathway And now you can see that all of these little boxes have a green color when the gene is found in arabidopsis paliana And you see that some of them are not there, right? Because they they they are not not every protein is needed to build these complexes Um, so, yeah, of course, we can now see that uh psb u psb v psb x These are three proteins which generally are considered part of this pathway and are more or less Well, not necessary for the function, but they they have some function in the uh pathway in the photosynthesis pathway But arabidopsis paliana, so this little plant which is called thail crest It does not encode them So which proteins are missing? So let me show you guys the answers that I had Just so that you can see it So here missing in arabidopsis paliana were psb u psb v psb x and a couple of other ones Um, yes, so this allows you to reason about Will it be able to do photosynthesis or not? Of course arabidopsis is a plant so it can do photosynthesis So what we can learn from this is that these proteins are not Necessary to do photosynthesis. They are probably there to either Enhance photosynthesis or they are there to um To kind of fulfill the role when another protein is missing, right? So they had a lot of these pathways, of course, they have backups built into the pathway All right, so now the next question was go back to the reference pathway for photosynthesis All right, we can do that. That's just clicking the back button And then if we click on the cytochrome complex 1.10.9.1 So, um, let me look for that 1.10.9.1 1.10.9.1. Where are you? Where are you? Where are you? Cytochrome complex, let me just search for that cytochrome complex Where are you because you should be in here photosystem 2 cytochrome complex So it actually got a new number again. That is really annoying Uh-huh. So let me click on that. So photosynthesis So what did I? So why did it change the number again? Huh, interesting. It happens sometimes, right? So sometimes like the Dewey decimal system that they use gets updated But this is indeed the cytochrome Oh, this is just one of the subunits, not the whole thing. So where's the whole thing then? Cytochrome pathway, cytochrome complex Oh, that should be okay All right, so it did it did change the number, um, which happens from time to time So now the question was let me look at the question again So if we click on the cytochrome complex, we can see which reaction takes Which reaction it takes part in or catalyzes. So what is this reaction, right? So when we scroll all the way down, we see that we have the name of this enzyme is called plus the we know And then if we scroll down further, it should show us the Let me see. So here you see the reaction, right? So the reaction is also in cag. You can click on it So if we click on reaction, um, then you see actually what it does, right? So you see here the metabolite that is the input of this, um, complex And then the one which is the output, right? So this is the iron subunit So what it does it says that the reaction that it does it takes plus the quinole Plus to oxidize plus the cn2 hydrogen at our two hydrogen or less positively charged hydrogens And then it makes plus the quione Right. So that's what it does. So, um, let me shoot Guys if you're looking if I'm saying that look here, um, Then if you're looking at the notepad window do say like dude, um, we're looking at the wrong screen Because I'm not watching the stream all of the time. So I'm just clicking on the thing So let me do that again for you guys, right? So here we have the complex Unfortunately, the number has changed. So it's not 10 point something anymore But it's still called the cytochrome complex. So if we click on the cytochrome complex, right? We see more information about this complex If we then scroll down, right, then we see the enzyme, right? So all of these different proteins together form a single enzyme And then we can just click here on the reaction. So when we click on the reaction, it gives us the reaction So it gives us the input and then it gives us the output metabolite, right? And of course, um, it uses some of some other things as well, right? So you can see here that the equation is, um, c16693 which stands for plus the quinoa Two times this oxidized plus the cn2 and then two times a standard positively charged hydrogen atom And then it creates plus the quione which has this structural formula Plus two times the reduced plus the cn2 and in total this now Gives you four positively charged hydrogens Right. So, um, if we see, um, in the answers, so that's kind of what I wrote down So the reaction that is, um, that is catalyzed by this by this protein complex Is going from plus the quinoa to plus the quinone And it just has this formula Right. So in every enzyme in keg has this information. So if you want to know, I have this certain protein Which catalyzes a certain process What are the input? What are the outputs? Then all of these things you can track down in keg And of course, this is really useful, especially if in the future you need to do something like bacterial manipulation, right? So if you have a certain bacteria like an E. Coli bacteria and you want to have this E. Coli bacteria produce cocaine for you Or some other substance that you might be interested in Then you can use keg to figure out what the closest compound is to the compound that you want to produce And then you just look at the coca plant see which enzymes they use Take those enzymes put them on a little vector and then put the vectors into your bacteria and then ta-da You have a bacteria like an E. Coli bacteria, which can make cocaine for you Right. So that is the usefulness of keg It allows you to reason on how to make or how to use a biological symptom system to make a certain substance So not saying that you should make bacteria or plants or other things that make Cocaine or other drugs. I'm just saying that if you want to You can use keg to do this, right? So you can just see what is the closest substance that this animal can make And then which Proteins do I need to give to the animal to build up the pathway leading to Whatever you want to make, right? And this is the same thing that people do when they make These big bio reactors and they say well, we want to make this substance. It's really hard to make chemically So we are going to use bacteria or other animals to make these substances All right. So next question. Um, so go back to the reference or that we are, uh Clicking on the reaction itself will bring up the chemical formula. Um, and that that's what we did, right? So the chemical formula, um, let me switch back to firefox. This is the chemical formula that it catalyzes. So relatively easy to figure out All right. So then the next question was, um, if we navigate to the tryptophan biosynthesis pathway and mouse Okay So when you look at this pathway, can you tell if a mouse is able to create tryptophan? So let's just go all the way back to keg, right? Um, so go to keg Then we go to pathways. Um, then we search for tryptophan So we go to tryptophan metabolism Um, of course, this is a massive massive pathway, right? There's there's literally almost a hundred different proteins in here, which all kinds of different reactions So we want to create tryptophan itself and I think unfortunately we cannot just search in here Because this is just a picture, right? So we have to find tryptophan, but fortunately I looked at it before. So here is tryptophan Right. So to create tryptophan, there is only kind of one way of creating tryptophan and that is Following the arrows We have the arrow, which is tryptophan biosynthesis, which then leads to here, which is l tryptophan Which can then be transformed into tryptophan. I don't if I click on here. I should be able to see Okay, so this is just tryptophan. So we want to go to the tryptophan biosynthesis, right? Because we want to know if we can synthesize it. So here tryptophan should be one of the outputs So the outputs are generally in these round boxes where you go to another one So let me see I looked at tryptophan in the previous one, but here Ah here l tryptophan, right? So l tryptophan can be made from indole or it can be made from three indole glycerol phosphate Right because these have arrows. So this protein is able to go and take indole and make l tryptophan This one actually is a reaction which goes both ways. So it's a it's a chemical reaction Which is in in in balance and this enzyme can be used to steer the reaction one way or the other Okay, so let's look at mouse, right? So I'm just going to click the change pathway type again And then I'm going to select mouse, which is called mus musculus And here So if we click on mouse musculus, we see that there's only a couple of enzymes that are encoded in mice So this means that a mouse is definitely not able to synthesize l tryptophan, right? Because it it it doesn't have these two enzymes So the question was can a mouse synthesize tryptophan? No a mouse cannot synthesize its own tryptophan Next question. How about soybeans? Can soybeans make their own tryptophan? So again, we go up we'd say change pathway types Then we go to soybeans. So let me just search for that. So soybean actually is called glycine mux. That's the official And here we see that soybeans Have these two enzymes, right? And they also have the other enzymes in the pathway So probably soybeans can make tryptophan So hey imagine that I am a tryptophan dealer and I want to search for the best animal To make tryptophan for me Then mice are not a good option soybeans are soybeans can make my my tryptophan The question was the next question is and when we look at entrochoccus fecalis Which is a bacteria which comes from human poop and then it's v5-8-3, right? So it's a very specific type of bacteria and that's the nice thing about cac because cac doesn't just have entrochoccus fecalis in there Now it also has a whole bunch of genetically modified organisms in there, right? So entrochoccus fecalis v5-8-3 is a very is a is a type of entrochoccus fecalis Which has been genetically modified to create create some some substance. So the question is if I can find that Easily because of course, there's literally hundreds of bacterias in there Enterochoccus, so I'm just looking through the whole list of So those are stephalococci The bacillus Enterochoccus, where are you? I'm just going to search for v5-8-3. That seems to be the one that is probably there. All right, so if we switch the pathway, so I just click the button, right? It reloads the pathway then you can see that this entrochoccus fecalis v8-5-8-3 Is having a lot of the pathway encoded It just misses some of them, right? So again this animal this this bacteria is probably not able to make L-tryptophan But you see that if we add 1, 2, 3, 4, 5 proteins it should be able to make it, right? So if we just take these five proteins we encode them on a bacterial vector Transform this little vector into the bacteria, then we could make a bacteria which makes tryptophan Good, so let me see What the answers were Let me see And switch you guys there, right? So the tryptophan biosynthesis mouse can most definitely not make it, right? So glycine mux or soybeans are very probable So i'm never answering yes, right? Because like i'm not a biochemist So hey, i'm not going to say soybeans make tryptophan But here the answer is yes, they most probably will be able to synthesize tryptophan Because you never know if anything upstream of the process is missing or not But at least hey it contains all of the enzymes to make tryptophan from indole Good, and then entrecoccus Also, probably not at least not if have but by adding eight Eight enzymes to this bacteria. We could have a back we could make a bacteria which which encodes this Huge Testosaurus redeemed dig still sketch All right A puffer fish. Oh my god. Oh my god Sure, we will do a puffer fish Do you mind if we first finish the assignments then after that we will make you a nice nice drawing You just have too many points All right, thanks for giving me some time. All right. So, um, let me see the next question Right. So let's go back to keg next question is Navigate to the biosynthesis of plant secondary metabolites So let's go to the main page. We can go to keg again We can go to pathways and then i'm just going to search for secondary Might be the best No, that's other So biosynthesis of secondary metabolites. No, it's biosynthesis of plant secondary metabolites Uh biosynthesis of various various various plant secondary metabolites. So there it is, right? So and just looking at it. So again, you can see that This is like a massive massive pathway, right? Right, there's literally like hundreds and hundreds of enzymes and and the nice thing about this pathway is actually that All of the structural formulas are here Because they are really, um Important when you look at secondary metabolites Okay, so now the question was from which substrate is flavonol produced So again, we have to kind of play this game of search where it is. I think I know where it should be because I'm actually Pretty familiar with this pathway because I did study it in the past. So here we are falling alanine Uh flavonol. I hate this. I hate searching for these things because they're so big that I looked at it this morning quickly So this is the indolay glucosinolate from tryptophan I think it should be in this part of the pathway On the bottom left, I saw it. All right, so left bottom left here flavonol All right Good. So we then have the answer also because here we see flavonol, right and flavonol is produced from flavonol Beacon. Thank you. Yeah on the left side. Yeah found it. So here flavonone is transformed into flavonol and flavonols are actually very important. So, um In plants you have something called, uh flavonoids and flavonoids are these little substances which are In like plants and they are very good for your health and other they have all kinds of other medicinal properties. Um, so There's like hundreds of thousands of these compounds But they all are created first by making the flavonol and then flavonol is then Transformed into all kinds of other substances. So there are all these like flat surfaces which function as a kind of molecular key All right So now the question is is download and save the citrate cycle pathway in humans and save it as a key gml file So that we can use it later in cytoscape. So actually I try to do the live demo at the end, right? Like two weeks ago and I failed horribly But I found actually that I just had a too old version of keg installed to do what I want Um, so citrate cycle pathway. So we just again go to pathways We search for the word citrate citrate cycle and then here we have the pathway, right? And then we can actually say that we want to download the pathway. So downloading the pathway should be um Pathway entry and then uh, here's the map Here's the ortholog table and then we can actually export it as well Where was the export button pathway menu? That's what we are. So that's the citrate cycle uh, show description Hey, where did the download button go so we can highlight all of them Why is there no download button anymore? I hate that they change the website every year There used to be just a button here at the top, which is um download pathway. Let me actually open up the help file Pathway, that's so horrible. They actually remove this whole thing. Oh, that's such a shame That is such a shame This is the pathway, right? Yeah, and then the pathway entry Can I not just download the whole thing? He used to be able to have like a single button download Oh, that's the db get of course, we can use db get to get it, but we don't want that. We just want to have the Let me search if they actually uh removed it Download keg Yeah, so it should still be there markup file is an extension blah blah blah um Okay, so we have to Use not the map, but we have to do the ko Entries so we go back here to the pathway that we were interested in and then we go to pathway menu Yeah, so that's the one that we want. We want to have this one. We go to change pathway types Um, then we have to go to the ko And now it should have a download option, right? So, um, unfortunately, you guys can't see that but when you change Let me actually capture you guys that screen once. Um, just so that you guys can uh see the uh Window capture. All right, that's the window that I want to capture. So the the pop-up looks like this, right? So you have just the uh the map, which is the reference pathway, then you have the The reference pathway when you have the keg only, um, then you have the ec only and then the reaction only So head they are three different ways of looking at the pathway Um, but in this case, I just click on the ko right and when I click on ko Then it does allow me to download the the ko kml file Good. So here we say download kgml And then we say save file and we're just going to save this for later All right, so that was the trick. So the trick is to click on the change pathway type and go from the Kind of map pathway, which is the more or less default pathway to the other one. Um, okay So the next question is about reactom. So let me open up reactom Good. So it's always good to search, right? Like google skills are very very important. Oh, that looks a little bit weird Um, so google skills are very important in bioinformatics like googling stuff is like Well, it's important like in any field. I think that it makes sense to be able to To to figure out if you don't know something just throw it in google and google will tell you what you should do Um, ah, ha ha, let me let me show you guys the answer Download it trick is select either key ko ec or reaction So I did put the little trick in here. So um, yeah, so for the keg pathway Good, so let's go back to firefox. So this is the reactom database very similar to keg It's just more high level, right? So keg really is metabolite enzyme other metabolite But the reactom has a much higher view. So a pathway in the reactom can for example be, um DNA replication right DNA replication, of course involves like very big enzymes Which are made out of hundreds and hundreds of different proteins. Um, and then of course It's not as clear that you have metabolite protein and then the output metabolite All right, so let me read you guys the question if I can find the window actually I can't but Okay, first get familiar with the structure click on a couple of pathways and observe that you can drill down on a pathway by opening A different pathways which your subnetworks in more details. All right So let's just look at the citric cycle pathway, right? Because the the same pathway that we have here Should also be in reactom. Um, so let's just go to reactom and look at the citric pathway, right? So we have citrate which can head so there's three reactions in total So we can just click on one and then it opens up this. Well That's not the best pathway to start off with. Um So This is a very very small pathway. So let's say DNA replication, right? So to have a bigger pathway Okay, so here there's two pathways So if we click around we click on the DNA DNA replication pathway, right? Then you can see here a picture of the pathway Um, and if we click on it here On the image then it actually opens up in the pathway browser. Yeah, so here you see that And it starts zooming in already So here we have the pathway that we were just looking at and of course this is only a sub pathway of a much much bigger Structure, right? So what Keck tries to do? If we then zoom in a little bit, right? Um, then we can see that there's different complexes. There's different Proteins which are involved, right? So you see here that ork one binds and then you have the ork thing and then that that binds cd cdc6 and cdt1 Right, so it gives you the whole kind of DNA replication cycle Which goes round and round and round, right? So if we then are interested in some of the sub pathways And then we can actually just click on them and then hey it goes into this little sub pathway Which is again the assembly of the Pre-replicative complex and then you have the activation of the complex, right? So it it does have the same level of detail as keg if you drill down enough. Um, so let's just Double click here, right? So to zoom in a little bit on this part of the pathway, right? So you see that in this case these two pathways are kind of overlapping So you have the assembly and then the activation and the whole thing is called The replication pre-initiation complex, right? And again, if we really want to know More about it, we can actually click on these links and we get a summary And also here on the side you see that actually sub pathways start opening up Where you get more information. So again a very very useful database All right, so click the search icon Here you can input your own genes of interest search for HALA and project it on the different networks in which pathway is cox 15 active All right, so let's go back to reactom. Here we have the search thing, right? And we search for HALA We say go so we have HALA, HALA clause one, clause two, so we just click the first one just to make sure And then it is located here and we want to Look at one of the pathways, right? It zooms in a lot And then we are here So the question was In which pathway is cox 15 active? So why didn't I just search for cox 15 then that makes more sense to me actually Where is the search button here? I'm having the feeling that I'm not seeing the whole thing because I've I've cut it in a little squidgy screen So let's go back to reactom and just search for cox 15, right? That's probably so cox 15 is a protein And then here we learn that it's located in the mitochondrial and the inner membrane at least it is in humans And then if we look at the pathway, so the question was in which pathway is cox 15 active So cox 15 is active in the metabolism of porifrofins Heme biosynthesis and then then you have the the transformation, right? Can we actually go to this pathway? Not so we could only Can we zoom in on the Let's load the pathway browser. I like the fact that it's just coming at you So here we see the cox 15 gene and this is Involved in the biosynthesis. So what it does it makes from heme O It makes heme a right and if you want more information about what cox 15 actually does Hey, you see here a whole description Um, besides that you can also see if the same thing as in keg Oh, you guys can see that but if you click the button here, it opens up all of the different species So again, just like in keg it allows you to reason if a certain species is able to do it or not But if we just go back and we have we just say the cox 15 then actually the pathway in which it is Located is in the heme biosynthesis pathway, which is the one of the pathways which is Responsible for Synthesizing the heme protein of course the heme protein is one of the main proteins in hemoglobin So it's the one that is able to catch oxygen using iron atoms And of course here you could figure that out by just looking at the gene and looking at the pathway and reading the descriptions in the pathway Good next question So question for rektom is in which pathway is it active? Well, it's active in the heme biosynthesis All right, so download install cytoscape. I hope everyone was able to do that. I also did that So I also have cytoscape open at the moment Um, let me actually capture that window No, I want to capture cytoscape. All right. There's cytoscape Make it visible get rid of firefox get rid of notepad plus plus Move it a little bit bigger so that you guys can actually see what's happening A little bit more and then I'm making it a little bit more so that feels good, right? Okay. So first things first um, so the question was Find the app that will allow you to load keg files and install it then load the citrid acyl cycle pathway that you download From keg into um cytoscape. So cytoscape has kind of an app plugin system, right where you can use multiple apps So when we go to the app manager a window opens up, which I Probably can show you guys Window capture see if it captures the right one. Yeah, so it's This one So right, this is the popup window that opens and then hey, you can see that it has actually an app store Where you can download all kinds of plugins for cytoscape. Um, I have nothing installed because I just installed it But of course, I can just search and I can search for keg, right because that's the one that I wanted to load Why is all of these empty currently installed check for updates. That's also fine Oh I am using a slightly out of date version so it It it doesn't have the app store anymore Um, I did install a newer version of cytoscape though today So I installed which version am I using currently I'm currently using 3.4. That's not what I want. I want to use the 3.9 set escape There are you Okay, so I'd escape 3.9. So let me just close the old version and That's also one of the things that went wrong last time when I wanted to do a live demo Um So starting up Takes a little while. It's a java program java can be really slow in that sense. Um for starting up But once it started up, it's fast enough Righty then there we are I don't want to do that like just go to app manager, right? So now So let's close that one close that one These and then all right. So now when I look at the app manager in cytoscape It looks like this and now I actually have all of the apps that I can Search for right because a lot of people are there Making plugins for cytoscape. Um, so I just want to search. I want to search for keg And then you have your cytok keg or keg scape So find keg pathways. No, I just want to file reader and pathway visualizer for keg xml files right because in keg we downloaded one of these keg xml files So I'm just going to install this one. Um, it takes a little while, but it's generally small, right? So All right, very good. So it's installed Then let me actually capture the main window from cytoscape And when I open up the new version, it kind of looks like this It falls on top of me, which is not the best thing in the world, but it's also not the worst thing in the world So here we see the uh cytoscape, right? So we just installed the plugin. So now when I go to apps I haven't uh, I have a kml reader. So I should be able to now Import my network So Let me see. Where's the uh currently installed App description not found. That's fine So where's my keg scape app? keg scape app I should have installed this beforehand, but Um, let me just try to open it up. It might be that the plugin just detexted So I'm just going to say file open and then I'm going to go to downloads. Um, because that's where I save the kml file So let me see the file. Where are you? Why is this not sorting it in a normal way? I hate java java programs have such a weird way of showing files and folders So sort by date modified Go all the way up All right, open up Has the wrong extension. I already thought that. Where is my kml kml App actually restarted to see if it actually I know there's a whole bunch of updates. That's not the issue So where did the app go? Because generally when you do apps then when you install an app when you click on the app button, it has just an additional um An additional so let me see if there's another Cag reader Yeah, so why? Okay, so I I need to Restall site escape after installing it. So let me close site escape and then restart it just so that it activates the app Something that they actually could have mentioned in the like help file All right, so let's open up the right side escape this time. All right starting up again This might be also the issue. All right, so The app that I downloaded is for site escape 3.8 And I have site escape 3.9 installed and I have site escape 3.4 installed So This is not going to work. So the app just doesn't work under the version that I have installed Why is that? Why is that? Why why does it not? Why? Why computer? Why can't you just work with me a little bit work with me a little bit? All right, so forget about the cac pathway loading. Um, let me actually remove this one and then say properties and Good then close it. All right So that's a shame, but you can use the app plugin But you have to install the right version because that's not the version of the app It's not compatible with the version of cytoscape that I'm currently in that I have installed And of course if you use a version which is too old the app store is not even available um, okay, so says site escape 3.8 or later Yeah, here it says like works with cytoscape 3.8 Which should mean that it actually works with 3.9 as well. Um, but Like let me show you the the window that I'm looking at so here. I'm looking at kekscape, right? So and here it says works with cytoscape 3.8. Um, it's actually very recently released. Um, but it it just It just doesn't seem to do what I what I what I want Because generally you go to the apps right and then for each app that you have installed You have just a button that you can click which opens up the import window um So for some reason, I don't Understand why this doesn't work with my version of cytoscape then Let me see cytoscape 3.9 Because it should work with 3.9, right? That's also the way that That I actually expected it to work because there was an older version for 3.4 Um, but I can't install that anymore because they took offline the whole app store for 3.4 All right, so I'm starting up cytoscape again So just the 3.9 version so that we can actually try this once again See if a reboot of cytoscape actually makes the app work Um, check the window for you guys. So there it is again again too big. It doesn't remember the Size that actually gave it. So let's just puzzle around, right? Okay Good, so now we go to apps App manager currently installed kexcape 0.9.1 App description not found So it does give me an error in the uh in the app window So just for for you guys if I go to apps app manager, um, let me Capture that one right then if uh, let's make this a little bit bigger All right, so when I go here, right then it says that I've currently installed the kexcape But then when I click on it, it says that the app description not found So it it seems to not work that well with the version of cytoscape that I'm using um Let me see if I can just file open up because it might be that it's smart and that it just integrated with the open button instead of having the uh Downloads do a list of details sort by last modified open up the xml file And it still says wrong extension and I can't go to two apps because when I click apps I I don't get the one that I want Anyway, not too important. So probably I just need to downgrade my cytoscape to 3.8 And then it should work because it it seems to be just a little bit of an issue with the uh Um with the version that I'm using so it seems to be a version conflict um Like last time right like last time we also had this little issue with uh with cytoscape because I was using an older version Which didn't load in the file type that I wanted Okay, but now what we did want to do is we want to create our own pathway, right? So let me show you notepad, right? Um, and Don't show you this one. Don't show you guys the firefox and Open up notepad plus plus Right, so here are my answers. So here we made uh, we want to make our own little pathway, right? Because it has this very flexible network definition So last time that we tried this we wanted to say something like oscar loves food Denny loves oscar Right, and then we want to say something like, um, denny loves Anna and then we can have different types of interactions as well. So we can then say for example oscar Hates water Right because he's a cat so he doesn't like water and then we can say water Is wet, right? So it's just a three column structure Um, so we can save it and i'm just going to save this as um On my d drive and i'm just going to say small network dot txt Good. So now let's open up cytoscape and let's open up the version that I know I can use because I Tried it this morning. Um, so that was actually, um This one I think Which is 3.6.1. By now I have like five different versions of cytoscape installed Which is not the correct way of doing it, but the it's a really useful tool It's just that it's very finicky sometimes with the formats that it supports or the apps that are available All right, so it's booting up, um, and then once it's booted up I will show you guys the cytoscape window and then we will try and go and load this little network that I made And it's waiting. It's waiting. It's waiting waiting waiting Like I could do the drawing in the meantime while we're actually waiting for cytoscape to boot up. So it's actually stuck here I hate java programs. All right, just like Yeah, I know that there's some problem with this Plug-in that you have cytoscape. Stop bothering me with it. All right good A newer version of cytoscape is available. No Screw you guys. Like I just installed that version and it didn't work either Window capture two properties Capture the cytoscape Session. All right, so now it even opened up much wider. So I'm totally gone All right, so we made this little network, right? So we have the network where we have different types And we just want to um go through it, right? So let me close the welcome So we have no networks. Um, and now we see that we have the network the style panel, right? Which I was was struggling with last time. Um, that the style panel actually did not Show me or show you guys Did not allow me to show you guys what I wanted to show you guys. So let me actually put it up Better so you can see the whole window So you can guys can see what I'm looking at. All right. So now first things first We want to say import the network, right? So we go file import network file file import No, we go file import table file Right. So then we say our file which is on the d drive go to details Sort by last modified And then here we have my small network So if I do this, right then I think the window capture should capture that Let me see if that works That's Just black. Come on computer. Don't make it so difficult. All right. So then it looks like this, right? So here's the import window that I'm seeing, right? So and then when I do this, I can now say, okay, so this is my, um, um My little file that I created, right? So the first thing that I do is I go to advanced option and say I separated things by spaces, right? So now, um I also can go to advanced options and say I do not have any column names, right? So I just say column one, column two, column three, right? So now we go to column one and then we say that column one is a um is a key I did this changing answer. This is the key Uh, this isn't No, no, no, no, no, no, no, this is not No, this is the wrong one import columns from table. We go file import network from file, right? Then we select the network that we want So again, sort by date modified small network open up All right, so we enter up in the same window, but now it's saying import network from table And now we go advanced options. It is separated by space. I don't want to use the first column name So now it looks like this Right and now I can say column one Is what is the meaning? And you guys can see that again. I hate that it so it's a source node, right? So now where you see here that it got to this little green dot So when I click this button here, it gives me an option to select What is the thing that is in this column? So column one contains the source node column three contains the target node and then column two contains the um, Not the edge attribute, but it contains the interaction type, right? So now I have source node Interaction type target node and now I press okay Right. So now it loaded my network. So now we see that oscar. We have oscar. We have water We have denny we have ana food and wet, right? So those are the different nodes that I defined Now when we go to the style tab now, I can say Based on these attributes Let me zoom out a little bit. So based on for example, the edge attributes, right? Because we have different types of edges We have an edge which is called love We have an edge which is called is and we have an edge which is called hate So now we go to on the bottom here. We go to edge and now I want to say I want to change the line color Where's the line color? Edge arrows to color color unselected All right, so then just do the line type Um stroke color. Yeah, just do this stroke color Okay, so the line type so I now want to say mapping values All right, so we have the default value. Then we have the mapping. So we're going to change the mapping So Why is color unselected? That's so weird. Okay, so but in have we go to the line type we say go to the mapping What mapping do I want to do? Well, I want to take the Interaction column and then the mapping that I want to do is a Discrete mapping right, which means that now I get the option to set The different line types for hate is and love. So let's do that. So let's make hate um, like a contiguous arrow thingy Let's make is a dots And then let's make loves Um An equal dash right. So now you see that based on the type of the edge It starts doing the lines differently So you cannot so it's not only the lines that you can do that you can change But also things like labels and if it has a label, right? So if I want to map the label onto the thing, then I say again So what do I want to do? Well, I click mapping And then I say take the column which is called interaction The mapping type is just pass through Right. So now what it does it takes the label and passes it through to the it takes the the name of the edge And it passes it through as the label of the edge. So now you can see that it says is loves loves loves and hates right And this is how you can structure your networks. Of course, we can also add different attributes, right? So that's the the step that I did wrong at the beginning So now for example, we can add attributes to each of the nodes, right? So here we have a node which is water here We have a node which is called oscar, right? So if we go back to notepad plus plus So let me just hide these networks for a minute and we say we make a new file, right? And now we say oscar Is a animal Right. Um, denny is a human Anna is also a human, right? So now for every Every edge Or for every node, right? So it's node edge node source interaction target So now I have to say something like food, which is off type Organic or something like that, right? So I can just annotate for everything Nobody talks about hoop. Yeah, that's true I didn't put the fish in right like let's keep the network a little bit So water is not organic, but this is a A fluid Right. Now when I save this, I can now save this as node dot attribute Right. So I'm just making a new file saving it as a node dot attribute file Now when I go back to cytoscape, right? So when I go back to cytoscape Denny cyborg. Yeah, you could do something like that as well, right? But you can you can define all of these terms and all of these terms cytoscape can use Right. But now what I can say is I can now go to file. I can go to import I say table from a file, right? And now I select the new table that we have So I just have this node attribute table, right? And now I can say again Advanced options. I say do it by space The first is not the column name So now I can say so the first column I can now say this is the key Right and here we say, okay, so where to input to the network collection node table columns, right? So it's a node table columns and it's not edges Because I want to for each node I want now want to add a property, right? So the property that I want to add is that I want to say that oscar is an animal Denny is a human, Anna is a human, food is organic and water is a fluid, right? So now when I say okay, then now when I click on water, it now has this column two Which says that oh water is a fluid when I click on oscar then it says oh Oscar is an animal Anna is a human and food is organic, right? So now I can go to the node attributes and now I can use these just imported attributes to Change the node, right? If I want to for example, take the fill color and I want to change the fill color I can say well, which column do I want to take? Well, it's called column two because I didn't give it a name I can say the mapping type is again discrete, right? Because I don't want to pass it through But I want to for each Each discrete element in the column. I now want to select a color so I can say well all of the animals that I have I want to mapping value. So I just want to say rainbow colors, right? So now it is signed a color to each of the things which have an attribute, right? So now all of the humans are colored purple all of the organic substances are called red And all of the animals are called a colored green Right and of course wet here, right? It I it didn't have an option in column number two So it doesn't get a it just gets the default value So this is how you can build up your own really nice really colorful networks Using cytoscape and that's the thing what cytoscape really excels at right? And this is just like a little bit of basic introduction Hey, you have many default styles where you can say oh, I want to have like a relatively fancy gradient looking one Or I want to have like a minimal network layout But head the nice thing is is that even using These the standard layouts, right? You can still Color them the way that you want, right? So here if I have this network, which now looks like this, right? And it's relatively fancy and even moving But again, I can say if I want to change the fill color of the nodes, right? So the nodes are the round things I can say do a mapping Use column two The mapping type is discrete and then I'm just going to say Do some rainbow colors in there and then it will start coloring each of these nice nodes with the colors And I can even change the colors, right? So I can just change the the gray color to be anything that I want So I can just say edit and Select something else So it's a it's a really nifty tool to Visualize networks any type of network and you can come up with the network Just remember that you have nodes and edges So the nodes are these little bubbles here The edges are the things that connect two nodes, which is kind of the interaction. So it's object interaction other object And then you can make two additional files one Which for every node gives it additional properties like we just did saying that oscar is an animal Or denny is a human However, we can also do the same thing for the edges, right? So we can say that well Loves has certain properties or hates has certain properties Good, I've been talking for an hour So with this I am going to consider the cytoscape part done And the r-assignments is something that we will leave for next week So unless people really really want me to do the r-assignments as well But I think that we should start the lecture By now since I've been mocking around too long in cytoscape altogether But first but first of course we are going to have a little break So anyone watching here on youtube or if you're watching it on twitch back later I will see you guys in around five to ten minutes The first um Let me go back to the overview slide. So the first break that we have Will be animated gifs of pigs So I will stop the recording. So if you're watching this on youtube see you later if you're watching this on twitch See you later