 Hello, if you are a virtual attendee and you can hear me, can you give me a thumbs up or write something in the chat? All right, I got a thumbs up from Charlotte. Thank you, Charlotte. All right. Good afternoon. Let's go ahead and get started. This is the last session and let me introduce you, Janja Darinevich. She is a senior bioinformatics scientist at the University of Chicago, I'm sorry, University of Illinois, Urbana-Champaign, yes, all right, and she has been a member of Biconductor Teaching Committee for maybe two years, and Janja, please take it away. Thank you, Mikhail. So in true teaching fashion, I want to make sure everybody knows where these slides are because I have lots and lots of embedded links in them. So if you go to the BioC website, so it's BioC2022.bioconductor.org, hopefully everyone has seen this. And if you go to the workshop and demos, we have links here for all of the workshops and the package demos that we can add links, and if you've already given yours and you have any links, so you're still going to give yours, let us know what they are and we can put them in. So I am here in the beginner section, and so this link will take you to the slides. So I am, I said, giving this presentation on behalf of the BioConductor Teaching Committee, most of them are probably asleep right now, a lot of them are physically located in Europe, so I got drafted. So what is the BioConductor Teaching and or Education? There was a thing, and now we're actually calling ourselves the Teaching Committee more. It was formed in early 2020. They report, we report to the Community Advisory Board. It's currently chaired by Laurent Gatto and Charlotte Sonison, but it is open to any interested member of the BioConductor community. Don't have to be a developer. Don't necessarily even have to be currently a teacher or trainer, but someone who may be interested in education. We have monthly virtual meetings. Also we have the Education and Training Slack channel on the BioConductor Slack. The original aims of the committee were to provide networking opportunities and to coordinate training activities. We also wanted to establish the connection with the Carpentries, which I'll talk about in the next slide, and with them assemble BioConductor-focused training material that are consistent with the Carpentries' guiding principles. We also wanted to coordinate delivery of training material at BioConductor-related events, and this talk here at BioC 2022, and then I'll show you in a minute that they're planning on doing a workshop ahead of the Euro BioC later in September. The Carpentries is a global consortium that their mission statement is to build capacity in essential data and computational skills. Efficient open reproducible research and their mandate is any area, so not only sciences but engineering, library sciences, social sciences, any area of research that does any sort of computation. To do this, they want to train and foster an active but an inclusive and a diverse community of both learners and instructors, and they want to collaboratively develop openly available lessons and deliver these lessons using evidence-based teaching practices. So this dovetails extremely nicely with what a teaching committee is we're doing for BioConductor. So what has happened over the last couple of years, we have had initially five community members became certified Carpentries instructors, and we have been actively developing three different training modules. I will go into each of these in more detail in a little bit. But we've developed them in concert with the Carpentries. We've had Toby Hodges, who's our Carpentry liaison, who's helped us quite a bit with this. So the next step, as the Dean mentioned earlier today, as of August 1st, BioConductor will be a Platinum member of the Carpentries. And this link here goes to the new blog announcement. Again, this is supported by the Chan Zuckerberg Initiative. Among other things, what this gives us is we can have spots for 15 instructors to go through their instructor training per year. And these are going to be any one of the BioConductor community can apply to become a certified trainer. So we are the link. This is a link here. We move to the slideshow because then I can just double go ahead and fill out the application. These are going to be done on a rolling basis. The trainings happen throughout the year. And you can pick one at your schedule. They're held in either a two full day or a four half day format, and they're all completely online right now. Say that the BioC intro module is going to be given in Heidelberg, Germany by Charlotte and Ron, and it's going to be prior right before the EuroBioC. We also are planning or naming the BioConductor Teaching Week, which is earlier in September, six to eight. Well, we say week. This is actually it's just going to be a series of one hour community calls staggered through different times so that hopefully no matter which time zone in the world you are, you can join one of these calls. And this is just to have a discussion with the BioConductor community about your educational needs and ideas. So some ideas or questions or what community resources do you use? What resources do you think are missing? What's the best learning resource experience that you know about? And then kind of, you know, what's the hardest thing you had to do? Had you had to learn how to do in BioConductor and what kind of training materials do you think could help that out? So we're working all this final details and the call links is going to be widely advertised in August. All right, so back to the carpentries. They're pedagogical methods. This link right here goes to their instructor training materials. These are excellent. If you do any teaching or training at all in any area, not even just by informatics, this will help you become a better teacher. I really think they have just done an amazing job looking at this. So the number one thing that they espouse is that you have to be extremely welcoming, particularly to novices that have this sort of fear of getting in and not knowing what to do. You need to be proactively inclusive to the community, asking ahead of time if people need accessibility, aids or needs or anything like that. They also rely heavily on evidence-based teaching practices. And so this, that their workshops are less theory-based and more applied approaches, trying to solve a specific problem. Your learners are practicing what they are learning in real time. And periodically, we provide assessments and training exercises or multiple-choice questions that not only see, you can see if they can answer it correctly, but in a correctly-worded multiple-choice question, the wrong answers will give you an idea about what they have not learned correctly and what they're still having trouble with. They also espouse the idea that you start with a kind of a small, simple, no-more-than-six-points mental model of a particular point. You build that up, particularly if you are, is the, I forget what they exactly call it, but as experts, we forget what we already learned or how much we've already learned. And we already have a very complex model. So fitting in a new piece is very easy because we can easily see all the connections to everything else we already know. A novice starting out doesn't have that mental framework. So we need to slowly build up small pieces and then show how they can start making connections. And then from that, they can form deeper understandings. The other thing that I really like and started employing in all my teaching is the feedback from learners in real-time, aka sticky notes, where if it's in person, you give everybody a red sticky note and a green sticky note. And if they're having trouble, they put up the red sticky note and one of the helpers comes to help them. If they're on an assessment and they're working on their own, when they're done, they put up their green sticky notes that way you can tell if people are done or not. One of the things I have found harder to switch to is that they really advocate live coding instead of just presenting slides and actually slowing yourself down and making yourself type what seems like very, very super slowly. Part of this is that in teaching, we tend to go super fast, too fast. And that's actually detrimental because they are actually learning less when you cover more than if you just slowed down and tried not to get through as much and then they would actually learn what you did go through. And again, you need to co-teach with many helpers so you can have one person up being the main instructor and then other people helping out. So the current lessons we have in the Carpentries Incubator is the main, the BioC Introduction. So this is a general introduction to R. It assumes that they have no knowledge of R ahead of time. The Carpentries has many different flavors of these introductions to R and we're coming on R's with a focus on omics data. So that's kind of the domain area that we're coming in. At the end of it, we introduce experiment data containers and we end up with a summarized experiment. The BioConductor project is more actual BioConductor focused. So it's kind of an overview. There's some history about BioConductor. The specific building blocks, we talk about what are the landing pages, what are vignettes, what are the BioC views. You can even find a package that you're going to use and it gives an introduction to some of the base S4 classes that BioConductor has come up with. And then the last one, still work in progress is the BioC RNA-Seq. That's the analysis of RNA-Seq data using various BioConductor packages. These are all under an attribution 4.0 international license. So it means anybody, not even a member of the BioConductor community, but anybody is free to share. You can grab it, you can copy, you can redistribute it in any format. You may adapt it, you can remix it, you can transform it, you can add things onto it. You can even do it commercially. So the question is like, if you're going to run a workshop and you are charging your attendees and you're using our materials, that's completely fine. You just need to give proper attribution. So give proper credit linked to our original license and you need to indicate what changes were made. And you cannot add any additional restrictions on our materials. So how do we use these if you're interested in either running through them yourself or using them to teach others? The easiest way is probably to go ahead and teach from the rendered GitHub IO pages. And I will show you the one for the BioC introduction. And I need this bigger. So again, we have followed the Carpentries template about how you put together a lesson. And so they always start with a homepage, the list of what are the prerequisites for the learners in this course is not much. Although they should be familiar with tabular data and spreadsheets. There's a schedule. Again, these are all set for two full day workshop. That is the timeframe. We have not, we have big estimates. I thought someone was supposed to start putting in. So these would actually show you how long they thought each one would take. And so we're still beta version, but not quite to production yet. From these, they also give you a setup. And you see all the stuff here. Oh, so the code of conduct is also a highlight this very important. The Carpentries code of conduct is probably even more extensive than the bio conductor code of conduct. And so it's really good. But the main thing is not just there's a written code of conduct. There is a framework for incidents reporting and people will follow up on it. This again, really key point is an inclusive community. Yes, question, Nadine. So the bio conductor code of conduct also has like a whole instance reporting thing as well. At what point do we connect if there is a code of conduct issue, could something happen in the Carpentries that would never be reported to the bio conductor code of conduct and would that ever be important? Or is that something we need to consider at all at any point? Or is that completely outside the bounds of this presentation? A little bit outside the bounds. I didn't mean to apply that bio conductor didn't have a reporting because I know that they just revised the code of conduct and that was a big part of it that how you report violations. I don't know that's something to bring up if we're running a bio conductor Carpentries workshop and hopefully it would never be an issue but if there was, which one is the more appropriate place or you'd put it in both? I don't know. Yeah, okay. There's also a nice setup and this is ideally what your learners will do ahead of time before they walk into the workshop. Some really good details about how to install our and our studio. Also it's platform dependent and if you already have it, what do you need to do? You need to check to make sure you're running the most recent version. What do you do if you don't have it? And so for all the major platforms and then everybody, there's just a few lines of code. They just say run this. The other thing which often you will say to do is at the beginning of your workshop say we will be there 20 minutes early if you're having trouble with the setup. So come early and we will help you get your machine working. All right, and then there's the link to the various episodes and they're kind of following in a linear order. Again, they start out with an overview of questions. What are the objectives that we're gonna learn through here? Obviously I'm not gonna go through this right now but there are challenge questions. These are assessments. Some of them are just discussed with your neighbor and maybe we'll talk about the carpentries is also very big in a group learning, communal learning, you're working with somebody else and you're helping to work through it with each other. So while this is a self-contained, anybody can like read it and kind of follow along on their own. Like I said, this is where the instructor is not supposed to have this up necessarily and they're supposed to be live coding on the side of that. I'll show you in another ones. There's different kinds of challenges. I'm gonna scroll down here to the bottom to show you at the end of every one of these, there's kind of a summary about what the lesson was and then a key points and then you would go move on to the next lesson. You can also up here and I believe it was the starting with data show you that the other things that we can do with the assessments which are useful is you can have a question, a challenge and you can have the solution but you can have it hidden. And then you can, so the learners can get the answer if they're working on their own. All right, so what about if you're using these and you find any arrows or typos? How do you make changes and modifications to this? So there's a carpentries guide very extensive guide for novices, novice contributors what to do. Small arrows and typos are most easily fixed by that improve this page every single page at the top. If you notice one on that page we'll have a improve this page which will take you directly to that page. I don't have a count logged in. I don't know I can do it on the fly but if you're not familiar with GitHub if you haven't a GitHub account you'll need to do a if you make the change you're actually gonna fork the repository it'll do it for you on the backend you submit the change and then you push do a push for a pull request to fix it. If you don't have, I guess everyone has to have to GitHub even an open an issue. We will note that we had a very well intentioned helpful people pointing out typos that were actually just the British UK English spellings of words and that's actually the carpentries style. So we thank those people anyway they would really take the fine going through every single one to find the arrows and typos. If you have larger content changes in addition we will also welcome these but usually that's not best to do in a pull request. You can potentially open an issue on the discussion so we can get into it. There, let's see if this will show up if I'm not. Ah, okay. So this is the issue section and you don't have to have a GitHub to see this that we have populated many of these with help wanted these are things that we know we need help with to improve the lessons. And so if you're looking for a way to contribute you can in any of the lessons look at what these are and potentially start working on those. And if you really have other ones that you wanna do you can start love for you to attend the teaching committee and discuss it with us in there. Ideally what we'll go to next is if you what if you wanna set up your own customized page the carpentries has a wonderful template instructions for I now want to set up for this workshop that I'm gonna have on September 15th and 16th and I'm gonna call it this and here's my information about where we're meeting. They have a nice template for that and from there you can link to not only the general carpentry lessons but I think also our incubator lessons. Now if you wanna personalize any of our bioconductor workshops we do not have this template system set up yet. You can fork your own but I think the forking in GitHub is more intended to then push the changes back not just I'm forking it and then I'm just gonna keep going down my own path. Ideally we'll add a template option that you can do this and at the end of this if you have your own template what's nice is that you can get your own rendered GitHub IO page that's an HTML page you can use. At the end you may take any materials at all however and use them like them. If you need the data set that we're using if you like our examples, any of the figures that we use, any of the challenges it's super hard to come up with these challenges. Just make sure that you give attribution and the carpentries here they have a workshop for how to set up not only either an in-person or an online workshop. It's extremely detailed and it's wonderful. If you've never organized a workshop I would strongly point you to look at this and consider many things that you do. If you are a certified instructor you can fill out a form and get the carpentries to listed on their site that you're running a carpentries style workshop. Okay so quick wrap up we'll have some questions. Please apply to become a bioconductor community certified carpentries instructor. You hopefully will be able to find training that works on your schedule and of course it is no cost to you. We haven't quite completely ironed it out but I do think that from this is the interpretation that you're gonna turn around and help run workshops to train other people in bioconductor in R. We think about attending one of the community calls that we're having upcoming during the teaching week and or join the teaching committee and we are happy to take anybody from seasoned teachers to a brand new person. I have to teach my first graduates, as a graduate student I have to teach my first workshop or lab or something and I've never done this before and I wanna learn more. So we're happy to have all levels on the teaching committee. Right now we're meeting the second Monday of every month two to three p.m. central European time. Contact us so this link will go to the Google group or get in touch with us on the education and training slack manner. It's all I had so thank you very much and I'll take any questions you have. Yeah I had a quick question. So you mentioned that there were 15 slots for training is that just for the Germany training or what is that? Like what's the 15 limit? No no the 15 slots is per year we can send up to 15 people and have them they're allowed to go take any of the carpentries instructor training. The workshop that's being held before EuroBioC I think they're pretty much full they have about 25 people signed up for that. But this the 15 per year is to get so at least the two years that we have it we can get up to 30 more people trained to become carpentries instructors. Yeah all of them are virtual and they're spread out throughout the year and in different time zones as well. So it just strikes me that a lot of the workshops and demos that people do at the bio conductor conference are kind of workshops but are not following the style. I guess what's the is there a vision that at some point will be using like for example these templates and so if somebody is submitting a workshop or like a package demo or whatever to the bio conductor conference it would be in the carpentries form or. That could, I was noticing that as myself too where you know we're like okay well it's just time we're gonna just skip this place where we have you to stop and take five minutes and work on your own. I think what it is it's the scale that these workshop demos or even the long workshops are an hour and a half. The module that we're doing for the carpentries that's set for 14 hours of instructor training. So two full days minus. So again it's what can you cover in the scale of the time. I do think that we can have everybody improve the way that they give their workshops but I don't think we can quite go all the way to the carpentries just because of the scale of the time that we do here. Christian up here. I just wanted to ask a little bit about how the carpentries is adapting to virtual learning and how we can like have that level of engagement. For example, you gave the example with the post-it notes we can't, I mean yes we can do some like hands up and raise hands but do you have any feedback on just how to best implement a virtual and maybe even like hybrid class that we've learned over the pandemic? Yeah hybrid, I've taught a hybrid workshop. We've seen what hybrid is here, it's got its pros, it's got its cons. I don't think it's ever gonna go away because of the ease of remoteness but their workshop coordination, they have a whole section. As soon as COVID hit, they had recommendations out by I wanna say April about how to switch over to online, how to do this, how to, I mean they are really engaged in all of this. So whole section on online workshops and how best to do them. And so they have a lot of materials out there as well. So I think you already mentioned a little bit about this but for these 15 or 30 or however many members of the community that would be trained in this, so what would they then, like what's kind of the expectation then? Like I mean it seems like you're creating some of these workshops and then this is gonna be, I guess how you're doing this Europe thing that happens every year, right? I don't know much about it but I know there's some sort of training week and I guess this is how that's gonna be run but are you intending for there to be now more sort of training events or are you just sort of saying we want you to then go out and start just hosting your own stuff to basically we want you to use these, right? Yeah, I have a Dean, well that's because she was the one who wrote up the, so yeah, so myself and the CAB wrote the grant that's kind of funding the concept behind this. So we're also hiring or in the process of hiring a community manager and it will be that person's job to coordinate all of this. So there'll be 15 instructors trained, we hope that those instructors will be able to provide training not just in English but in other languages, in geographically diverse community and support or bioconductors not just within the US and Europe but globally. So that's the idea that these courses are virtual is very attractive to us and yeah, we hope to be able to set up these courses. We hope that we'll have 15 instructors that'll give 15 introduction to RNA-seq workshops throughout the world, yeah. I think that's the plan, isn't it? Yeah, I think in general with the Carpentries instructor training, there are some items that you have to do upon checkout, you've got to contribute to a GitHub lesson in one way or the other and you have to do a demo teaching but I think beyond that they, well not a requirement, they do think they would be good if somehow or another you'd be involved in teaching a Carpentries style workshop like within the first year and ideally people could go back not only to their home institutions, the community manager, we can kind of set up, okay, we're gonna have an online virtual workshop in this time zone and then later we'll have one in a different time zone and yeah, it'd be great to have these in not only also given in different languages and that's, I think we'll bring up at our next teaching committee meeting, I think our introduction to R is at a good enough state that it could probably start being translated in other languages. There's an online question? Okay. Who can be considered member of bioconductor community? Yeah. Okay, so the question is who is considered a member of the bioconductor community? Anybody that works with bioconductor packages do you actually need to have created and maintain a package? No, you do not need to be a developer. I've used bioconductors since almost the beginning of bioconductor about 2002 is when I first got my hands in it I have never developed my own package. I'm a power user, I teach a lot, I do a lot of data analysis, I could not do my job without bioconductor. So no, you do not have to be a developer or maintainer to be considered for one of the teaching positions. And also I would say you don't necessarily have to have much extensive teaching experience either. If you are willing and you're motivated and you want to get in teaching, like I said, their instructor training almost could work better on a novice instructor so you don't have to unlearn all the bad habits that you learned when you were just learning how to teach on your own. So anybody, it's open to anybody. The other, thank you all very much. No, so that concludes day one and we will see you all tomorrow morning. Oh, day two, sorry. I think you, we talked about it, but I did say I would make, not that there's lots of us here. We don't have this building anymore tomorrow and so everything starting at the morning will begin at Sound Garden up on the 11th floor. Yeah, so we will put out also an announcement to everybody, but.