 Hello everybody and welcome to the GTN Smorgasbord, a truly global galaxy training event. My name is Saskia Hilteman. I work at the Erasmus Medical Center in the Netherlands and I am one of the organizers of this course. I'm very excited to have you all here. Over a thousand of you have signed up and this will be an event that runs 24 seven across all time zones and this is possible due to a global community of volunteer galaxy instructors. In this video, we'll walk you through some of the logistics of this course and explain how everything will work this week. So what is GTN Smorgasbord? GTN stands for the Galaxy Training Network and this is a global network of trainers who use Galaxy for training. Smorgasbord is a Swedish word for a meal consisting of a lot of small dishes that you can then get a taste of and you can pick and choose which dishes you like. You can skip some food that doesn't look good to you or you can get a little taste of everything or focus on one kind of thing that's up to you. If you prefer a slightly simpler word, you can think of this as GTN Tapas as well. What this means for this workshop is that during this week, you will be able to get a taste of all the different GTN tutorials that are available. We have tutorials on a wide range of topics and you can choose which are interesting for you to follow and which you'd rather skip. So the Galaxy Training Network is a network of many, many Galaxy trainers who have collected their training materials in a single place and we will use these trainings during this workshop this week. And there are over 150 different contributors who have made over 185 tutorials across 21 different topics. And over 50 volunteers from this global Galaxy training community are here this week to help you work through these tutorials. Now, before we start, I want to remind everybody that we have a code of conduct and there is a link in these slides if you want to read it. But basically this means that everybody should feel safe and respected during this workshop. Basically, just be excellent to each other. Now, if you encounter any issues or violations of this code of contact, please report them and you can read how to do that in the code of conduct. Okay, so the program for this week, you can read the full program on the course website. Basically, we will start off with an introduction to the Galaxy platform itself and the basics of NGS analysis. Then on the second day, we will dive into RNA-seq analysis using Galaxy and using R inside of Galaxy. Wednesday is a half day. We will cover single cell RNA-seq analysis. And this is a short day, so it will give you some time to maybe catch up from the previous days if you need. And on Thursday, we will dive into proteomics. And on Friday is a Choose Your Own Adventure day. So here we have a broad range of tutorials you can choose from whatever sounds interesting to you. So the theme of this week is that you are in charge. It is an asynchronous event, which means that you can start whenever you want. You can take breaks whenever you want. You can end whenever you want. You can decide your own time. All the tutorials have video lectures, so you can just start watching these whenever you want. The same goes for the program. If you are not so interested in certain tutorials, feel free to skip them. If you don't have much time on one of the days, feel free to finish that tutorial the next day or even the next week. You can manage your own time and we will be there to help you if you need questions or if you get stuck on the Slack chat platform. Now, before you start, there are a couple of things you will need. So here's a link to the course website, which you should already all have. You're going to need an account on one of the three main Galaxy servers. So we would suggest you choose the one closest to you. We have usegalaxy.org based in the U.S. You have usegalaxy.eu based in Europe and usegalaxy.org.au in Australia. Each training session on the website will list which of these Galaxy servers support this particular tutorial. And lastly, you should join Slack so that you can ask any questions to one of our instructors. If you get stuck or if you just have general questions about the tutorial or about Galaxy, you should have received a link to join here via email. And if not, let me know. Once this course is over, everything will stay online. And then you should ask your questions, not in Slack, but in the GTN Gitter channel, which we'll also link to. Now, this is what the website looks like. If you expand one of the training sessions by clicking on the top here, you will get everything you need. So you will see the video. You will see some information about the speaker. Below the video, you see some more information and also which servers support this tutorial. So most of the tutorials are supported by all of the main servers, but please check here if you can't find your tools, whether it is supported on the server you are on. And below here, you see a link to any supporting materials, so any slides or tutorials that the presenter uses will be listed here. And there's also a link to an FAQ document. So here we will put the most common questions and answers in this document so that if you have a question, you can look there first to see if it has already been answered before. Okay, as I said, everything here is based on videos. So we have some video lectures and some video hands-on tutorials where presenters walk you through the tutorials step-by-step. You choose how to use these materials. Maybe you would like to just watch the instructor or maybe you'd like to watch and follow along yourself simultaneously. Or maybe you'd like to watch the video first and then try it yourself later on. Or not everybody likes videos. You are free to just skip the video and work through the tutorial on your own based on the manual that is linked below. Now just some quick notes about the video. So all the videos should have English subtitles. So you can turn those on using the gear icon at the bottom here on YouTube. You can also change the playback speed here. For example, if someone talks a bit too fast and you want to keep up because you want to follow along in Galaxy yourself, you can slow it down or you can speed it up. And you can also adjust the quality. So this is useful in case your internet connection maybe isn't great. You can scale down the quality a little bit. Okay, then if you are doing these tutorials and you get stuck, you can get support from our instructors. And I want to encourage you to ask lots and lots of questions. That's what we're here for. That's what this week is all about. There are no dumb questions. Don't be shy, ask away. So there are multiple ways to get answers. One are the FAQ documents for questions that may have already been answered before or you can ask our instructors on Slack. And of course, if you know the answer to the question of one of the other participants, please feel free to answer it as well. Now we have round the clock support on Slack due to instructors from all time zones. We may have certain time zones that have a little bit better coverage than other ones. So if you don't get an answer right away, please be patient. Someone will get to your question eventually. Now this is what Slack looks like. You see on the left here there are a bunch of different channels. So we have for every training session a dedicated channel where you can ask your questions relating to that particular training. There are also some general channels such as general or social. And here you can talk about things not related to a specific tutorial. Either you have general questions about Galaxy or about the course or you just want to socialize with the other participants and the instructors. You can do that in the social channel. Now, if you get very stuck and you can't get a good answer, you can't really explain what the problem is. It is also possible in Slack to start a one-on-one calls where you can share your screen with an instructor. Okay, each day we also have an icebreaker session. So we have a small question for you to answer on Slack. This lets the instructors know how many people approximately have joined today and have gotten started. It also is meant to sort of get to know each other a bit and encourage discussions. So feel free to respond to each other here as well. And also we have some social sessions. So once you are done with the day or if you just need a break, you can go to these channels and socialize. So there are things from games and quizzes to just chats about a certain topic or just talking with each other. And so please look at those in Slack. If you would like to organize something like this yourself, just let us know, we can make a channel for you and you can start your game, your chat, whatever your idea is. Now, we would also love your feedback. So if you have any comments, suggestions, compliments, complaints, did you see something as a typo in one of the materials? Please let us know. And there are two main ways to do this. If you have any feedback about the materials themselves, so the slides or the tutorial manuals, there is a feedback form at the end of the tutorial where you can give your comments. If you have comments about this specific course, about this week, please use the Slack channel named feedback for that. And after the course, after this week is over, all the materials that you see here today will remain online. So you can keep working with them if you didn't have time to completely finish or if you want to run them again later, you can always come back and do them again. Some of you have asked about certificates. These will be available upon request. Just make sure to do the icebreakers every day so we know you attended. And at the end of the week, we will send you a form where you can request your certificate. And also make sure to save the Galaxy histories that you've created during this week, performing the tutorials so that you can show us which tutorials you ran. And most importantly, have fun. Now, before we start, I really want to thank the Galaxy community. This has truly been a community effort. So a big thank you to everybody involved. This week would not be possible without the many, many volunteers from the community. So this includes people who you will see presenting tutorials here, people who help out asking questions on Slack, people who've worked on these subtitles for the videos, people who've created the tutorials to begin with and the slides, people who've made the tools in Galaxy, and of course the administrators of the Galaxy servers who have worked hard to support all these tutorials on the Galaxy servers. So next up is a video where you will meet some of your instructors. This is not all the instructors. Some of them you will see later on in the week during the training session. Other, you will see on Slack answering questions and lots and lots more people have helped behind the scenes to make all this possible. So thank you. Hello, my name is Anna Seym. I'm based at the University of Melbourne in Australia, working for Melbourne Bioinformatics and the Australian Biocommons and developing a lot of training material for life science researchers. So I hope to see you in the training session soon. Hello, everybody. My name is Florian. I'm responsible for the quality control session in day one. I'm a trained bioinformatician and I'm doing my PhD right now at the Rothbach-Auffengruppe slash Pyongurengruppe. So here and there I am mapping out the Galaxy project here in Frybook. And I'm doing half applied bioinformatics as well as also theoretical bioinformatics. So applying machine learning and creating some tools for data analysis. And I analyzed so far Eclipsec, Chipsec, Adaseasec, RNAasec. So a lot of data over the years. And hopefully I can give you there for a lot of insights for quality control. I want to advertise very, very briefly a short site project which we have here in Frybook which we started two years ago which is called the Street Science Community Frybook. It's an open science project and we created this with the intention to foster the communication between science and the general public. So this is a two-day workshop for pupils, students and really everybody who's interested. We have done this because we saw that there was an increase in spreading fake news and fears about science which you really see right now during the corona crisis. And therefore we wanted to foster this communication between science and the general public. And we carried this workshop where a group of students or pupils or whoever wants to join extract and analyze yeast from beer. So we analyze some microbiome of beer using nanopro sequencing. And if you want to know more about this project then please follow this link, the Street Science Community. There you get a lot of information. It's the workshops are currently on hold because we have to set up everything online which we are doing right now. But you can also help us or if you want to spread information about this project then please do follow the link and hopefully the workshops will continue this year. Thank you very much for listening and yeah, have some really fun days. Bye-bye. Hello everybody, I'm Bernice Batu. I'm a postdoc in the Freiburg Galaxy Team at the University of Freiburg in Germany. I'm a bioinformatician. I mostly analyze sequencing data from RNA-seq or metagenomics and I develop tools to facilitate this analysis mostly in Galaxy. I regularly give trainings on data analysis and I'm involved in several training initiatives. So for example, I'm recording with Saskia and Elena the Galaxy training materials project that you will use this week. And I will teach you this week the RNA-seq data analysis. So I really hope you will enjoy this week of trainings and have fun. Hi, my name is Fauci Samopoulos and I'm a research engineer to apply biosciences at the Center for Research and Technology alas in the Selma King Ries. My research focus is on bioinformatics and machine learning but I spend also quite a lot of time in providing training both at the national and international level. Some notable examples include Elixir and the Elixir training platform as well as the Galaxy project and Erasmus Flash project that is led by the Erasmus Medical Center in Netherlands. Hello, my name is Wendy Bacon and I work at the European Bioinformatics Institute in Cambridge, UK. I am involved in single cell analysis and single cell research and single cell courses. So I'll be co-teaching a bit of single cell analysis later in the week and I also really enjoy teaching martial arts. So that was my hobby. Yes, looking forward to you meeting you all. Hi, everybody. I'm Mehmet Teckman. I work in the private Galaxy team and I will see you all on day three of the GTN. My name is Melanie Full. I'm a postdoctoral researcher at the Institute for Surgical Pathology in Freiburg, Germany. In my research, I apply mass spectrometry to analyze the molecular tissue content of two more samples. I've used Galaxy for a few years now to analyze my proteomic data and I'm looking forward to show you in the course how to do the same. See you there. Hi there. My name is Tim Griffin. I am a professor at the Department of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota. My research interests are developing analytical and bioinformatic tools and focused on biological mass spectrometry and then using these tools to apply them to interesting questions in biology and biomedical research. My laboratory has been involved in the Galaxy for Proteomics or Galaxy P project where we've been developing galaxy-based tools for multi-omic analysis. And also, part of my position is to direct the Center for Mass Spectrometry and Proteomics at the University of Minnesota, which supports research efforts in biological mass spectrometry. Hello. My name is Subina Mehta. I'm currently a member of the Galaxy for Proteomics team under PI, Dr. Tim Griffin. My research interests lie in the application of analytical and bioinformatic tools focused on omics-based studies such as proteomics, proteogenomics, and metaproteomics. My current research focuses on developing proteomics-based analytical workflows in the Galaxy platform, debugging and maintaining bioinformatic tools, developing training materials for the Galaxy training networks and workshops and also helping disseminating open-source tools within the Galaxy platform. To know more about us and our work, please visit us at www.galaxyp.org. Thank you. Hello. My name is Pratik Dilip Jattab. I'm a research assistant professor at the Department of Biochemistry, Molecular Biology, and Biophysics at the University of Minnesota. I co-lead the Galaxy P team along with Professor Griffin. My research interests include developing analytical workflows for mass spectrometry-based proteomics applications such as metaproteomics, proteogenomics, and DIA data analysis. My publications can be accessed through Google Scholar link or PubMed link. I can be reached via email or Twitter. Hello. My name is Suley Narasha. I am a teacher in higher education at Avonce Hope School in Bereda, and I am also a PhD student at the Erasmus Medical Center in Rotterdam. My background is in biochemistry and bioinformatics. I worked for some years doing phage genomics, and as part of that work, I started the Galaxy Genome Meditation Project. I've spent a lot of time working on visualizations and sort of workflow summarization tools, and these things are very important to me. I hope you have a good week. Hello. My name is Andrew Oczewski, and I'm a graduate student at the University of Minnesota, where I work in the Griffin and Treticova labs. My research is focused on the application of multi-omics to inflame systems with a particular focus on quantitation of proteins involved in reading, writing, and erasing epigenetic marks. I'm also a part of the Galaxy for Proteomics group here at the University. For the Galaxy Training Network's Morgesborg, I'm presenting a proteogenomics tutorial focused on searching protein mass spectrometry data against custom-faceted databases. Hi, I'm Anne. I'm working at the University of Oslo in Norway as a research software engineer, and I'm developing tools and training material for the Galaxy Climate Workbench. I would be very happy to help anyone interested in the Galaxy climate. See you soon. Thank you. Hello, I'm Anthony Brottodou from Rennes, France. I'm working for INRAE, the French Agronomy Institute. I'm the assistant dean of galaxy.genoes.org and the usegalaxy.fr. I contribute to Galaxy and to GTA or IUC, and I'm also part of the Galaxy Genome Meditation Project. Hi, my name is Willem de Koning, and I'm currently a PhD student at the Erasmus Medical Center in Rotterdam, the Netherlands. I am doing this PhD now for almost two years, and I work on pancreatic cancer data. I did studies in bioinformatics, and for that I did an internship as well in the Erasmus Medical Center in Rotterdam, and for that I wrapped tools into Galaxy for antimicrobial resistance, and therefore I'm an instructor.