 Now that we've had a discussion about the computational essay, let's have a look at our first example here. We're going to start off by looking at the shoulder girdle, the upper limb, and we're going to start off with the bony elements that comprise the upper limb, and we're going to actually start with something very very simple, the clavicle. So here's my computational essay. We can see a beautiful logo at the top here. I've got a title in the cell here and subtitle on the right-hand side and the content that we're going to have a look at. So there'll be an introduction. We're going to have a look at Wolfram Alpha data. We're going to look at the parts of the clavicle, the joints that the clavicle form, or that the clavicle is part of, and we're going to look at the muscle attachments. And then every now and again I want to just introduce a bit of fun material. As I mentioned right in the beginning of this course or this YouTube playlist is the fact that I want you to become familiar not only with the anatomy or to create your notes as far as the computational essay is concerned, but also learn how to use a computer language to become familiar with it and to start using it in your everyday life. If you're involved in healthcare, you might be interested in research doing data analysis, etc. So every now and again I'm going to bring in something interesting, a bit of fun stuff. So we notice that we collapsed these cells. So if I look in the right-hand side here, there's a little downward almost arrow in the cell, or if I am here in the desktop version, we'll see these big double arrow signs here. If I click on that, that will open up for me. So let's have a look at the clavicle. Of course, it's a long bone that connects the upper limb to the axial skeleton. It is visually very prominent as it forms this double curve from the anterior inferior aspect of the neck towards the shoulder. And this very superficial position makes it prone to fractures. We see a lot of fractures of the clavicle. Now I classify this as a long bone, but note that it is special that it does not contain a medullary cavity. In other words, it doesn't have bone marrow. Instead, it's just a scandalous or spongy bone surrounded by compact bone. So let's use anatomy data. Now, I've already have these typed in. You know now how to type this. I don't want to waste your time by you looking at all my spelling mistakes because I make a lot of those when I type in. I'm not the world's fastest type. So there we go. So we're going to call the anatomy data function. Remember, I'm going to hit control, enter or command, enter or equal, I should say, control, equal sign, command, equal sign, and then type in clavicle and just accept the anatomical structure, comma, and the one of these properties that I want to look at is the function of the clavicle. So let's execute that. And we note it provides structural support of the shoulder, allows the scapula to move and protects the underlying nerves and blood vessels. We have this huge neurovascular bundle that runs underneath the clavicle. Let's have a look just at another property, and that is the latter name of the clavicle and we see it's the clavicular. Now remember, if I hover here over anatomy data, I can click on this I and that's going to open up all the information that I want on anatomy data. It gives me these quick and easy just showing me here what the arguments are, but I can ask for a lot more detail. And you can see, for instance, all the properties there, and that's why I got these properties from now. Not all the properties are available for all the structures. For instance, the clavicle is not going to have a depth, for instance, as a property. So only some of the properties make it into the functions here, but have a look through this. It'll give you a lot of these properties here and other arguments that you can set and how you can set them. And you see some beautiful examples at the bottom here. If we come to the brain, for instance, we can look at the volume of the brain or the function of the pancreas and also the mass density and typical morphology of the liver and we'll get to all of these. If you can't wait just to explore on your own, that is what this is about. Let's have a look at Wolfram Alpha. Now, Wolfram Alpha, you can actually buy the app just on your cellular phone or tablet. You can use it online and I can use it right here in the Mathematica coding environment. And the way that I did this was just to have a click on the plus there and say Wolfram Alpha query. That is going to just go to the Wolfram Alpha servers that contain a lot of curated data. And if I hit down shift enter, shift return, it is going to give me a lot of information that it has stored that Wolfram has stored about the clavicle. Let's wait and see what comes up. It is saying it's assuming that it's the clavicle's anatomical structure. I see it's printed that out twice. In a meta, we see that it is in the clavicle, the Latin name, alternate names bone of the clavicle, bone tissue of the clavicle, collar bone. That might be interesting. The functional description which we've already seen. And then the hierarchical relationship. So I'm part of what systemic group is it. It's part of the skeletal system, the anatomical group. It's part of the skeleton of the upper limb. It's a long bone. It's a skeleton of the pectoral girdle. So it's all these anatomical groups, these hierarchical structures that we use in anatomy when we start to classify and group things. It's going to give me a nice little picture there, just the morphology of that. It's going to show me where in the body I can find these. We can see clearly there. It's going to give me some of the constitutional parts. Now remember these are all functions that I can just ask for. And we see there's a total of 12. So if I click on more there, it's just going to show me all of these constitutional parts. There's the sternal end all the way down here to the endosteum of the clavicle. Let's look at the connections, the circulary system. We can ask for the arterial supply as the clavicular branch of the supraclear scabular artery. And we can get all that information here as far as the musculoskeletal system is concerned. We can see all the attached muscles, the originated muscles, the inserted muscles, the adjacent joints and the bone articulation. We're going to ask all of that and just for a bit of fun, it gives us a Wikipedia page history. So we can see from 2008 all the way to 2018. And we see these hits per day. And we see around about 2012, 2014 lots of hits per day. But it certainly tapered out on Wikipedia. People not looking for information on the clavicle and Wikipedia as much. Let's look at the parts of the clavicle. Remember, it's anatomy plot 3D. Let's just have a look at the clavicle up close, as opposed to what was given to us in the Wolfram Alpha. And we can see, we can turn it around and we can clearly see, if we look from the top there, this is the left clavicle. We can see, we can see this double curve here, convex, concave. If we look from the bottom here and the different parts, we can also see in the medial parts quite triangular. And as it flattens out laterally, it goes laterally, we see it flattens out quite a bit. So let's just look at the constitutional parts. And we see there's the sternal end. That's this triangle end. The difuses of the clavicle. Remember, that's where the growth is going to take place. The cromial end of the clavicle on the right-hand side here. The articular cartilage of the sternal end. It's going to be the cartilage on this side, on the cromium side and the other side. There's the actual bone. There's the cartilage of the clavicle, the bony parts of the clavicle, periosteum, vasculature of the clavicle, the cavity of the clavicle, and the endosteum of the clavicle. So that, as far as anatomical classifications concern, those are going to be the constitutional parts. So let's have a look at the joints. I can just ask for the adjacent joints property. So let's have a look at that. So there we see the acromio-clavicular joint and the sternoclavicular joint. That is where we mentioned that it just connects the arm, the upper limb to the axial skeleton. So let's plot these. I'm going to plot the clavicle. I'm going to plot the manubrium of the sternum. Because when we get to the sternum, we'll see that they're different parts. So I actually want the manubrium of the sternum and the scapula. And here we can see all these joints. So we see the sternoclavicular joint here immediately, where the clavicle is in triangular shape. And laterally there, we can see, we can clearly see the acromio-clavicular joint on the lateral surface there. So we can inspect these joints. Supersternal notch there, where we can feel for the trachea. Remember, is the trachea centrally located? We're always concerned about that when we have injury to one of the two pleural cavities. If we have a tension pneumothorax, we'll note that the trachea is displaced here in the sternal notch. So let's look at the attached muscles. So I'm going to use a computer variable. It's a name that I create. And I'm going to call it originated muscles. Now this is camel case. Camel case means I put all the words together as one word. And apart from the first word that starts with a lower case letter, all subsequent words start with an uppercase letter so that we can just read that as human beings. I use a descriptive name, because if I refer back to this, or give this far to someone else, I want them to understand what I'm trying to do here. So this is a computer variable. Now what it does, it creates a little space in memory by giving it a name. And I can always refer to the content of that little space in memory by reusing that name. So I'm going to use the equal sign. Now in computer science terms, this is not an equal sign, it's an assignment operator. I'm assigning whatever's on the right-hand side to whatever's on the left-hand side. The left-hand side is a computer variable. And it is going to be assigned a specific object. And the object is an anatomy data of the clavicle and its originated muscles. Let's have a look at that. And we see the muscles that originate from the clavicle are the sternocleidomastoid, the sternohyroid, the deltoid, and the pectoralis major, those four muscles. Now I'm going to use the append2 function. Now functions in the Wolfram language, they always start with an uppercase letter. There's almost 6,000 of them. I think there's probably more now with the newer versions coming out. Append2 is going to take two arguments. The first argument is the object that I want to start with, and that's this originated muscles. And this originated muscles object here contains a list. A list is something that is contained inside of curly braces in the Wolfram language. And these are elements inside of this curly braces, this list. So these are all elements of this list. They all actually numbered. This is number one, this is number two, this is number three, this is number four, it's called the address. So I'm going to append to that. Append means add to in English. So I'm going to add to that the clavicle. So let's do that. And now we have the original four, one, two, three, four, and I've appended clavicle. So that is just me adding an object, an element to a Wolfram language list. And I know it's a list because it's inside of curly braces. Now, because I've got all five of those, I can say anatomy plot 3D and then use this object, which now contains these five elements. So using that computer available name, which stores this object in memory, Wolfram language now knows to go look inside your computer's memory and it's going to take those five elements out and it's going to do something with it. It passes it as an argument to the anatomy plot 3D. And those are our muscles that originate from the clavicles. So we can actually look around and that's beautiful. As you study, you can just keep this handy to remind yourself all of these muscles. We see all the muscles here, sternocleidomestoid here, the sternohyway, these two strap muscles here in the middle that go over the thyroid. We see the massive deltoid muscles here on the side and even bigger pectoralis major muscle, which takes some of its origin here from this first part of the curve, the convex curve of the clavicle and then the deltoid here from the concave curve lateral here in the clavicle. So we can have a look at all of those. When you see a picture like that, put it in your mind as you study, you've created your computational essay, you will never forget these details. Let's do the same for inserted muscles. So anatomy data, the clavicle, I want to know. Inserted data, once again I'm creating an object by stating a computer variable name. Inserted muscles is what I'm going to call it because it'll be easy to remember. And we see there are two muscles that insert into the clavicle and that is the subclavius muscle and the mighty big trapezius muscle. Let's append to that the clavicle, shift enter, shift return so that I now have subclavius, trapezius and clavicle, those three objects inside my offering language list because if I just plot it, I will plot all three of them now. And this is the way we start thinking computationally. There's a way that we talk in a specific language. It has its own syntax, words, the way that we form them, add them together, verbs, adjectives, etc. There's the whole grammar, the spelling, etc. The same goes for computer language. So we have to convert our thoughts not into a spoken language but into a computer language. And you can actually see how easy this is. It's really not difficult. So there we go. We can see the tiny little subclavius muscle there that attaches itself there to the inferior aspect of this flat lateral surface of the clavicle. And then we see the big, big, big, big area of the trapezius muscle that starts here on the posterior aspect of this concave lateral curve right on its posterior edge. It starts and makes its insertion at least on the clavicle there. So we can see both left and right trapezius muscles there. So here comes the fun stuff. Let's have a quick look. So say we're not always going to do this, but I just want to introduce you to computational thinking, to writing computer language, and doing something useful. Of course, we're going to be studying anatomy here, and you can already see how beautiful this is. Remember, you can just click anywhere here, the plus sign, and say plain text or alt, and seven, option seven on your keyboard. And you can just write normal notes in there. You can put bullet points, so many things you can do with your own computational essays. Now remember, I will put this, this file will be available on GitHub, and here on this YouTube video, I'll put a link in the description down below, so you can download this file itself, but feel free to create your own one. So one of the 6000 odd functions is the word cloud function. So I'm just going to use that. It takes an argument, and that argument that I'm going to use is actually another function, and that's the import function, and the import can do a lot of things in the Warframe language. Here I'm giving it a URL, and that is just a website address, httpas-fort slash fort slash en.wikipedia.org, so you know it's Wikipedia page, fort slash wiki, fort slash clavicle. So that is the page you'll get if you search for clavicle in Wikipedia, and what I want to do is import that whole page, and then I'm going to create a nice word cloud, and again you can hover over word cloud, you can click on the information I there, and it'll tell you all the things you can do with word cloud. So it'll now do what's called scraping the web, so it's going to scrape all this information from this website, and it's going to create this beautiful word cloud for us. Isn't that, well I think it's a lot of fun, so we can see clavicle of course appears most often as a word there. We see collarbone, we see lateral bones, scapula, shoulder attachment, anatomical, humans, ossification, girdle, etc. All this information. Now let's do something even more fun. We're going to do a bit of biostatistics. Don't run away, it is very easy. So let's see here, a publication claims that they are on average 200 page hits per day for the word clavicular on an anatomy website. You collect data over a period of 30 consecutive days to examine this claim. So I want to know, is this claim correct? Now the 30 day hits are listed below. Now because I never did that, this is just a make believe website, but I can ask the Warframe language just to create simulated data for me. And the way I'm going to do that is to start off with this function called the seed random function. Now what that does is, if I put any value there, any integer value, I just chose 12, you can put in there whatever you want. But what that would do is every time I ask for random numbers, it's going to follow a specific pattern so that if you run this file again, you're going to get exactly the same numbers back. If I did not include this and just create random numbers, every time I ran this page, you ran this page, you ran this code, you'll get a different set of random values. So by setting a seed here, seeding the random number value generator here, we'll get back the exact same values every time. So I'm going to use hits as my object name, my computer variable name, which will create this nice little space in my computer's memory to store this object in and the object I'm after is a boyfriend language list. And to create this list, I'm going to use the random integer function and it takes two arguments. I'm using two arguments here. The first is a list inside of curly braces, which specifies the minimum and the maximum value. So it says choose between 180 and 230 inclusive. So from 180 to 230 and 180 and 230 are included and give me back city values at random in that range at random, but it's not really going to be random because I seeded the seed of random number generator and let's see what we get back. And there we go. We get back 30 values, 189, 180, 226, 213. So what I've done here, I am imagining that I really did the study and I, for 30 consecutive days, I looked at the page hits and these are the page hits. Now I want to know if I look at these, can this claim be true? Is the average close to 200? So let's look at this visually. Let's create a box and whisk a plot. We've all seen those. So I'm going to call the box whisk a chart function. I'm going to pass hits as first argument. So those are the 30 values and I'm going to create a nice little title for my plot with a plot label argument and you see a little arrow there and you know on your keyboard, although most keyboards will have a right arrow, that's not how you get a right arrow. In Mathematica, the way that you do a right arrow is the minus and greater than sign and if you type anything after that, it'll actually concatenate those two symbols into this nice little right arrow. So remember that. So I'm going to put a plot label there as a string. Strings go inside of quotation marks. So one number of hits per day. Let's have a look at that and if I hover over my box and whisk a chart I can actually see the maximum of these random values was 2 to 9, the minimum was 180 and I see the median there was 201.5. So it gives it as a fraction there and the first and third quartile values we can see there as well. So let's just have a look at the average because we want to know is this claim of 200 true and the way that I do that I'm going to use the mean function and pass hits as an argument but because I'm going to get back an exact value an exact representation is something like that the fraction that you see there 403 over 2 is tiny if you're watching a smaller screen you're not going to see that but the median is 403 over 2. If I use the n function first it's going to give me back a numerical approximation. So it says the average of those 30 numbers is 203.433. So two things important to note here that I can put a function inside of a function so this mean hits is an argument of the numerical function n. So first it's going to do the inside so it's going to calculate the mean or the average of the hits those three values and then it's going to give me back a numerical approximation. Look what happens if I don't use the numerical approximation let's take that away and just do this and you can see there it counted up all of those and divided by how many there were that's an exact representation now there is a little dirty shortcut we call it syntactic sugar just something to make it easier to type we don't always want to put the n up front sometimes you can do right at the end two forward slashes in an n there or any other function that is just an alternate notation it's just sometimes when you have to put one function inside of another it just becomes laborious and if there's something we want to happen over the whole thing we've put together it's very easy in the Wolfram language just to put those two forward slashes in an n that's one way to do it and now you'll see we'll be back with a numerical approximation and I want to show you a third little way to do it and I can just say n and then the at symbol so that at what it does is it replaces that at with a left bracket left square bracket and it automatically puts an invisible right square bracket right at the end so that's what it does also just save some time when we type so you can see the three ways there of doing it I want to show you something even more I hope you're still watching this is about anatomy but I promised to add a few more things of interest so now our null hypothesis is that the mean is 200 hits per day now to reject the null hypothesis and accept the alternative hypothesis that the mean is not 200 meaning this is a two-tailed alternate hypothesis it can be either more or 200 or less than 200 we choose an alpha value of 0.05 and now we can just do this I'm going to create this computer variable I'm calling it script H and the way to get that script H let me show you how to do that I'm going to hit my escape key which gives me those three little dashes I'm going to hit sc for script and then an uppercase H and then escape again and that gives me that fancy script like H so that's my computer variable and inside of that I'm going to add an object so my assignment operator and I'm going to do just a normal students t test and I'm going to pass my 30 values hits the average that I think it is 200 and I'm going to ask for property and that property is called the test data table so let's do that and we see a t statistic of 1.33394 and a p value of 0.19 so we cannot reject the null hypothesis so with a p value of equal to or greater than 0.05 we cannot reject the null hypothesis the claims the publications claim that stands that the value we got of 203 is not statistically significant from their claim of 200 there you go we used the t test we looked at some data we simulated that data we looked at some samples statistic statistics here the mean and we created a beautiful box and whisk a chart once you get into using a computer language and all we're trying to do yeah is learn a bit of anatomy for you to be able to create your own computational essay write your notes write inside you have these 3D graphics I don't think it gets any better than that but as I mentioned once you get into this there's the whole world of computation opens up to you there is so much you can do I hope you enjoyed this and I'll see you in the next video we hopefully will start looking at the scapula