 Welcome, everybody. My name is Saskia Hilton. I'm Clayton Rasha. And this is the third annual smorgasbord training course. This video will get you set up with everything you need to know to follow this course as we can get the most out of it. And all the course logistics. So let's get started. Thank you all for joining. It's nice to see so many of you signed up again. So for those of you who have not attended one of these events before, what is the GTN smorgasbord event? So the word smorgasbord comes from Swedish and it means a meal with lots of small dishes to choose from. And that way you can get a little taste of everything. But also you can choose what you would like to have and maybe if you want to skip something. So it's the same here with tutorials. We offer a wide range of tutorials in this workshop. And you can pick and choose which one of these you want to follow depending on what's interesting to you and what your experience is. So what's the GTN the galaxy training network is a collection of over 340 tutorials for galaxy analysis this is ranges from bioinformatics to life sciences to climate sciences and even now statistics and COVID analysis and more machine learning as well. It's a project that's by the community for the community it's been going on for eight years and we're really excited to bring you a lot of contact in the galaxy training materials. Today or during this week, we will be following the galaxy project code of conduct this we expect this to be a welcoming and friendly event for everyone. If you have any issues that you feel could be code of conduct violations there is form we encourage you to report them there. Please before you start the event make sure you've read through the galaxy project code of conduct and know what is expected of you during this week. Okay, then about the program this week. So this may be a little bit different than other courses you've been to. In this event, you decide your own program. We don't have a set program for you. What you need to do every day, but you can decide. So we have prepared a lot of modules for you around different topics to help you find the tutorials of interest. And if you're new to galaxy, I would suggest starting the first day with the intro to galaxy section. This will guide you through what galaxy is how it works and the first analysis. And then you can move on. If you are sort of new to genomics. I would suggest the sequence analysis basics module. And after that, you decide. So we have here bunch of modules they can are arranged by analysis types if you want to learn about transcriptomics meta genomics machine learning things like that, you can pick a module here. There are some also by sample types of you already know oh I want to analyze health data or plant data, microbial data and things like that then look at one of those modules. And we don't have just genomics data tutorials. We also have non genomics modules to have a look at those as well. We have a page and it can be found in the short link gx y.io slash more for three. We also have some new modules this year. So one of the ones is bio conductor and are. So these are a set of tutorials outside of the GTN, but they do use our inside galaxy contributed by the bio conductor team. And a great set of new tutorials so if you are interested in bio informatics with our, please check those out. There's a special bio conductor galaxy you will use for these tutorials, but you will find all this in the welcome video on that module. And we also have a new fair data and best practices section we have tutorials about our own crates research objects crates. If you're interested in this please check out that module. We also have the bio informatics buffet module. So this will give you a little bit of an introduction to all the different topics and introduction to genomics transcriptomics proteomics, and then you can really get broad range of topics. And other than that you are also welcome to try anything else so even go to the GTN web page find a tutorial you're interested in, even if it doesn't have a video, or if it's not listed here. So welcome to follow that tutorial and ask your questions in this in this course. So the format of this course will be an asynchronous course, we will be having helpers that are available online all week long in slack. So if you have questions go to ask your questions there. One of our helpers from across basically all the time zones in the world will be available to answer your question hopefully some tutorials have more or fewer instructors available for that topic so they may not be available. They may not be available immediately and they may take some time to get back. We're all here as a volunteer organization and volunteering during this week. All of the video, all of the resources for this workshop are available as videos and as text tutorials so if you prefer video watch the video to prefer the text, you can go watch the you can just read the tutorial itself. So this week there will be no live sessions so you can take breaks you can start you can stop whenever you want. If you have you know childcare responsibilities, the GTN smorgasbord hopefully can fit very well into your schedule. Everything you'll need for this week is available on the smorgasbord course page which we will link in a lot of places this has links to the video that you want the video, the training materials if you prefer that, and also links to the support links where you can ask questions. We recommend to you that she's the galaxy tutorial map for each of the galaxy servers you use during this week. There is a little icon at the top this little graduation cap icon, and this will open the galaxy training materials directly within galaxy itself. There is nice integration with this so when you go to access the tutorials you can quickly jump to tools and workflows that are referenced by tutorial authors. The video that the join tool is linked directly to the galaxy that you're accessing. So this makes it great for small screens you don't have to town back and forth between multiple different windows you can really just go to galaxy and also follow training materials there. Okay, so one note about some of these videos. Now let's see recently updated the history panel quite a bit, and some of these tutorials were recorded before that update. So it could be that for some of these tutorials, what you see the instructor on the instructor screen is slightly different than how it looks for you. So this is the case. Please check out FAQs we have about histories and this will tell you how to perform all the history actions like deleting creating new history, switching between histories moving data around everything like that. So the instructor does something and you're not sure how to do it in your version of galaxy. Check out these FAQs. And if you still are not unclear, you can just always ask us and slack of course. Most of the introductory videos the version should match but for some of the more advanced videos or maybe a mismatch between what you see in the video you see in your galaxy. Okay, so all these training sessions have videos, like we said, you can, these can be different types, some are lecture videos. So here an instructor just walks you through a slide deck and explains the topic. And there's nothing for you really to do but listen and learn. There's a lot of tutorials where really the instructor will guide you through the analysis and the ideas that you follow along on your galaxy. And you can pause the video if you need a bit more time. That's all fine of course, but it's really, yeah, for you to interactively follow. And there are also some more demo type videos where the instructor really shows something but you can just watch and learn from that without following along. And you should also have some automated videos for some of the slides. So some of the slide decks will have automated text to speech versions of it as well. And it's also up to you how you use materials. If you want to follow along, please do so. Remember to first watch the entire video and then do it by yourself later based on the written instructions that is totally fine first. Or if you're not a video person, you can just skip straight to the instructions and tutorial and just work through the entire tutorial on your own. So that's all up to you as well. So if you do watch the videos, make sure to use check out the gear icon here for extra settings. All our videos have subtitles in English. So please remember to turn these on for help for you. You can also change, for example, the playback speed if something throw a little bit too fast for you slow it down so that you can keep up without having to stop and restart the video. And if you're having sort of trouble with buffering or the quality, you can also adjust the quality of the video. And this can be very useful if you're on like a bad internet connection. So getting set up. There are a couple of different galaxy servers you can use. We have I think five supporting us this time hopefully the European Australian American Belgium and French galaxies these are all going to be available for you to use during the week. So if you can always check the get set up for the course section for more information on this, which server you choose does not matter. We would suggest of course that you choose one that's close to you in terms of where you are in the world. This means it'll be easier for you to get support more quickly and talk to people who are working on that server in your time zone. We also have training infrastructure as a service setup. So these are special URLs that you will visit once at the start of the course. This is a special queue that will let you run your jobs a bit faster. So for all of the different galaxy servers, they have they're very heavily used by a lot of other community members. However, for this event, a lot of them have set aside special resources just for the smorgasbord users. So if you're following on with the course we recommend you click the join to us link that is appropriate for the server you're using so if you're using the European galaxy server, then click the European galaxy TS link. So make your jobs run a bit quicker and gives you easier access to all of the resources available. Lastly, of course, you'll need to join Slack. We've seen some of you doing this already. So exciting to see all of you joining. But if you have not done that already you'll find the instructions and link for where you can do that within the course program. So if you run every tutorial, we also recommend that you check the supporting galaxies. So we're making an attempt that all of the galaxies will support the vast majority of all of the tutorials, but it can be the case that some galaxies do not support the tutorial you might want to run. So here in the training materials we will also display this on the video library, a list of supporting galaxies. So here we've separated them into known working where we know that galaxy has precisely the versions of tools that are used in that tutorial. There's also the possibly working category for galaxies which have a different version of the tool the tutorial may still run but the results may be a little bit different so watch out for that. But we recommend you always check this for starting each tutorial. Please note that you can make accounts on different galaxies, but please do not make more than one account per galaxy so don't have two European galaxy accounts just one. Okay, then for support we will use Slack this week. So Slack is a chat platform. We have a channel for tutorial where you can ask at least specific questions. And we also have more general channels like social waking like really talk to each other and get to know each other, general and random channels for other discussions. We will post important announcements to the announcements channels. We have received the invite link in email. If not, it's also on the course webpage. So make sure before you start that you join Slack and have a look around introduce yourself. Under each tutorial you will find the link to the channel for that tutorial where you can ask your questions. There will be instructors from around the world available 24 seven to help answer your questions, depending on your time zone and the time zone of the instructors who know the topic may have to wait a little bit for you to get an answer for your questions so please be patient. We also have icebreakers in Slack. So at the start of each day, we ask a question and we ask that you answer this question in Slack in the social channel. So this is a little bit to, yeah, to help us get to know each other to see with was there and was active, and especially if you would like a certificate at the end of this course, please make sure to do these every day so we can see that you were actively participating. The course certificates will work like this every time that you complete a tutorial, then you should run a slash completed command in the channel that is associated with that tutorial. This way we can get a receipt of your history to know that you've done the work and then we can record this and write up a certificate for you at the end. If you want to see which courses we have you recorded having done, you can use the slash transcript command in Slack. And then at the end of the course, once you're done with everything you want to do, you should run the slash request certificate command with however you would like your name to appear on your certificate. We will generate these certificates. We're going to try and estimate the ECTS that would be appropriate for that and this will all be included in the certificate that will be set up to you at the end of the course. If you have any feedback, comments, suggestions, complaints, let us know. All of the training materials that you're going to engage with this week are openly licensed and we're happy to make updates wherever we find something wrong. So let us know if you see anything. If you have any complaints or comments about the course, please let us know. There is a feedback survey and the wrap up of the course. So at the end of the week, we'll have a feedback survey that we'll send out. Please let us know your deep thoughts on what you liked, what you didn't like in the course. If you have feedbacks about the individual materials themselves, there is a feedback form at the end of every GTN tutorial. And then of course there is a hashtag feedback channel in Slack that you can join. If you have thoughts on any of these, please let us know. Course instructors, people who have written these training materials will be in all of those channels and they loved here that you enjoy those material or what was your favorite part. So please let us know your thoughts on each material. Yeah, and I think this is it for the logistics. I think you're ready to get started now. But before you do, I want to thank everybody involved in this. This is really a big community effort. And it would not be possible with all these volunteers from the Galaxy community. This includes people who are recorded videos who presented the videos, people who are around to answer questions this week. People who added the captions to the videos, people who wrote the tutorials in the first place, people who added the tools to Galaxy, people who run the Galaxy. Like so many people came together and worked hard for this event. So a big thank you. And then now I will leave you with the most important slide of this presentation. Remember to have fun and enjoy. Thank you.