 Hello, and welcome to this tutorial on trajectory analysis using Python in Galaxy. My name is Wendy Bacon. I am a lecturer at the Open University, as well as a visiting researcher at Emble EVI. I will be doing this tutorial in the Human Cell Atlas. Well, to start with, Human Cell Atlas, use galaxy.eu. Purely because that's my favorite one, because it's the first one I ever used. The Galaxy Notebooks or the Jupyter Notebooks work in many different instances of Galaxy, so you've just got to kind of check if that tool's there or not, and if not, follow on to usegalaxy.org. Usegalaxy.eu can both perform this tutorial. This video is purely if you're struggling to click or find the right perimeter or find which buttons to press to get through the tutorial. Right, onwards we go. I'll start with creating a new tutorial, and then we need to upload some data. So I'm going to copy the links. That's a little bit too zoomed in. And we're going to rename both data sets. That scene is H5AD. Fantastic. And that scene is a Jupyter Notebook. All right, and then we have the issue of the data set. We want to create these lovely trajectories and see how the cells are related to each other. However, it currently has cells that are not related to anything. So the red blood cells, we need to remove them. Come down here, filter. Ops. Pull in. I'm going to set up the next one as well. And we're done, and we can then look within these objects and see hopefully the number has changed. Yes, I guess. I'm going to download that onto my computer. And if you're using the tutorial within Galaxy, so if you're using this, you can just click on the tool button. So remember that's a handy little feature. You don't have to be searching all the time. Okay, we're going to start a fresh Notebook. And this may take a little while, particularly if the server is incredibly busy, but just give it its moment and it'll appear. And it's here. It always does this to me. It's absolutely fine. I don't know why. And then we're going to save it. And now we're going to upload that file, that Notebook that we've downloaded already. Well, hello, old friend. Okay, and this is quite simple. All the code is here. So essentially what you do is you go line by line running it. And this is where you sort of transition from the Galaxy tutorial into a Notebook tutorial where it'll give you lots of lovely information about each thing. Because it's not wrapped in these lovely wonderful Galaxy tools. It is using proper code, proper Python. You do have to install a few things at the beginning to make sure that your code will work. And it always says you may need to restart the kernel. Don't worry about that. I'm going to save how I'm doing. That is not hugely useful. What's very useful is to download these files. You can come over here. Phil, let me click on it. And then you can download them directly onto your computer. And then you can share them around. You can put them into a history that you can share so that people can download them. Yeah, so saving it here is great. But if you ever shut down this tool, because it's still in your Galaxy history, if I pop over here, you can see it's still here. So if you ever exit that, you'll lose all your beautiful work that you've done in the Notebook. So make sure you don't exit it until you're ready. Until you've downloaded whatever Notebook you need. Onward we go. And I'm not running these all at once. That might be my own superstition. Or someone's a bit smarter on the back inside of Python could tell you more about this. But I find if I run them all at once and try and install them all at once, sometimes it doesn't remember to do everything after the first one. So I've just gotten in the habit of doing it one by one. And then here you're just sort of importing those lovely tools into your environment so you can use them. All right. This is fun. So this is where we're getting our objects. So if I come over here, our object's actually number four in this history. So I need to change this to be number four. And it's going to pull that, that data set from my Galaxy history. It's a big data set. So it's going to take a little while. And we're there. It did take a little while. And now we need to read it into the understands the object that we're working with, creating our graph coordinates with the force directed graph. And we're back. Okay. And now we can do the fun bit, which is plotting it. And you'll also notice it has the save output as well. So we're going to be saving our images. Figures. There we go. So it's creating a little folder of these images as well. Do the rest of the calculation. See what happens. And we're there. Yeah. Well, it's not great. Okay. You can, if you're working in a group, you can mix this up a little bit. We're on the home stretch of all the cool images. Plotting time. Oh, that's just so cool. Right. And then compare. You can see the two branches. That is very annoying. In the original of this, it has quote marks here as opposed to one post of face. So don't let that get you. And then now we're putting those objects into our galaxy history and sorted flawlessly. Okay. And then we can go back and we can now see that we've taken our Jupyter Notebook and we now have our plot. And we also have our H5 ID objects. So they're all back in our galaxy history. So we've got everything that we want from here. You can, you know, add in all the plots to your delight if you wish. And then when you're done, you go to those tools. Oh, I had another one. And then you're going to stop that tool. And it'll still look like orange in here. So I usually just delete it so I don't get confused. All right. That's the end of this tutorial.