Today, we're going to be talking about PATRIC's annotation service. The first thing you have to know for the annotation service is you have to have files that are appropriate for it, and those are contig files. Now, if you've run an assembly in PATRIC, that will automatically give you contig files. Let me show you by going to my jobs page by clicking down here in the lower right. A recent assembly, highlight that row, click on "View". You can see that I have that build. When I run an assembly in PATRIC, it creates the contigs file. But let's say you have assembled the genome outside of PATRIC or you've downloaded something for GenBank and you want to annotate it in PATRIC. How do you get it into PATRIC? Well, there are three ways you can upload data that can be used in the service. One is down here in the lower right. Upload monitor shows how your uploads are going, but you can also upload data there. You can upload directly in the workspaces that you can get to from going to this tab at the top of the page. Also, if you happen to be in a service like annotation, clicking on services and annotation, I can directly upload data here. But first, let's talk about uploading data from the upload monitor. This icon here is our symbol for upload. Let's click on that together. You can see that that opens a popup window. First, it's asking what type of file you want to upload. Now, in PATRIC, you can upload anything here. Excel files, PowerPoint files, PDFs. If you have a collaborative workspace that you're working on with other people, this is a great way to share data. If you click here on this down arrow, to run the annotation service to generate an annotated genome, that service requires contigs. I'm going to click on contigs, and why do that? For the PATRIC services to read certain files, they need to be tagged appropriately or it won't recognize them. If you have read files and you go to the annotation service, you won't even be able to see it when you search for it. So it has to be tagged as contigs for the service to see it. Let's click on that. Now, immediately, you see it generates a message here. It says that these files must be provided in fasta format. Typically, those end in a.fa, a.fasta, or a.fna. This is important to note that GenBank formatted files are not currently accepted. I know everybody would like it that way, but that's not the way our service works. You can see that there's a check box here that says "Restrict file selection to comment extensions for this file type." So it's only going to search in my computer for this. I could uncheck that, but then I'd have to see everything that was there. So this will make my search a little bit quicker. Filter it down. You could drag and drop files here from a window in your computer; from your Finder, if you're on a Mac, or you can select files. Let's click on that. This opens up a dialogue box with my computer. You can see I'm in my Downloads folder and it's automatically showing me those files that have the correct extension, fasta files. I'm going to click on this one and open it. Then you can see here it is. I'm going to start the upload. Now, let me tell you that when I do start this upload, it's going to go into the home directory of my workspace. Click on "Start upload" and it's off. I can monitor the upload by clicking here. I'm looking. It's telling me that this file has already loaded. While we're talking about uploads, let me talk about another place you can go to upload data in PATRIC, and that's directly into the workspaces. Let's click here, your workspace, and let's click on "Home". This is my workspace. You can see that it is rather disorganized and quite messy. I use the uploads monitor a lot, and it goes directly into my home directory, and I never take the time, I'm ashamed to say, to clean it up and to organize it. Don't be like me. Organize your data. You'll just be a happier person. I want you to be happy. I want two things. I want you to use PATRIC and I want you to be happy. For organizing your data, look up here in the upper right, add folder. Let's create a folder that we want to put on [inaudible]. I'm going to click on "Add Folder" and that creates a little pop-up window where I can name the folder. Because I don't want to scroll through everything in my disordered workspace, I'm going to call it "A contig folder," so it'll be at the top. I'm going to create that folder. It says that folder is created. Let's scroll through some of the mess to look for it. There it is. I'm going to click on that. It opens it up, and the folder's empty. I could drag and drop files under this window, or I can use this Upload button to upload directly to this folder. So let's upload here. Remember, it looks just like the window that I showed you when we were using the upload monitor and the upload icon right here. But here I am in this particular folder so the data is going to be uploaded there. I'm going to leave it unspecified this time so I can show you another function, ''Select Files'' and see when it's unspecified, look at all the things I can upload. I'm going to upload this again and I'm also going to upload this guy. I'm going to upload them both, they're both listed as unspecified and start the upload. I can look at the upload monitor again, I can already see that it's uploaded. But you could check it again and it's saying that it's 100 percent uploaded. Now look, there are these files here, when I click on it, notice it populates this vertical green band with a number of downstream icons of possible actions that you can do with this. But it also reveals some information beyond the green band. Here it says the type is unspecified. I've told you that it has to be tagged as contigs for the annotation service to be able to read it. How do I change that? You see this down arrow here, click on that, and it opens up a new window, I'm not sure exactly why it does that, but let's click on this again and I can mark it as a contigs file, so I click on that and I click on ''Save'' and now the services that use contigs, we'll be able to see it. Here I'm going to do the same thing to this one, I highlight the row, click on the ''Down Arrow'', click on the ''Down Arrow'', click on Contigs, and click on ''Save''. Now that I have contigs in this folder, I could go ahead and delete it from the home directory, which I'll do it some later time, I'll show you guys how to do that so you can see how to clean up your mess. There's one other place that you can upload files and that's from within the services. Let's click on Services here and click on Annotation in this pop-up window because that's the service we're going to concentrate on today. I click on that and it opens the window to the graphical user interface that allows me to submit an annotation job. Notice that the annotate button is grayed out. I can't submit a job until I fill in the parameters and it will not turn blue until I fill in all the data here and then I'll be able to annotate it. First, let's give it some contigs. Now if I know what these contigs are called I could write it here, but we want to upload some data, so let's click on this folder icon that's at the end of the box. Click on that and here we are within the workspace and it's going to get loaded into my home directory. I can click on the ''Upload Monitor'' and it's the same thing that we've had before and I can select a file. If I selected one I've uploaded before already in my home directory, and I say ''Open'' that and I say ''Start Upload'', I'll get a message and it says, are you sure you already uploaded that earlier today? Are you sure you want to do that? Just for example say character, sure you'll say, ''Okay'', we'll upload it and now I would have to scroll down and find it, and I wanted to avoid. Now can you see how disordered my workspace is. But then it's been uploaded, I click ''Okay''. There it is. It appears in the folder, or the end or the contigs. The first step is there. So that's the three ways, from the upload monitor, from the workspace or from the surface itself, that you can upload your contig data into PATRIC, into your own private workspace so that you can use it in the annotation service. Next, we'll talk about submitting the annotation job. Okay everybody, now we have our first annotation assignment. If you did the assembly tutorials earlier, you could also use this as an opportunity to upload contigs of that or get yourself acquainted with it. But here's your first assignment, it's got three parts; you need to create a folder in your workspace to hold this job. In that folder, I'm going to need you to copy this file, the MOOC_Test_contigs.fasta. Then the third assignment is to make sure that that folder is tagged as a contig file. Now where is it? Well, go into Workspaces and click on Public Workspaces. Then when you're there, find the MOOC PATRIC Course, and click on that globe. Then when you're there, you'll see now there are two folders. Click on Annotation, and there we have the MOOC_Test_contigs.fasta file, I want you to copy that folder to your private workspace. You just click on it, you'll be able to figure it out. Then there's the third part of your assignment. What is this thing tagged as oh, oh, right now it's tagged as unspecified. The annotation app can't see it. You need to change that to contigs. I know you can do it. Good luck.
