So this is great to have the last presentation of the day. My name is Jesse Beach. I work at aquia. I'm one of the front-end developers. They're working on the spark team and For the most part I work on JavaScript CSS and HTML. I wouldn't say that I am at all an accessibility expert But what I am is someone who's very interested in data and access and people getting two information that they need and information that they want So I kind of fell into this accessibility space in October of 2012 at the Toronto Camp the Drupal Toronto camp We were working on the toolbar and we had to meet the accessibility gate the Drupal accessibility gate. I Had no idea what that meant at the time So I spent a full day working with Everett as you felt Mike Gifford a bunch of other people And I really got a sense of how far from the mark we were in Terms of accessibility and how rich the space is Providing means of access to complex applications like the toolbar in Drupal core And it started me down this road of wanting to Make all of Drupal accessible. I know I'm not the first person who's wanted to do this I'm certainly not Perhaps the best person to do this, but I'm someone who jumps into something You know, even if I'm stepping on toes and knocking over glasses who Wants to see you know Good UI be made so this is a Talk about what we're doing at the moment in terms of accessibility in Drupal and what we might do into Drupal 9 with perhaps Setting up, you know an initiative something bigger that gets us formal structure behind these efforts So if you go to this bit.ly URL I set up a Google document With notes, I would love it if you know You feel like you have something to say or something to add if you could add your comment to notes on this page I'll lock down the page afterwards and open it for comments But it'll be a place where we can go back to and find names of people or organizations Ideas we can incorporate into later plans So just give everyone like two seconds to jot that down What I'll do is talk a little bit about what we're doing at the moment and then some efforts Beyond the reason we want to improve accessibility in Drupal Core is because it is simply the right thing to do There is you know, you can talk about perhaps Economic reasons you can talk about You know you as a provider wanting to move into a space such as government that requires you to be accessible But from my perspective as a developer there is no Justification for building something that someone cannot access in my mind so if we look at a project like WordPress and I think Mike Gifford for bringing this up during our conversation yesterday if we look at This plug-in in WordPress called WP accessibility has 3049 downloads out of 20 million downloads for WordPress core and About five million six hundred and eighty-three thousand domains that are running WordPress The reason I bring this up is it was suggested in our conversation that the accessibility support in WordPress is not ideal And if you think about that as a percent there are point zero five three six percent of WordPress sites running this module Potentially to improve the basic accessibility of WordPress There are currently six hundred and fifteen thousand domains running Drupal and to my mind Solving this problem in core means that we hit all of those domains all of those sites It's not something that we want to push out to contrib space in terms of support So we are building the standards in Drupal core One of those is the WCAG the web constant accessibility guidelines and the a tag or the Authoring tool accessibility guidelines There's a page on Drupal.org that specifies that we support these two guidelines in terms of accessibility But we really don't know if we do that's the problem The problem is we we don't measure our support of these two guidelines in terms of Drupal core And what I'd like us to do as we approach Code freeze in Drupal 8 and then the cleanup phase is to think about how we might measure our support of these two guidelines Before we produce the official release of Drupal 8. So what we might do is a full review of all core admin pages every route that we have run it through a Ballotator an HTML balladator run it through a tool like the wave tool on Firefox And just get a baseline Number of how many errors there are on that page and Then log an issue for it We would also want to do a full review of the core templates to make sure that things like field templates Have the attributes that are necessary to make those things accessible And then what I'd really like to see is an effort similar to the HTML 5 effort and the twig conversion effort Where we create essentially a scoreboard of every template and every page in Drupal and Give it a grade, you know, or it's percent of support if it has three errors in the wave toolbar then it has you know a Negative three score and we want to get them all to zero. I'm not really sure how we would measure this But we want to have some way of comparing them and knowing when we get to done for Drupal 8 and I would say that the number of people working accessibility in Drupal core that I see regularly which is definitely not everybody but You know, it's maybe a dozen Who are there in the queues every week? I Would love to see people who are Actually accessibility experts jump in and help us do testing help us do reviews I don't think you would need too much knowledge of code to jump in load up an admin site run it through a toolbar to check for errors and then Log those somewhere on triple org So I mentioned a couple of tools. I was just introduced to the wave toolbar and Firefox Essentially what this does is it looks at your rendered HTML page and it Indicates through Warnings and errors on the page where you might have problems such as missing an alt tag on your images We also have markup validators These to me are useful They won't bring out errors and highly dynamic pages because they're just going to look at the rendered content that comes back from Drupal And then moving into the future. We might look at more automated means of doing testing The quail module. This is a JavaScript framework that does testing Talked with them Peter Drogman's about perhaps working this into the test for a module which we've begun developing front-end tests against and then moving something that like that perhaps into the text test spot for Testing patches as they're proposed another interesting Tool for the content creation side would be whizzy wig integration letting authors know at the time of Authoring that an image that they've just added to the page is missing alt tags So at the moment there are about 116 open issues with the accessibility tag against them Some of these are meta issues. Some of these are highly specific issues But to my mind they don't represent at all the full amount of work that we have to do against Drupal 8 and then we get down to this Idea that the guidelines themselves are extremely difficult to understand. I myself Have read them perhaps, you know four or five times over and I still don't really understand what they're trying to make me Do or what they would like me to do Those being the the WCAG and the a tag guidelines so what I've tried to do is and This is through talking with Mike and Vincenzo is to understand the principles behind the guidelines and to Apply those in my work rather than the specifics. So those are a UI should be perceivable You should know that something is there If you come to our talked women are giving a talk tomorrow about views oral UIs Backbone will give you really stark examples of how things are not perceivable currently in Drupal core Operable refers to being able to take action against something in the UI Understandable if you could imagine a Link in a comment that just says one new, you know There's one new comment and that link repeated ten times on a page with no further context You've eliminated the possibility of understanding what that means to an on-site aduser And then I think robustness is just the general principle of UIs in general, but especially for The UIs we don't spend the most time on you know the visual UIs for oral UIs we want to make sure that They Are accessible and Usable always in the same way. We don't want to be introducing new patterns or anti patterns Into these UIs so I would say that as Front-end developers were extremely invested in producing highly polished usable visual experiences But when it comes to building Experiences that are non-visual oral UIs keyboard UIs We don't have the experience and we don't have the patterns available to us to do those That sort of work. So if I was to list the major Components or the systems in Drupal that need Work at the moment like actual design work views is at the top of the list and thankfully the views team is in complete agreement that the accessibility of that subsystem of Drupal is We'll say nicely lacking at the moment. We know that what the major issues are They're going to be hopefully addressed during this Drupal con one of them being switching to using the dialogue API That was introduced to Drupal 8 in views that will open up the possibility to work on further issues That are sort of blocked at the moment by that there's still a bit more work to go with the field API and specific fields to to make sure that they have all the attributes and The descriptive accessibility elements and then I really want to look at The subsystems like content creation Block placement the things that people are going to do on a daily basis and make sure that those are highly refined usable There's nothing hidden everything can be found and it's kind of a dream. I would love to be able to have an Oral UI for field states in the same way that we introduced You know Ajax support for fields or states for fields where if you know you click a checkbox you you can associate Another set of field items with the the state of that checkbox. It would be great if we could have automatic Informative information based on fields produced orally as well as visually Yeah, and views we have to fix that. I don't know if there are oral UI designers I think it's Exactly so When we say UI designer, we're implicitly saying visual UI designer, right? Someone who comes in produces boxes and arrows and you know layouts but that's just one way of Producing data output a view of data an oral UI is something that you hear is another way of accessing that information and We tend not to think of an oral UI as something you can design because I don't think We've really taken the time to design it if you think about visual UI 40 years ago when the first mouse and click interfaces were introduced No one knew what they were doing. They were inventing metaphors. They were inventing patterns to take bits and present them to people in visual presentations and I want us to do the same thing in Drupal. I think we are going to be pioneers in this space of presenting information through oral means And by the same token we need to think about How we access information from a keyboard consistently throughout Drupal Are there hotkeys and combos that we can build in so that if I press C or S or A they do something consistently in views and content creation across the board So if anyone knows of an oral UI designer or someone who produces spoken UIs Bring them into Drupal. I think they have the opportunity to really impact a lot of people around the world So the short-term plan this is to do with just getting us to Drupal 8 launch Meeting our proposed or our professed support of WCAG and ATAG Is to make sure we're testing and this is where we need everyone in the community because we do not have the resources at the moment to both build and test at the same time People out here if you work for a university if you work for a company if you have access to testing facilities Anything at this point will help us log an issue and once the issue is logged There are folks who will address it You know, we have a small number of folks, but they're highly efficient and they they really burn through issues And then what I really think we need are folks Who develop in the modality that is their primary modality my primary modality is visual I? want to understand how people interact with data in different ways, but It's very hard for me. It takes a lot of interaction and Learning and I feel like I just I will never get the UI perfect for someone who wants to access data in a non-visual way We're starting to see that people coming into our community whose modality of interaction is non-visual Who are also developers and this excites me so much because they bring? Patterns of usage to our community that we are lacking at this moment. So if you know someone developer Who wants to spend a little bit of time volunteering bring them into Drupal let them know that there are developers who will teach them all of the You know intricacies of working with Drupal in order to get them being productive and producing code The long-term plan. I really think we need Something that has the formality in the structure of an initiative in the same way that we had mobile whiskey scotch For Drupal 9. I want to see meetings Well, I hate meetings, but they're very useful. I want to have people getting together talking about these issues Laying out priorities. That's what I really like priorities Getting issues in the queue in order and addressing them, you know tops about them All right, so I'm gonna open it now to questions That we can save for posterity and if anyone is inside the notes Please take notes on questions and we will address them later Wanted to bring up. I hope this is appropriate Perhaps a larger movement that's around this that's often referred to as universal design And I wanted to point out. I think this is a great no pun intended visionary effort that's going on not only for Blind users or for people with motor limitations for using websites But also for the future of Drupal when it comes to vision This is an oral UI And it's very hard It's very hard for blind users Common It's really hard for blind users to use Typical devices and these typical devices will become harder for visual, you know for visually Normal people also to use as they get smaller And if we are actually ready with universal design, we'll be the We'll be the first CMS on the Apple watch for example or for other devices that Rely less on our ability to touch them and see them and more on our ability to hear them and interact with them Vocally so for what that's worth So following up on the previous point there Would Oral design do you think also include, you know, the device in that case is speaking Functionality of the system and that's hard enough as is but if you're dealing with a touchscreen or Something like that where you don't have a physical keyboard then Inputting data of some form is just as hard if not harder Should we be looking at? You know, what would it take to make Drupal Voice capable for when there is such a tool that allows that I have no idea what that would look like I have no idea what the standards are there if anything, but is that something we should be asking about at this point? Yeah, definitely. Okay. I mean that excites me as a developer So I don't know. Are there any specs along those lines for, you know, browsers not just outputting data In the audible format, but also inputting data. I don't know if anything there. That's not Google proprietary So just to repeat that Mike said that Dragon naturally speaking is one such input modality there was an effort by Everett Sioux felt to Collaborate with them, but that didn't go anywhere Okay, and personally I don't know anything beyond Google proprietary, you know voice API's builds into Chrome where we could do that, but Yeah, I would love to see. Yeah, I mean where I'm kind of going is You know, what would it take to give a Drupal site the kind of interactivity that something like Google now has probably an awful lot But it'd be really cool if we could Definitely everybody Thank you also for your all your hard work This is something that's been on my mind as long as I've been working in web But I've like I've never found anyone willing to pay for it.  I mean, there's nothing hard in there like technically Like as there, do you know of any work around automated testing of scan this page for accessibility errors? and because I mean if we could make that a feature where You check this box and every time you have an accessibility error, you get warned or you get whatever to me that that would make That would bring the at least the awareness level up and you know, that would it would give us a place to start Yeah, so Falcon brought up yesterday this idea of doing almost like an error log of accessibility problems during content Authoring so that if you did have a workflow We know where an individual content creator didn't produce the optimal output You could have an editor come by and perhaps fix that or at least maybe inform it out to a third-party service That would do that sort of thing if you needed to the the two realms of content creation and site building To me aren't defined well enough yet in terms of our community to understand what the different Responsibilities in those two areas are and I think that's something that we need to suss out still So my question is sort of about the I guess the known unknowns and the unknown unknowns I work at a university and I'm curious to like do we have the Tests in place in the real-world stuff like I can I have a usability lab So I could sit students and people in a library who are using JAWS or Any of these tools down in front of a in front of more or something like that and actually test them and get that I guess distributed to the community But do you guys have that yet is does anybody have that as a post anywhere or do we is that a contribution that needs to be made? I think that's a contribution that needs to be made posting those videos Somewhere would be some that's completely valuable something that someone could run through and Create issues off of and have as a physical artifact to go back to yeah if you could do that Awesome, so I thought I'd give a status update because I'm the person responsible for making accessible content And then disappearing for a year But also run quail. So quail actually has a branch with key with Q unit integration now So that it would be really easy to integrate with test swarm But I think a challenge would be it as a community is to Identify test suites beyond just straight accessibility guidelines But also that incorporate best practices that are not Necessarily encompass and we cagger 508 And I think it would be we we have had in d6 Modules that gave feedback to theme developers and to content creators So those should be catching up with d7 and d8 shortly, but I think it even beyond test swarm integration even looking at Some form of like qa.drupal.org For people who are just writing interfaces would be also interesting thing to look at Do you think we could support dynamic interfaces? So quail too, which is in JavaScript already does support that and we have tests written and that are working in Travis CI that that do do a lot of dynamic interface Ajax loaded stuff The challenge is figuring out how to You you do need to train the test about what areas of that content Do you want to look out for and what events you want to react to so that would be you know another challenge? Awesome, let's talk after this. Yeah, I just want to say um, you know I think it's great that we're talking about getting testing in place to make sure that we're Satisfying accessibility standards. I just had an audit done on my site and I am I was trying to think about what can we automate in terms of future Pages and I realized that a lot of that stuff just can't be automated like a lot of them are design-centric, you know color contrast issues Sensible navigation order so a lot of these things have to do I think Design and I'm wondering You know is the appropriate path of that education towards like Drupal designers Or like on the contrib space is there way that we can evaluate like contributed themes in terms of their accessibility Because I think that's a big piece of it that can't just be automated Yeah, there's good points. I don't think I've answers To me anything that any sort of educational material needs to be so immediately perceivable and consumable That folks don't have to you know think about it too much But that doesn't mean you shouldn't do it at the very least we can make sure the core themes Satisfy the design definitely to me those those are part of core and those would satisfy but I hadn't Really separated the two in my mind yet so I thank you for bringing that up that there's only so far we can take automation and then Education is the only way to to bridge that and and testing like with usability labs as Mentioned before I mean that's a big part of it. Definitely even exposure. I mean that just produces exposure to the larger development community Has a value Thanks Thank you very much. Jesse. This has been good. I just wanted to to add the yeah No one level in terms of the the automated testing will get you so far. So there's a lot of stuff that we can do to go off and to To help with automated testing that identify the low-hanging fruit in the basic basic elements But we need to To also try and engage with the communities who have the people with expertise who can deal with this It was great to have somebody at the back was was talking about you know trying to engage their their usability lab and trying to go off and bring in students with with Disabilities to be involved, but there's a lot of different kinds of people and a lot of different kinds of disabilities that there are blocking people from having access to to to your website and and the Blind the blind community certainly one, but it's not the Necessarily even the hardest of the the the types of people that you need to that The WKG is dealing with so there's dealing with people with cognitive issues and learning disabilities and with people with multiple disabilities There's a range of potential people to try and and to try and work towards being able to to make your content make the content accessible but wanted to go up and to talk just briefly about the was about Looking at at the the the standards and a lot of these things are becoming Are still forming and I think that that I'm in conversations with people at a tag who are or the WC3 You're sort trying to define these these definitions and define best practices There's a really interesting opportunity to go up and have a tag be reference or to have a tag reference Drupal and Drupal's admin interface as as sort of the This the best best practice by defined by the WC3 in terms of implementation of these these tools I think where we're further ahead than any other CMS out there and there's still so much more to do But the WC3 doesn't have that many implementations to to sort of point to so Maybe just wanted to raise those those issues So what could we do to help people who want to test but are faced with you know the totality of Drupal and They need to somehow distill that into a 25-minute session Do you think we could put together a list of? You know subsystems or even just list like our top 10 admin pages That we would love to see tested and that will get the ball rolling. It would certainly help if we we haven't had a Full audit of Drupal 7 period that it has not been audited by an external party for accessibility And there was an effort that the accessibility team tried to put together to have a An audit, but it comes down to Who's who's gonna fund it and it's something that you know somebody who is a good auditor will charge In the range of you know $400 a page to go off an audit And there's a lot of pages just in core if you're looking at you know all of the different admin screens And that's you know potentially thousands of dollars if you haven't prepared and organized and I mean It's you know hundreds of thousand dollars if you haven't prepared and organized But you know it's a it's a it's something that that needs to be thought through strategically And there needs to be a team to are willing to commit it to deal with that and again with Drupal 8 You know it's it's many of the same problems are We're relying on people to go off and to give their feedback to the Drupal community There's an issue and trying to make sure that we've reached out to them So if there are problems that they they know that they can can reach out to the Drupal community and get a positive response and and we've Certainly for most modules and most themes when we've identified an accessibility problem People are really quite generous to go off and to deal with to try and address that so yeah All right, let's talk about that more. This will be the last question. We're four minutes over This is actually I guess more of a response to the question of how can we get people to do testing and Get some coverage one thing that I'm working on a distribution at a university Customized distribution that we have developed a training guide for And the training guide covers a lot of the core things that content creators do every day in Drupal and so something like Taking a training guide and pointing something to that and say okay you can evaluate the process of using this of this this process by following this training guide and how you might you know to With whatever your assistive technology is and can you do these core functions like adding users creating content editing content and Rather than necessarily looking at it as we have to evaluate all these admin pages To more look at it in a usability standpoint of we have these tasks that people need to do and we already have a lot of documentation Help documentation that we could just point people to and say hey, can you evaluate this process using your technology? That's a great idea. I think that would really be a great place to start To make sure I get your card before you leave Great. Thank you everybody While I still have power of the microphone. I told Brian Hirsch that I would announce a sprint on Friday Tonight 730 coders lounge in the double tree hotel Drupal cons Oklahoma tornado support codathon We'll be working to help the victims and emergency responders on the ground We want to develop a website that will coordinate the transportation and help deal with housing issues. If you have time tonight double tree 730


Welcome to MOOC course on Introduction to Proteogenomics. Welcome to the hands-on session of WebGSTART. In today's session, Dr. Bing Jain will teach you about how the results and jobs summary can give you useful information. He will also show you how the enrichment analysis can be visualized in different forms. He will discuss about different types of network-based methods like direct neighbor-based approach, module-based approach or diffusion-based approach. So, let us welcome Dr. Bing Jain for today's hands-on session on WebGSTART. Go SLEEM summary. So this is not, first, this is not enrichment analysis. Don't use this to report as your enrichment analysis. This is just simply a classification of the genes you submitted based on some pre-selected biological process, cellular component and molecular function categories. Give you an idea of how many, for example, how many genes are related to biological recognition and mathematical process or response to streamers. These are the high-level categories. Yeah. Well, again, that is I think you are very good representative of the users. We got this request from a lot of users. So, yeah, that is our to-do list to add to, yeah, we will do that in the 2019 release. And it is just basically similar to the pie chart you typically see, I mean, to classify genes. And then the important part is this enrichment results. Let's don't do the redundancy reduction yet. And then the default view is a pie chart. So basically, this shows you the enriched categories because we choose the top 10 options. That's why we get the 10 categories here, right. And on the y-axis, you have the enrichment ratio from the vicious analysis. And then you can, this one can be downloaded if you right click. And then you can download this as PNG or SVG for your presentation or for, and even for publication, I think the quality is good enough. Or you want to maybe visualize in another way. You can visualize all your results in a book kind of plot like this. And then you see these are the goal terms highlighted the top 10 categories. You also have the option to change it. You can change the label from the gene set like the gene ontology, which you don't understand what it is to something is more descriptive like the description of the gene ontology terms. If you don't have this volcano plot, then you are still using the old version probably. So you have to go to the website and if you, the old website is like this and you have to use the webcast dot 2019 beta version or you just put the 2019 in your URL. Yeah, next, this is a completely new feature. So and the programmer also did a very nice job as you can see because these labels are crowded and sometimes you won't be able to see it right. But the good thing is you can actually use your mouse to move this around, to move this to the right place that you want it to be. And of course, now it's difficult to see where it's, where you can draw the link and then basically you can rearrange them in the way that it can be used for publication. Click on the draw link yeah and the yeah the axis is the log 2 of enrichment ratio. So basically this is you have expected the number of genes right if you do random sampling and then if you have a enrichment what is the enrichment ratio this is this and then the y axis is FDR in the log scale. But after you move this around you can see now you basically have a very nice view of everything. You can keep the link or you can remove the link to get a clean view and then you can download this plot that is very yeah minus log FDR yeah yeah. So the smaller will end up with a higher yeah. So this is a deck of a kind of view and then you can also do the deck of view because these genes are all guys thing directed a cyclic graph in gene ontology you can actually see this as well but this is available in the old version as well. And from any of these and sometimes if you end up with too many categories some of these are quite redundant as you can see in go right they it has this hierarchical structure I mean the parent term and the child term. So you want to simplify this and for example you can do the affinity propagation based on simplification let us look at this if you let us do a bar chart you originally have 10 10 significant terms but if you do the affinity propagation you end up with 3. That means this will group the 10 terms into basically 3 clusters and only pick one from each as a representative that will simplify your interpretation and another algorithm we implemented is the weighted set cover this end up with 4 either of this is useful for you to simplify your for 10 I mean it is not a problem at all but you can imagine when you have 200 and this would be a very useful feature to look at. And now we have the overview of the results and you can download and save but of course you want to understand why this is enriched right you want to look at the detailed result you can click on any of this bar that will show you the detailed results for that bar at the bottom bottom part of this. For example this shows the apoptotic process and then you can click on this it is linked to the database Emiko so this will give you a description of what is apoptotic process and then here you have the FDR result the p-value before the adjustment and then you have the gene set size you have the expected value and the overlap the number of genes and the enrichment ratio so basically the enrichment ratio is the overlap divided by the expected and then you have also very easily understandable one diagram to help you to understand this result and then all the genes in overlapping genes here in this table you can browse all the genes and you can also sort them in different ways. So, yeah and then let us say you did this analysis and you want to share with your colleagues or if you want to share with your supervisor he just does not have time to run this analysis so and then you can click on the result download. So, this will save the result as a zip file if you open this zip file it will include the html file and other files and if you click on that html file that will basically reproduce this exact result. So, it also provides a very easy way to share your results with others. So, yeah it is very simple like this, but you can explore this in many different ways and you can go back and then change the let us say we did the analysis against the biological process right. Now, we want to do pathway let us say we do change the functional database to pathway type and then we use a wiki pathway for the analysis and maybe we change the cutoff from the top 10 to fdr.05. So, and then you can submit. So, basically this will compare your gene list with all the wiki pathways let us see what we get. I am using wiki pathway as a demo yeah you can choose a rectum if you want or a keg, but yeah I am using wiki pathway here. fdr yeah I think you can do 0.05 for example yeah it is up yes yeah, but usually I mean you can you can do up to point some people use 25 percent 0.25 that is a not just I think you can go yeah, but I think usually you go with 0.05 or 0.01 this is a result I got. So, basically it is very similar to the gene ontology analysis, but of course, we do not have the dag because I mean this is not gene ontology. So, there is that directed a significant graph structure anymore, but you still have the volcano plot and then you can still put the description here. And now you can see because we have a lot of enrich the categories. So, it is more useful to apply the affinity propagation for example, you have a lot right and it is difficult to go through and then use affinity propagation or with it will give you a reduced set that can represent basically highlights the representative ones. And yeah that will make your volcano plot easier to look at as well. And another difference between the this analysis and the gene ontology analysis for gene ontology and they just put genes together, but without defining the relationship between genes within that gene set right. But here and we can have the pathway map yeah this is the result. So, but if you click on one of these pathways and then if you click on the pathway ID it will also show you the overlapping genes here there are 6 genes here right and then you have the pathway map and the genes will be highlighted in the map. I do not know why only one is highlighted here. Let us try another one. So, the highlighted ones are like because sometimes one load might have represent a complex or something like that there might be multiple genes in one load. But this provides a very easy way that you have not only have the pathway identified, but also you know where your genes are located on the pathway. And this highlighting function is available in all of the pathway analysis like Keck, Reaktome or Weki pathway. So, that is the first example and I think you can change the parameters in different ways. For example, we only look at the gene ontology biological process and the Keck Weki pathway and using a specific cutoff, but you are free to change those and do your own analysis. But in the next example and I want to show you how you can do the gene setting enrichment analysis in Webgestot and the specifically what we have here is a pre-rank based analysis. We do not do the differential analysis in the system, rather you do you choose your statistical methods and you do your differential analysis and after that you get a statistical p-value that will allow you to rank all the genes. In this case for the ORA as I said let us see if ORA and the input is very simple, it is just a list of genes. So, that is basically you do a differential analysis or correlation analysis and you identify 100, 200 genes and then you copy paste here or you put that in a text file and upload here. But if you want to do GSEA, let us see let us click on this GSEA sample run and what you need to have is something like this. You have every gene has a value associated with that gene and in this case for example, this could be t statistic or minus not p-value or something like that. So, that will allow you to rank the genes, but notice this and in this case you do not set any cut-off if you do a proteomic study and then you identify 5000 proteins and then you have t statistic for all the 5000, you need to put all every single protein in this, but in this format one gene or one protein and the value this and then the system will sort the genes and the identify the location of each gene for specific gene set where the genes are located in the ranked list. So, yeah because of the time let us just do the GSEA sample run I think that would be easier than getting the file and upload, but when you prepare your file is basically same as this just a file text file with two columns remember for ORA is just one column or just a gene list GSEA always you have to have a gene and a value from your statistical test. For example, you can calculate the correlation of the genes to drug sensitivity and then for each of those you have a Pearson's correlation and then you can use that to rank all the genes. So, this is if you succeed in getting the result I mean the top part will be very similar to the ORA analysis basically you still get the bar chart of a kind of plot or if you do the go you get the deck of your enrich the go terms. The major difference is here and rather than the the Venn diagram that shows you the overlapping genes between your updated gene list and the genes enrich the gene set. For example, let us see if we are interested in this focal adhesion we click on this and then it is you let us say this is the rank the list this is the data you in this is your input. So, basically now because every gene came with the value then the system was able to rank all the genes from the largest value to the lowest value right. Here you can see this is ranked list metric this is the number one gene this is the last gene basically from the positive values to the negative values. And now for the focal adhesion genes this bar basically represent where are the focal adhesion genes located on this ranked list. As we can see there is a tendency for this genes to be located on this part rather than this part basically that means, there are a lot more up regulated focal adhesion genes than the I mean the very few down regulated focal adhesion genes that is why it is enriched at this part. Also it has this scoring plot enrichment score plot and this part is the leading edge meaning these are the genes that give you the enrichment signal and these are the genes that are listed in the table at the bottom. There are a total of 53 genes out of the 128 genes that are in the leading edge that is giving you the enrichment signal. So, the so basically I mean if you think about the one diagram and this you can probably can help you better understand the difference between these two approach. One approach you have a cutoff and then it becomes two sets and then you do the overlap and then you use a facial test or hyper geometric test to check the enrichment of the overlap. But here you are not setting a cutoff then you get all the values for all the genes and then you are testing their enrichment in the ranked list. So, I think this is again I mean you can also at the top there is a download button and then you can also save and the download and then save and share your results. So, finally, let us take a look at the NTA sample run. So, the NTA sample run the input is also very simple is just an again a list of genes you are put let us say you have a list of differentially expressed genes or some genes you can just put here. The idea is to say I mean if I identify let us say we do a association study we identify 300 genes that are potentially interesting which one should I test first right do an experiment first and this will help you to answer that question. So, in there are two options one is to do network expansion, but the other is network retrieval and the prioritization. This prioritization is when you have a lot of genes you want to pick the top and then you do this. But this can also be used let us say I can show you another example later let us say you have one gene, but you do not know the function of this gene then you can just type the name of the gene here and then you can do the same analysis that will help you to retrieve the neighborhood of that gene and then to go enrichment analysis to help you to predict function for that gene. But let us look at this first yes I think the analysis probably will take very long because of there are a lot of people submitting job at the same time. But this is the result and if you do the analysis later you succeeded in getting the result it is like this and at the top you have the job summary and here you have the sub-network. So, yeah if we go back to here we see where basically this is our input gene list right and the network we chose the PPI biograde. So, this is a protein-protein interaction database. So, basically we are mapping these genes to a protein-protein interaction network and then first first we retrieved all the genes that are included in the network and then you get a sub-network like this and then you notice that and the top 10 genes because of your parameter is and you want to get the highlights the 10 genes top 10 genes right. Then these are the 10 genes that are highlighted and then you can zoom in and it will tell you and for example, the FN1 and ELM collagen A1 and TGF beta 1 I mean these genes are the top genes based on the network diffusion analysis that means these are probably the half genes or the have more connections to the other genes in this network than the genes that was not selected as for highlighting. On the right side so basically this is an enrichment gene ontology analysis for the network and it will tell you what are the enriched functions for these genes and you can click on this for example, this is response to wounding and then that those genes will be highlighted. So, basically it provides you a way to retrieve the network and also understand what are the major functions associated with the network and then you can also visualize and which genes in my network has that function. And at the bottom you have the all the genes you submitted and the rank like here you can get all the rank like FN1 is the number 1 and then THBS1 is number 2, but basically you can have your complete list here. Yeah here this is a gene ontology enrichment analysis result for the network you have so basically the typical gene ontology overrepresentation overrepresentation analysis report result similar to the ORA analysis, but focusing on the genes in the network and using the gene ontology biological process for evaluation. So, these are the three I mean major functions for the webgestot. So, again the ORA and NTA the input are just genies it is very easy you can just copy and paste to your list to here, but make sure you understand the parameter setting and get the right parameters and then the result is very simple to understand I think you and you can download the figures for very easily from the interface. I hope today's session was useful to you where you got an idea about exploration of Webgestot result. So, we learned that Webgestot gives you data of gene enrichment, gene ontology, protein-protein interaction modules and pathway analysis. In pathway analysis we learned that we can choose different functional database such as keg, reactome and wiki pathway. The filtering of pathway analyzed data can be done with stringent criteria such as 0.05 fast discovery rate. I hope you appreciate that resources like Webgestot are so precious open access available to the community where from your complex mass spectrometry or even NGS dataset you can try to now further get an idea about what is the best biological sense of a data. How to really get the best biology out of that the complex mass spectra? How best now you can try to address the biological question which you originally wanted to start with? So, these resources are highly valuable of course these short lectures and hands on sessions may not be able to provide you all the information but more and more you make yourself familiar by using these tools you will then appreciate that the same dataset which you have obtained from these high throughput technologies can now give you some very novel insight and probably the right answer to the biological question which you wanted to address. In the next lecture Dr. Bing Zhang will teach you about network analysis. Thank you.


When you think of an extrovert, odds are you're imagining a loud, obnoxious party animal. Instead of falling back on old, often inaccurate stereotypes, we want to focus on the strengths of extroverts. We encourage you to do the same. Here are six things extroverts are best at doing. Number one, extroverts are enthusiastic. According to research, extroverts are actually wired to be enthusiasts because they strongly associate their environment with rewards. This is why they're often known as the life of the party in some circles. Studies have shown that when people find themselves in a positive experience, they are likely to move faster, remember better, and take on an optimistic demeanor. This is very much instant gratification for an extrovert who is motivated by their impulse to be happy. Number two, they're natural risk takers. While risk is often negatively associated with reckless and unhealthy choices, in healthy doses, risk taking is actually one of the best things you can experience. Extroverts are always searching for the next exciting adventure, whether it be traveling the world, having an unconventional career, or creating the latest invention. Extroverts are one of a kind. Thanks to biology, dopamine is more active in their brains. Dopamine is the neurotransmitter in our brains, which motivates us to seek external rewards and take risks. This makes extroverts natural explorers and the least boring people you'll ever meet. Number three, they're able to make friends from all walks of life. Their friendly and easy going disposition makes them easy to talk to, which often attracts many people to them. They enjoy variety and rarely fall in with clicks too. Since extroverts are not intimidated by large social gatherings, they are also skillful at navigating their way around like a butterfly and network while also making it a fun, enjoyable experience for everyone. Number four, their curiosity brings them unique experiences. Adventure is always out there and extroverts take the leap to embrace it. Their curiosity helps them gain knowledge about the world that can make them wise, informative individuals with great stories to tell. Number five, they're likely to succeed in their career. Extroverts make great workers because they're highly conscientious individuals. They're constantly figuring out how things work and are motivated by challenges. This enthusiasm and creative problem solving sets them apart from their peers, making them approachable leaders, but also great team players. Since extroverts are people oriented, they value interpersonal connections with their coworkers and are always willing to reach out to check in with someone to see how they're doing. This mutual openness really helps a company grow closer as a unit. Number six, they're open with their feelings. Making a good impression is what helps land a job interview or score a first date, but vulnerability is the essential ingredient for cultivating deep relationships. Because extroverts are open about their feelings, as well as the feelings of others, they open the line of communication easily. While introverts are widely considered interesting because of their mysterious nature, the more underrated extroverts transparency makes them endearing and honest individuals. What are some other good traits that extroverts have? Let us know in the comments below. If you liked this video, be sure to check out our website and other social media, as well as our Patreon account. And don't forget to like and subscribe. As always, thanks for watching.


Ionic polymer metal composites, IPMCs, are a type of artificial muscle material that can be used in biomedical devices, flexible robots, and microelectromechanical systems, men's. These materials consist of a proton exchange membrane sandwiched between two electrodes, which allows ions to move from one side to the other when electricity is applied. This movement causes the material to expand or contract, depending on the direction of the current flow. Recent advancements in the fabrication and characterization of conductive materials, such as carbon-based materials and conductive polymers, have led to improved performance of these materials. Additionally, modifications to the proton exchange membrane and electrodes have been made to improve their functionality. These improvements have allowed for the development of new applications for IPMCs, including robotics, MEMS, and biomedicine. This article was authored by Hao Zhang, Xiao Huolin, Yonghu, and others. We are article.tv. Links in the description below.