 Okay, so good morning, good afternoon, good evening everyone thanks for joining us for the webinar today. Some ground rules here. Let's see please use chat for comments if you have a question you can post it in Q&A. We'll take questions at the end, but you can enter them at any point. And what else we are being recorded. Okay, so this is the second webinar in the series this is for galaxy resources for educators and trainers in two weeks we have galaxy resources for tool developers so if you're a tool developer. Think about joining us for that. Let's see. So today we have five speakers, and it's really an all star cast. And here's what we're going to cover today. Saskia who's one of the founders of the galaxy training network is going to give us an overview. And then we're going to have five presentations with examples of teaching with galaxy and what the cool resources are. We're going to walk through this as we go it should come in right around an hour. We sure hope. Let's give that a go. So, GTM for instructors, I'm Saskia has a conflict right now. So this is pre recorded but she will be here for Q&A. So, let's play that. And I'm going to go here. Full screen. Okay, and if you can't hear Saskia type something in chat and I will panic. Hi everybody. My name is Saskia Hilteman. I work at the Erasmus Medical Center in Rotterdam in the Netherlands. And together with Birnys Patu and Helena Rache, we have spent a lot of time optimizing the GTM for instructors, which is what I'm going to talk to you about today. So first of all, why should you use Galaxy for teaching. So there are a lot of features in Galaxy, which make it ideal for teaching. First of all, it enables students to focus on the science instead of the technical details of the tools. So they don't have to worry about typing the exact right command in the command line, worrying about where the spaces go, things like that. This is also a very useful skill that can be taught in a different class. But if you really want to focus on the science on the bioinformatics concepts, Galaxy is perfect because it abstracts away that technical layer. There's also no installation required. So students, all they need is a browser and internet connection to participate. And of course, in the Galaxy training network, we have a huge library of free to use high quality tutorials, which you as an educator can reuse in your classes. And it also has a ton of visualization tools and visualization options. So you can visualize your results and the workflows themselves. It's a little very easy to share data in Galaxy. So you can share your results with your students, and you can have them share it back. So for example, if they get stuck anywhere, and they need some help, you can, they can share their history with you, you can have a look and help them get back on track. So all this really supports remote teaching as well. And there is also a thing called TIAS, Training Infrastructure as a Service, that lets you really follow the progress of remote students. But more about that later. And there's a lot more. So Galaxy of course has a ton of different tools. I think there are around 8,000 tools in the Galaxy tool shed right now across a bunch of different scientific domains. And something that's also very cool is you can combine Galaxy with various programming environments such as Jupiter in our studio. So if you also want to teach analysis using some coding with Python or R, you can do all of that without leaving Galaxy. There are shared data libraries where you can share input data sets for tutorials. So students don't have to each individually download those data sets and re-upload them to Galaxy. It's already there. And there are also a bunch of interactive tools in Galaxy such as genome browsers or other visualizations that support more interactive exploration of the data and playing around getting a feel for the data. And of course, a really nice thing is there's a very large global community of Galaxy instructors who you can discuss with, ask for help, things like that. It's really, really a nice community. Now, as I said, we have a large catalog of tutorials available in the GTN. So you can always find the latest stats by typing slash stats behind the GTN website. Currently, we have close to 200 tutorials made by over 170 different contributors across 21 different topics. So we currently have 16 different scientific topics and five technical topics. So you see here the scientific topics range from anything from biology, we also have climate, we have statistics and machine learning, and new things are added all the time. And this graph is one I really love. So you see that constantly new contributors are adding their tutorials and this community is really growing. And all these tutorials are completely free to use in your classes, in your events, whatever you want. And they're all designed to also be suitable for self studies. Students can also just go there, explore, find a tutorial they're interested in, and work through everything themselves without help of an instructor. And we always welcome new contributors. So if you want to teach, want to add your own tutorials here for teaching, then you can do that too. This is the homepage of the GTN tutorial website. You can find it at training.galaxyproject.org. And here you see it starts with the list of all the topics. And you see how many tutorials are in each topic. And here you can start to explore and find different tutorials. And on the right side, you see the bottom of the page, we have a really nice new welcome video that explains a little bit more about the GTN, so I would encourage you to watch it. And also a video here describing how you can connect with the Galaxy community. And there's some latest news, so whenever there are new tutorials or new features, you can read about those here. And of course you can follow us on Twitter. Now each of these GTN tutorials usually follows a scientific story. So a lot of the time we take a published analysis, and we recreate this step by step. So we go over all the relevant concepts, the science behind everything. And we have hands-on sections that really explain what to do in Galaxy is exactly where to click, which tools to open, which parameters to set, and explaining why you're setting these parameters, and things like that. And all these tutorials are designed with teaching in mind from the start. So at the top of every tutorial, you will see a box like this, an overview box, which describes some learning objectives, some questions that are addressed during the tutorial, a prerequisite training, an estimate of how long this will take, level, and link to supporting materials. Some tutorials might come with slides, most of them have some input data sets, the full workflow of everything that's done in the entire tutorial. And there's a list of all the galaxies you can go to to run this tutorial. And at the end of the tutorial there's a similar box describing the key points, the conclusions, just some take-home messages that the students will have learned during the tutorial. And there's a section with some references for further learning. Another thing that we have are question boxes. So throughout the tutorial, you will see these kinds of boxes asking some questions. And the solution is also included. It's collapsed by default. So students can look at the questions, have a think, try to formulate an answer, and then they can check if they were correct. And of course this also helps you as a teacher to maybe get some ideas of how to check your students' comprehension. This is a really cool feature. I think Dave showed it last week as well. But if you go to Galaxy and you click on this top hat or this graduation cap, you will open the GTN website. Here you can browse to different tutorials you might want to follow. And if you click outside that box again, you will go back to Galaxy and do something. And then when you click on the icon again, it'll show you exactly where you left off in the tutorials. You can easily switch back and forth between the two. And the really nice feature is when instruction is to start a specific tool. You can now just click on the tool name and it will pop back to Galaxy and open the tool for you as well. You don't have to search for the tool manually. You always have the right tool open. So that's a really nice feature. So this is also great for people who maybe have small screens, especially in other people who are following from home a lot. So you don't need two screens or maybe your screen between the tutorial and Galaxy. But you can really lay the tutorials on top of Galaxy. And now we have more support for instructors throughout the GTN. So for example, the slides have speaker notes. So if you press P for presenter mode, when you've got the slides open, you will see a view like this. And some speaker notes to help you prepare for teaching this in the slide deck. And what we also do is for slides that have really high quality speaker notes, we can auto-generate video slides using text-to-speech. So this way you can have students simply just watch that auto-generated video, or you can use this to prepare for teaching yourself. So if you would like to see one of those in action, I think Dave showed it last week as well. So if you haven't seen that webinar yet, I would highly recommend you go do that. There's also a link here in the slides for you to check that out. Then there's another fairly new feature. We've added now for every tutorial an FAQ page where we list some common questions and their answers. So things that students have often asked when someone was teaching this tutorial. And this again can help you prepare for teaching a tutorial like this, especially when it's maybe not your area of expertise. And the idea is that this is also very much a community effort. So if you teach something and you get the same question a couple of times from students, or just any question you think that might be useful for other learners to see or other teachers to see, please consider contributing that back to these FAQ pages to help others. And yet all of this is really a community effort. So here you see our Hall of Fame. We have 176 contributors right now who helped create all these tutorials and keep them up to date. And with such a big community, we have new tutorials added all the time and new topics even added regularly. And based on feedback from these instructors and contributors, we often add new features to the GTN and even to Galaxy. So yeah, it's really cool community driven project. Okay. Well, once you have a tutorial, I'll figure it out. You found one that you would like to teach in your workshop or in your class. Then you need a place to run it. So you need a galaxy. Well, the good news is you don't have to run your own galaxy. You don't have to be a systems administrator or talk to the IT department to run it. There are plenty of public Galaxy servers that you can use. So every tutorial at the top you see in this overview box, there is this under supporting materials. You have the section called available on these galaxies. And if you click on that, you get this list of all the galaxies that support this tutorial. So where you can just go and all the tools you need for this tutorial will be available. And another very nice thing is something called TS. TS stands for training infrastructure as a service. It's currently available on the European Galaxy server and soon to be available on Galaxy main and Galaxy Australia. But what this is is you can sort of apply for special resources, dedicated resources for your event for your workshop or your course. There's a little overview here. So normally all the users of the Galaxy server, they do their analysis, they start jobs, and those jobs go into queue and you might have to wait a little bit of time before it's your turn. Now, of course, during a workshop, you don't have a lot of time to wait around. So if the server is busy, you might end up waiting a little bit longer than you would like for your jobs to finish. So what you can do is you can apply for TS and then you get sort of your own special dedicated queue with some special resources behind it, so that your participants, your learners don't have to wait in the regular queue. And it also provides a nice little dashboard where you can monitor the progress of everybody who joined your event. Now, if you want this, this is a really nice service. I use it all the time myself. I love it. If you want to use this, you can apply. It's all free. They'll ask you for some information. So when is your workshop? How many people are you expecting? What exactly are you going to teach? So if you're using GTN tutorials, you can just provide them the link and they'll know exactly which tools you're expecting to run and based on that, they can estimate how many resources they should preserve for you. So that they will handle. What you get back is a URL, a join link. And the only thing you need to do is get students at the start of your training or of your lesson to click that link. So to join the special queue, to tell Galaxy, hey, I'm part of this training, put me in this special queue. And that's it. The rest is all hidden behind the scenes, but it works really well. So if you're going to teach a Galaxy event, whether that's like a single day or a longer running course, it doesn't matter. But I would highly recommend requesting TS for your events. Now this is the dashboard I was talking about. So you also get a link to this sort of overview page. So you see here at the top, there is an overview of the tools that have been run. You can see, for example, here, the tool feature counts has run 27 times and nobody got an error. So if I know that I have 27 students in my class, I think, okay, everybody's done. If I know that I have 50, I can see here that, okay, about half the people have reached the step in the tutorial. So this is good to get a little bit of an overview. Below you see more detailed information about individual jobs. You can see green means it's okay. And if you see a lot of red, you know, okay, people are having difficulties with this particular tool. Maybe I should go check on that or re-explain things like that. This is actually for remote training. This is very useful because, of course, it's a little bit harder to see the progress when you're not physically in the room with people. You can't walk over and look at their screens anymore or ask them. So this is really a nice feature for that. And if you do want to post a Galaxy workshop, you've picked out your tutorials, you've found Galaxy Server to run on, perhaps requested TS. And then you're going to go into the other details of organizing your workshop. And we also have a special topic in the GTN with some tutorials and guides to help you do this. So we provided some checklist of things you might want to think about before your workshop, but during your workshop and after the event. Some tips and tricks for instructors from the day. Just some things that different people have learned from doing this that might be useful for others. We have a slide deck that you can use to start your workshop off that explains a little bit how things might work during the workshop. And if you do want to configure your own Galaxy Server to support the training, if you already have one running or for whatever reason you would like to run your own. We have tutorials for that as well. And a Docker image per topic to maybe make this a little bit easier. So maybe you want to teach something that you can find in the GTN, but you have your own materials, maybe somewhere else, and you would like to add these to the GTN. We would love to have any in all tutorials. And we have a special topic that really walks you through everything you need to know about how to contribute your own tutorial to the GTN. How to write these tutorials, how to write your slides, how to use GitHub. And we are very happy to help you here we know, especially the first time you might need a little bit of extra extra help so you can always contact us. And of course this big community of 200 others who have done this before. So they're very happy to help you here. Now if you do contribute, you will of course get credit for it for your edition so you'll be listed at the top of all the tutorials you'll be listed on the slides, and everybody gets their own contributor page listing all their contributions across the GTN. And if you're curious to see like okay I made this tutorial but are people using it. You can also view that so we track metrics for all these pages. So if you go to the extras menu at the top. And then go to page metrics, you will get a page like this a little bit you can see the number of views of the tutorial over time. You can see where in the world, people are viewing it from the devices they've used and all sort of stats like that. The community is the greatest thing about this so we have a get our chat channel where we can just talk to each other, both about the GTM materials or running workshops, or finding events to go to. Also, if you might would like to maybe get a few extra instructors to help teach your event. Feel free to ask here and then you might find some people willing to help or to travel or anything. So this chat, you can find here and it's also accessible from the web page of the GTN itself. And if you want to see any upcoming galaxy related events including trading events. There's a link to the events page, and we really encourage anybody who is using Galaxy for teaching to also add their events here. Of course, we're very curious to hear from you, your experience using Galaxy for teaching using the GTN materials. And so we have a special forum for people who have used this as an instructor. It's also found at the end of every tutorial in the feedback section. Or maybe you want to start maybe a discussion about certain topic around Galaxy or how Galaxy can be improved how the GTM materials may be improved support teaching further. You can do that on GitHub. The links are in here. So you see we have different just different instructor discussions with with Galaxy instructors. We also have regular collaboration fests cofests. So every three months on the third Thursday, we have a day dedicated to working on GTN related activities. So we have three community calls in three different time zones. So here we just have a zoom call together we discuss a little bit. We'll tell you a little bit about the changes to the GTN in the recent months and our plans for the future. You can give us feedback. Tell us about any events you've hosted or planning. What things you need help with things you are just wondering about all that. Yeah, you can come to those calls. And we'll be available all day for support on GitHub. If you want to do some hands on work creating your own tutorials or updating tutorials, or maybe just you would like some help in organizing your workshop. Feel free to drop by one of these calls and then and talk to us. So the next one is May 20. And really everybody's welcome whether you're brand new to the GTN or I've already made several tutorials. Yeah, just join and talk to us. So if you want to join this there's a link in the slides to get more information including how to sign it. So the next part of this webinar will consist of several examples of using Galaxy for training using the GTN materials. So I will start off sharing very briefly our own experiences with fully remote and hybrid style trainings. And some of the other speakers will cover using Galaxy in a high school setting in a university setting, or in research institutes to educate later career scientists. And we have one nice example about using Galaxy as part of the citizen science outreach activity. Okay, so remote global training. And of course with the COVID pandemic recently, we in person events weren't possible anymore. And so we've experimented a bit with using Galaxy completely remotely. This actually worked very well and in February we had hosted the GTN smorgasbord event together with Helena Russia we organize that. The GTN event was a five day 24 seven nonstop event across all time zones. We had 1200 registrations from 78 different countries, and we use a completely asynchronous format. So this meant that all training sessions were pre recorded and available on YouTube. So we had over 40 sessions of more than 25 hours of video material. And the idea was that participants could start these sessions whenever they want they could stop they could take breaks, they could really manage their own time around everything else in their schedules. And they would come to Slack chat for support so they're following these video tutorials following along on Galaxy. So if they had questions about the science or they got stuck. They went to Slack they typed the question and one of over 60 instructors from around the world would help them answer their questions. So this, this format really worked well to support a global audience. And we really hope to make this an annual event. So hopefully next year we'll do the same thing, pandemic or no pandemic. With this there's a link here to a blog post. It's really a nice training for us to organize. Now, since we did this event, we now have a very big catalog of video tutorials as well. So all these videos, because it's an instructor basically running through the tutorial step by step and guiding instructor or guiding participants through a tutorial. And now these are all freely available on YouTube. And these are all free to use if you want to reuse some of them in your own course in your own event. You're free to do so. The event webpage is also still up and usable. So here you see, for example, you see your schedule. We had these sessions on day one. And if you click on one of them, you get a view like here on the right. You get the video is embedded. You get some information about the session where to run link to supporting materials like slides and everything. You might need a FQ document where to ask questions on Slack and things like that. So this is a nice additional resource for other instructors as well. And if we're going to do this type of event every year, these videos will also stay up to date pretty well. So our hope for the future is to sort of offer this catalog as sort of a shopping cart style interface where you can sort of select which modules, which trainings you would like to teach in your workshop. And then you get a website like this, but tailored specifically to your event. And we also want to offer all the other things that sort of we developed as part of this training and that we discussed with other people doing similar events. So you have, you would get a website like this very easily, you would get a Slack space where people can ask questions that's already configured. We can share our communications plan with you so we can just show you this is what we did in terms of promoting the event, sending emails to participants, things like that. And we can also share our registration forums or feedback forums, all that to hopefully make it even easier for you to post a similar event for your for your event. Now something slightly similar is hybrid training. And the Australian bio commons bioinformatics community has become very experienced at that and we do something similar for a project called gallantries. So present those two to you now. So in Australia they've used this approach a lot of course Australia is very big place and it's not so easy necessarily to travel between different cities in Australia. So what they've been doing for years now is hybrid training. So hybrid training is a combination of remote and in person formats. And how they do that here is you have one instructor teaching behind a camera. So here you see Anna and is facing a camera, but you see she's alone in a room she doesn't have a class in front of her. But she is teaching these tutorials. And that is live streamed to several classrooms across the region. You see here, Anna's view so she's teaching here about assembly on zoom and she sees a feed from the different classrooms in their screen. And then in one of these classrooms you see there's a group of students, they have their laptops following along. And you also have dedicated helpers to communicate maybe back to Anna. If people are falling behind maybe tell her great, can you slow down can you repeat the step or explain a little bit more about that. So each classroom has instructors to help these students if they get stuck and helpers to communicate back to the main presenter. So this is a really nice format and works really well for them. And if you want to read more they have published here and there's a link in the slide. Now for another project we have been at employing a similar format this hybrid training. So, and the project is called the gallon trees and it's called up because it's a mix between galaxy and the carpentries. Now for those of you who don't know the carpentries. This is by informatics training, but it focuses more on coding and using the command line. So for the gallon trees project we've tried to combine both these things. So we have a set of tutorials for RNA seek that start off with the initial analysis in galaxy, and then do some downstream analysis, using our and Python, both inside the galaxy so without leaving galaxy. So for example, using our for some some nice visualizations and things like that. So this is, yeah, a really nice little set of tutorials. If you want to combine coding galaxy. And our plans also to deliver this with this hybrid format, except with the COVID pandemic now we've changed this in the past year to fully remote format. So we have a couple of years to get back to hybrid when it's possible again. And over the next couple of years we will also expand the number of tutorials that sort of combine this coding with galaxy to other topics as well. So beyond just RNA seek. If you already want to try sort of these programming environments inside galaxy. You can do so, for example by going to live use galaxy.e you. So you can click on these and you will get our studio or Jupiter notebook right inside galaxy. And there are some special, special functions to sort of move data from your history to to the coding environment and back. And that's really cool. And that was all from my side so now we'll hand over to the other speakers of today, but I'll be available for Q&A session at the end of this webinar. Thanks. Thank you Sasuke. That was great. Next, we have Christine Kuchinata of the Fred Hutchinson Cancer Research Center. She is a postdoc and she's working with high school students and using Galaxy. Okay, Christine take it away. Can you hear me? Yes. Fantastic. Thank you so much. And first of all I just want to say the Galaxy training network is amazing and I feel like I've only scratched the surface of it while working with high school and undergraduate students using Galaxy so I'm just going to give you all kind of like a case study of how I've used Galaxy to train high school students. And as was mentioned in my postdoc Fred Hutchinson the Sukiama lab and our lab focuses on how gene expression changes occur during the cell cycle, and we focus on the chromatin environment on that. So the program that I am mentoring with is one of Fred Hutchinson Cancer Research Center's Science Education Partnership, I apologize, it's a little early here in the West Coast, for high school students. And what the idea of this is to allow high school students to work with researchers at Fred Hutch, and this year as many programs have become it's completely virtual. And so the way this works is mentors can be group leaders, staff scientists, postdocs, grad students, technicians, and it runs throughout the entire school year. And for me, I meet with my students, I have two students and I meet with them one on one and in a group setting each week and then they work with program leaders and talk about other topics. So about students spend about six hours per week in total reading and working on their analysis from projects. And so, as I mentioned earlier our lab is focusing on gene expression programs in the model organism budding yeast. And like many genomics labs we have a lot of data to analyze and probably more than we can handle right now so it's been a great opportunity to incorporate the use of galaxy to mentor high school students and undergraduate students and helping us complete create new projects and analyze data. So a lot of the data sets that we focus on our chip seek M&A and RNA seek data sets in a mixture of paired end and single end so they can learn a lot of sequencing concepts through those as well and I will say the galaxy tutorials have been fantastic for this. So the overall project that I've given them is to understand how cells re re express their gene expression from a state of dormancy and so I've given them data sets that have already been published in the lab and they are now taking these raw data sets of Paul to are any polymerase chip seek single end data sets and looking for basically learning how to align the reads and do further analysis and I'm going to tell you what they did here in a second but just kind of get an idea, not going to the biology behind this at all but the idea is that they're looking for genes that are getting activated and then asking questions regarding those genes are they controlled by specific transcription factors for example so it's kind of an exploratory project centered around this data analysis. So, as I mentioned, the students can use this Paul to chip seek data so they're only working with one type of data in the very beginning single end. It's a bit more simple. And they, everything usually for the most part has been contained in deep tools which is available on galaxy and this has been a really great environment for the students to explore their data. And so this point of given students freedom to choose gene sets of interest and have them formulate their own hypotheses so they can kind of diverge in their projects at this point. So they can ask which genes are induced which genes never induce from this cell cycle progression stage. And then again like because we're chromatin lab they can actually look specifically at what is the chromatin state so then we can introduce a new data type M&E seek data and paradigm data, and then they can also look at that sequence motifs of these genes of interest. So one of my high school students has actually done a lot made a lot of progress or both of them have made a lot of progress, but it's going to talk about one of their projects. So they, one high school student basically found about 800 activated genes that have a common have a common motif for trans a use transcription factor and this motif with or the genes, the targets for this transcription factor were 30 fold high, the expression of these genes was about 30 fold higher higher than what has been seen during normal growth conditions so this was very new information for us. And so at this point he decided that he would focus on this transcription factor and what genes this transcription factor might control. And then he wanted to know what is the chromatin environment here and so he looked at paired end M&E seek data and found that the chromatin architecture was likely rearranged during at these locations. So since we're a chromatin lab we went ahead and we actually had a lot of chromatin data so he then went through all of our data sets on his own and found actually some very interesting co localizations and reminder this is a high school student and actually kind of glossed over the fact that we did spend some time going over the central dogma what is what is DNA what is RNA. So we're going from very basic understanding to actually doing this analysis and coming up with his own hypotheses. And so here he found some co localizations with this transcription factor target and chromatin remodeling factors. And so now in the lab we're actually testing his hypothesis that this transcription factor candidate can actually target these remodeling factors. And so far this has been basically, you know, giving them a lot of freedom to ask their own questions. And having the tools and the tutorials, especially from the galaxy training network has really given them their own like empower them to ask their own questions and actually come up with these hypotheses. And while this has been all remote in the lab, I am able to be there and I can type it and so actually right now I'm testing one of my students hypotheses specific for one example is do these transcription factors to target certain remodelers, for example, to these genes that are activated. And so I was really excited because he actually found these 800 genes and where they are targeted here. And the, he found very striking co localizations here. So I was really impressed with how quickly the students were able to get up and running and I think taking away the, you know, the, the technicalities of like programming command command line really allowed them to think about as Sasuke mentioned earlier. And I think that this is really a testament to how useful galaxy can be in training students, especially those who haven't learned even what, what a gene is yet so I think that this was really exciting. I kind of spoke a lot faster than I intended, but I kind of wanted to end here, mentioning that there are other. There are a lot of reasons to use galaxy and in training high school students and undergraduates and this galaxy training network has been very useful with all of the tutorials, especially for chip seek their, their really great tutorials on how to analyze chip seek data sets. And the other great thing has been you're able to outreach a lot of students across the country or the world, depending on what kind of mentoring program you don't need to require any university access since we can even just do this on the main galaxy platform. And you can get projects up and running really quickly thanks to not needing to have a special environment set up for each analysis pipeline. And I just wanted to leave here there are actually a couple of virtual mentoring programs where you could actually institute similar ideas where you're giving students data from published either published data sets or if you're in a lab situation and you have data laying around that really needs to be analyzed you can actually like use as a teaching tool and give students an idea of how to create their own high. And so two of them are one is geared toward undergraduate level and it's called the national summer undergraduate research program or NSERF and you can apply to be a mentor there and NSERF work. And then a global high school level program is called Athena women in STEM and I've participated in both and had excellent students in both programs so with that I guess I will finish and I think we're taking questions at the end is that correct so I will answer questions and I apologize if I spoke too fast. That was good. That was great. Thank you Christine. And you have a question at the end so this is good. Okay, let's see I'm going to start sharing I hope share screen good. Okay, and then. Okay, let's try. Okay, so up next is me I'm out Jean. I tried. She's a she's faculty at the Evans school in the Netherlands and she's going to talk about galaxy in a university setting. Yes, thank you Dave for your introduction. Hi, everyone. I'm Miao Miao. So I'm working in the Evans University of Applied Sciences. We do have English name. We are located in Breda in the Netherlands. So yeah, our university has 18 academies and I work in the Academy of Life Sciences and Environmental Sciences as the data education coordinator. The purpose is to use Galaxy in a few years. This is the fourth year we use Galaxy for teaching. So things are going quickly. In our school we have four departments. That's a biomedicine education, chemical engineering, chemistry and environmental sciences. So I will introduce a little bit what we are doing in the biomedicine education. Please next slide. Yes. So we start to introduce Galaxy in year two. We give students a 20 weeks project. These students team up and their project is half wet, half dry. They spend four wet lab sessions. So actually those are days, four days in the wet lab. They will have to grow their own materials and afterwards they use Minion for sequencing. After that it's always six days of dry lab sessions by using Galaxy. This year we've chosen the topic to be bacteria drug resistant bacterial strain sequencing. Our students got four different strains from REVN, which is our National Institute of Public Health and Environment. So it is a real true identified drug resistant bacteria. But the students will have to re-identify and recreate the scientific funding that people already found in the labs. So this works. For the Galaxy part we decided to make our own Galaxy tutorials because the students are year two. They are very enthusiastic but when the tutorials go too deep they get lost. So we made our own tutorials and more will be available in the Galaxy training hub because we want to dedicate to the community. So yeah, this year we do drug resistant bacterial strain sequencing. Next year maybe we will do environmental DNA sequencing. In this way we can roll down and attract more students. So this is for year two setting and for year three. Dave, can you please go to the next slide. For year three students. We use the shmugashboards, videos and training materials really effectively. We try to. So one of the examples that I list here is the ARNASEC course that we give to our students. There are eight sessions that they have to complete. And this is two ECTS, European Credits, that's 28 hours per credit. The course is set up with a really pattern. So the students always have to prepare by watching the videos provided by the training hub. I would like to say thank you all for the speakers. Those are great videos, much better than myself in the classes. So afterwards, during the classes, students will have a PowerPoint provided by me and my colleagues to give them a theory. Afterwards, students use the online tutorials. They build their own workflows by using the materials. So for example, ARNASEC, they are using the fruit flies. But by using the fruit flies, they have a workflow to evaluate their outcomes because this is a two ECTS class. We give them a novel data set from cancer research that we just published. So everyone gets a part of that data set. They have to reapply the workflows that they built by using fruit flies on these cancer data sets. So they have to revise, work together, brainstorm, ask questions, write a small report. And this is one of the cases that we apply to the students. We also have the NGS class. We also have the Metabolomics classes. And at the moment, we are trying to build up a course in a similar fashion by using existing galaxy training materials for our environmental sciences students. In the ecology class. And the rationale that we have here by using galaxy is that we want to focus on teaching ARNASEC. We do not want to teach students programming or BASH in a limited amount of time. We have only 56 hours. If we spend half of that to teach students BASH and most of them get stuck with a very badly documented error message in the middle of a BASH command. Hey, where is the part of ARNASEC? Our students are biomedicine students who will end up in the lab becoming a person who's going to sequence all the samples. There will be bioinformaticians to help with real hardcore bioinformatics questions to analyze the data and go straight forward to the answer of the questions. Well, we say galaxy is one of the best options. And Dave, can you please go to the next slide? So that was the part that we use for teaching our students. Now I'm going to show you what we are doing with our teachers. As interesting as it sounds, we have 85% of our teachers have a PhD diploma. Many of them worked as a researcher before they came to our school as a teacher. However, teachers started to get nervous because nowadays in biology at least the technique renews really rapidly. Every four to eight years, there's a complete renewal of techniques and the data that we are generating is getting bigger and bigger. People are starting, people starts to be nervous. So we decided, okay, we are going to teach our teachers how to generate big data with new technology and also how to analyze your data properly. So luckily, we were selected with the Dutch National Funding Scheme for Education. The project is from the sub-city category called Comenius. It is €107 for 18 months. There we choose for the subjects big data, we use Galaxy. There we let our teaching assistants, those are technicians in the web lab, our teachers, our project leaders and students. We let them learn side by side because the technology is new. Then it's new to everyone. So the perspectives between teachers and the students get exchanged rapidly. It's really fun to see them sitting next to each other, try to find out how Galaxy works. So by far we use the NGS data input. We use Galaxy workshops in this project for Metabolomics because we generate a lot of data by using LC-MS. So this is another part that we are doing, not only with students, but teachers and students together. Dave, if you move to the last slide, then I will show you a little bit what we are doing only for the teachers. So we just started a new project called ABCDS, so it's advanced bootcamp of data skills. There we focus on upgrading the data skills in our teachers. Meanwhile, when teachers are upgraded hopefully with the skills, they will automatically upgrade our curriculum. We have an ambition. So our school always has this five years ambition. And this before 2025, one of our ambitions is to add data education everywhere in our curriculum. And there for data analysis and big data, we decide to use Galaxy again. Meanwhile, we will upgrade our own dry lab facilities, which we will have a dedicated Galaxy server. Because in our students' projects, sometimes we receive samples from the hospitals, then the data will be confidential. So that's a little bit an overview of what we are doing in our School of Life Sciences and Environmental Sciences. I hope this will give you a little bit of the flavor, what we are doing and with the existing materials of what we try to produce in the coming years to support the community. So that's a thank you very much for your attention. Yeah. Thank you. Yeah, that was great. Let's see up next is Sabina Maheta, who is with the University of Minnesota and she's going to talk about training for research scientists. Hi, hello all. Thanks Dave. My name is Sabina Maheta and I'm a member of the Galaxy for proteomics team. We are at the University of Minnesota. I think by now all of the panelists have already shared how great Galaxy training network is in their experience with teaching. So today I'm basically going to share my experience and a few pointers for training research scientists using the GTN, which has definitely been a great experience for myself. Next slide please, Steve. Thank you. So the first question is why should you use GTN training? Firstly, I would say that it is to introduce new topics to researchers, could be earlier career researchers or later career researchers. It is easy to use with slides or videos. Secondly, to keep everyone up to date with the latest tools and workflows available. For example, I usually teach at conferences or at the university-based setting. We usually conduct workshops when we want to introduce the work we have been doing in our lab, following the latest developments in the field. Sometimes we cover the happening topic or we want to share our thoughts on a particular topic. The benefit of such training is that we can usually foster interest in fellow scientists who are part of the same field that could eventually lead them becoming your collaborators. The second question is how to do the training or conduct workshop. In my experience, there are two ways. You could use a demo wherein the trainers can record their videos, post it on YouTube or Vimeo or any other publicly available resource. The benefit of these demos are that the trainers can use it in their own case, their own galaxy instance, and the attendees can also learn at their own pace in the case of, like in the case of the GTN Sparng School. Or we can also do a hands-on in-person workshop wherein the trainers can use any of these, any of the instances mentioned on the right, or request Tias to use Galaxy EU, which has been really a great experience for us. The benefit of in-person training is that you can provide a step-by-step instruction while the trainees are following you. And it also helps you explain each of these steps very clearly. The only issue or drawback that I have seen that is that you have to mention prior to the workshop that they have to bring their laptops with them. Next slide, please. Okay, so once you decide on how to train, the next plan, next part is how to plan. You have to plan your training. When we are planning our workshop, we usually develop our own tutorials as most of the time they are a part of our new scientific publication. For example, the Metatranscriptomics tutorial that you just see on the screen is a part of our journal paper. So what we do is we create this GTN as a part of our journal article to make people familiarized with the topic and also to give them a step-by-step instruction on how to use the workflow we've developed and the benefits of using it. However, you can also decide on using a tutorial that is previously developed by others, which you might have found interesting and thought it was beneficial for everyone to know. And if nothing else, you can decide on creating your own tutorial, as previously mentioned, and there is a lot of help for that. Next slide, please. Now, a few pointers before conducting your training or workshop is the first thing is test the tutorial yourself. Make sure it works. If you are the person who have written it, then ask people in your lab or someone else with less experience to test your training to ensure it works well, as well as they will provide you with valuable feedbacks. Frequently during our workshops, we use trim data sets or like smaller data sets for training purposes to ensure that the workflows are not time consuming. We also try to test how long our workflows run so that it's in the time constraint. If for some reason we are not able to trim our data sets or the workflow is too time consuming or there are some tools which take too long to run, then we provide a walkthrough or something called a cookbook style workshop, for example, what are the different attendees, what the input files are needed, how to run the workflow, what the parameters are and show them the output that they get from the workflow. In that case, the most important thing is to prepare example histories as nothing could go wrong if you have example history showing the output of your output of your tool or output of your workflow. Next slide, please. So first in your workshop or training in person, the first thing is to make sure is you give the users or attendees enough time to follow the tutorial. A few basic things to remember is that from my experience is that firstly give basic introduction to Galaxy and its features. Secondly, provide basic background pertaining to your topic. Be very slow. Ensure that everybody is on the same page. And at the end, allow a question and answer session because that's how you will know whether the attendees have understood your topic or not. Next slide, please. Now, if most of the questions are already answered during your training session. Sometimes what happens is that the attendees still have more question and there's not enough time to do it during the workshop, then we can offer them channels such as Slack or Gitter where they can interact with the trainers. You can also provide them with FAQ Google Docs. Next slide, please. Once your workshop is over, please feel free to ask for feedbacks. It's not just to know how many people attended your workshop or the quantity of your workshop, but also to attend, also to understand the drawbacks. Like, was your workshop too quick? Was it too slow? Was it informative? Was it productive? Was it valuable enough for them to perform their own research? Where shall you improve in your training? If you're using the GTN for the feedback, then at the end of each training tutorial, there are feedback forms. Or you can also decide to create your own feedback form. Personally, I have benefited a lot from these feedbacks because they have helped me improve the content of my tutorials. Next slide, please. Just to wrap up my part, if you take home messages. Why to use GTN training? Because it's truly user-friendly and provides a step-by-step instruction which is very beneficial. Second, preparation, preparation, preparation cannot reiterate more than that. It's just needed for your training for sure. Third, test your training material and be mindful of the time. Fourth, user communication is very important. Communicate with your attendees during and after the training. Lastly, feedback is truly important for improving your quality of your tutorials, making your content better. Thank you for listening to me. If you have any questions, please feel free to contact me at my email address provided here. Thank you. Thank you, Sabina. That was wonderful. It is a very common case to use Galaxy for training of researchers. Okay, our last presentation today. Oh, first of all, if you need to go at the hour, you're late because we're two minutes over the hour. But don't worry, we'll record stuff and publish it later this week. So if you need to go, go. Otherwise, stick around for the last talk and for Q&A. So last talk today is from Bernice, excuse me, Batu from the University of Freiburg, and she's going to talk about Galaxy for Teaching Pupils and Citizen Science. So let's go there. Hello everybody. So I'm Bernice Batu, a researcher at the University of Freiburg, and now I will show you how we use Galaxy for reaching and teaching pupils, a broad audience, mostly pupils and citizens with the Street Science project. So the Street Science project was started by researcher and some teacher at the University of Freiburg, and one of with the aims of introducing biology and genomics to a broad audience. And one of our key project currently is the Biodegraded Projects, which is an immersion into biology, bioinformatics and science via beers and daisies. So in this project, we organize one or two, one, mostly two days of practical workshops on Biodegraded to give pupils that we reach through the schools and citizens, the way that they can learn about DNA, sequencing technologies, bioinformatics, open science possible and their possible application and the impact of all of it in everyone's life. So all of these workshops are organized. So we take some beers, we extract the DNA of the yeast there directly with them so they do it on their own. So we teach them, we show them how to do that, we do that with them, we develop some from a simple protocol for that. In sequencing, we're using Minion, and once we got the DNA sequence, we do the data analysis to try to identify what yeast we can find in the beers. And so we're not good in details about the first steps of extraction and sequencing, but for the data analysis, you will expect so we use Galaxy, and we develop specifically we had a dedicated interface using the street science dot use in the EU, and we developed so some workflow for that using microbiome available tools, we share a data that regenerated with sequencing in shared data libraries. And we managed to organize one or two several workshops where we did that with pupils and citizens. Because it's not possible since the beginning of the pandemic to organize workshops, we are now moving to, we are currently developing online games using Galaxy in the back, where we could teach there where the people can learn about microbiome data analysis within Galaxy. But currently it's still ongoing project if you are interesting and we would like to participate feel free to reach me. And, and otherwise, we will share the news about that later when we will have more details about that on that I would like to thank you, and thanks. Okay. Thank you very nice and thanks to everyone. All the presenters. Let's see. Yeah, that was great. I do have to say very nice that a whole set of cool talks. You had the coolest topic. So thank you. So we have time for question and answer. We have one question so far well we had to but Sabina answered one of them. The question is for Christine. So if the panelists want to turn their mics that would be great. How steep is the learning curve for the students. So, I would say galaxy wise, it's pretty. Thanks. I, I sound like a preacher but honestly it's really very, very helpful. Honestly, I think the bioinformatics side has been very low learning curve and I think that that's just a testament to the beauty of the interface. The biggest learning curve has been more in the biological concepts but I think spending these one on one meetings, not just going over analysis but also going over the basics and allowing the students to ask questions, being super approachable and friendly I think has been very helpful because then they're not afraid to ask questions and then you can really help them get up to speed. I think on these concepts. Okay. If you have questions you can paste them in the q amp a post them in the q amp a. I have a question for for everyone. And this touches on the question that was just asked on Christine. How do you deal with classrooms full of people that have a huge range of experience, a huge range of background both in biology and in, you know comfort with computing per se. So this, this happens a lot, especially when I teach researchers so some are very tech savvy and some aren't so often I have a mix of like master students who, you know the computer well and older researchers who have trouble like copying links. So, it's hard. It's always hard but having lots of helpers around to help so it's easier in an in person event but if you have go slow. As the main teacher but also have some helpers that it's okay someone falls behind and they can sort of get help to get them back on track. I think that's the main thing. And same you could do with with online classes if you have sort of a second channel for communication chat or zoom. A helper could could help give individual help to people. Thank you. Anyone else want to touch that I would second saskia we usually have a group members like coming and helping us like walking around the room basically to make sure that everybody is on the same page. Everybody is able to follow we that's what I mentioned during my talk is initially we have to give them basic galaxy background to make sure everybody knows how to navigate things around galaxy interface. And then during the tutorial we have people going around and talking to people so that we make sure that they are understanding because yeah everybody is on different wavelengths most of the time. Thank you. Um, question. So Sabina included some things about support like getter and slack. I have a more basic question backing up so today we're using zoom and zoom is a popular choice but do you all have a preferred platform for the, you know the live feeds, you know things like this Christine you're nodding so. It's called it's sort of similar to slack but it's for video gamers and I find that it's a little bit easier for students, like younger people because they actually already have usually accounts. And you don't have to have a separate login for each like server platform or channel so actually usually we have that going while we're discussing or actually students will ask me questions very similar to slack like in a direct message but the cool thing. And I don't want to start selling discord but you can also really easily do voice chat and screen sharing in that. Um, so if the student or anyone has a quick question you can be like, we can just hop on you don't have to make a separate zoom meeting or anything like that so honestly it's actually pretty great tool for teaching. I recommend and if you have any questions we actually have a temp. I run a discord server for chromatin people and give a template. Wow, my community if anyone's interested. Thank you Christine. Have you. How we're using teams. Very good. So our school has just decided we will move to Microsoft everything including Azure. So that's really well, but the nice thing about teams is we can create the classroom teams. You can give assignments to students. The file folder than all the students can upload their files. So actually we use that to check their performance and the results can be exported easily in the format that we can using our. Study records system code or series again so then easier to do. If you have a non sessions with students and each time you have 160 students. Well, that that that you need something that's automatic. So don't we use teams. It's fine. Very good. Thanks. I'm very nice. Have you got something to throw in. No, okay. Already before the pandemic for the hybrid trainings. So it's, I mean, I like it, I like it, but so I cannot, I cannot recommend or something else for the smugglers bought they used slug, which was quite useful there. Especially to organize so Sasuke and then I did an amazing job to organize the channels by two by topics so by tutorials. And it was really great then for the people to find where to ask for to ask question there. And really, it's was really nice. That was amazing how well that's scaled. So 1100 participants and in Slack you could figure out where to ask the question and you could figure out, let's see where to answer it. The easy part was where to answer. But yeah, yeah, that was amazing. Okay, we are at 12 after the 13 after the hour and time flies. Let's see we do have an acknowledgement slide let's see if I can get there. And I will throw that up. Boom. Okay, and I will share that. And then, first of all, while I do that, I would really like to thank all of you. For joining today. Some of you I did not even know. So, thank you for doing that. And thank you for responding for that it's very indicative of the galaxy training community, the network that people are always willing to help so that went really well. I'd like to thank the funders for each of our speakers, as well as for the galaxy training network itself. And I'd like to thank all of the participants for spending an hour and now 13 minutes with us. So, thank you very much. I'm going to stop recording now if I can figure out how, and we'll close down the webinar. Okay, thanks everyone. Thank you Dave, you're a great DJ. We'll see if I can figure this out. Okay. Thank you everybody. Okay, bye. Have a nice day.