 Okay. Hi everyone. I'm just testing to make sure the mics are working and the visuals are coming through. Let me know that. Maybe pop it in the chat. Perfect. Great. Thank you so much and thanks for coming. Today's webinar is about using the OSF as an electronic lab notebook. I'm Nikki Piper. I have my colleague with me, Sarah Bowman. We're both on the product team here at Center for Open Science. So Center for Open Science, if you're not familiar, is a non-profit mission-driven organization. Our mission here is to increase the transparency openness and reproducibility of research. The objectives of our webinar today are to sort of introduce the reasons for using the OSF as an ELN, demonstrate some of those essential features that the OSF encompasses and how they can be applied for the use case of an ELN, and to also give you some additional resources that you can take after this and go do some exploration of how this can be applied into your workflow. So quickly, we're going to talk through an overview of using the OSF. For those that may not be super familiar, if you are, I'll keep it really brief so I'm not spending too much time on it. The OSF is a tool that is used throughout the entire research lifecycle. So at the beginning of your research, where you're doing search and discovery all the way through data collection and finally publishing a finalized manuscript, today we're going to focus in mostly on the areas where the active research is happening, where you're working through development of an idea and collaboration, designing your studies, working through materials and data collection, even storing your data, analyzing it and interpreting your findings. So some of the key advantages that the OSF offers, besides the one I just referenced, which is that it's an all-in-one tool for your research lifecycle. It's cost-free. There's no cost to the researcher. It's open source code. It offers public and private use, meaning you can start in a private mode and do all of your collaboration there, but at some point when you're ready to maybe publish your work or send it out for peer review and you want to give some private link access or public access, you can do that very easily. It encompasses provenance tracking, including activity logs for all of the actions that are taken by all of various collaborators. It's also a very collaborative workspace where you can add various contributors and give them different access permissions all the way from admin, the full control down to just read access where they can see private content but can't change it. Also, there is a nice structure within the OSF that allows you to build hierarchies of a project where you can break apart different pieces and get those controlled accesses as needed, and you can even turn on a feature called request access, where somebody may have access to one aspect of the project but want to be more involved in other aspects that they can just ask you through the interface. Okay, so now we're going to jump into more of a live demo, so as you know with any live demo situation, there are opportunities for things to go slowly or not work. We've practiced and tested everything, so hopefully that won't be the case, but if it does, please just bear with us or use that sort of downtime to put some questions in the chat and we'll be sure to answer them. Okay, so now I have to figure out how to, okay, here we go. Beautiful, okay. All right, so here is a private project. We made it public, so you can actually access this on your own if you want to explore while we talk through some of these cases and features. This is a project, obviously it's created for demonstration. Some of it isn't actual or factual, but for our purposes today we'll pretend that it is. So I'm going to see if Sarah wants to kind of talk through some of this as just an intro into how an OSF project is structured. So this is from the perspective of a user that is logged in and has created a project and is now beginning to work with others in their lab to collaborate on a research project. Thanks, Zinke. Yeah, this is an example project to give you something to look at and understand how you might know about structuring your own project for your own research. So what I've done here is created a top level project that states my particular research project. I've added Nikki as a contributor to the project. You can add all of your contributors and to the project and give them particular permissions depending on what type of access you want them to have. You just want to be able to read, for them to read the materials, you want them to be able to edit the materials, and if you want to give them administrative access, which would allow them to add other contributors and manage public-private setting. So I've added Nikki to my project, created a number of components for the project to try various parts of my research. So I've got one component that is my lab notebook. I've got a component for my microscopy images. I've got a component to manage my reaction data. I've got a component. Maybe I'm at the end of my project, and I'm ready to write this. So I've got a component just for all materials related to my manuscript. And then I've got another one related to my protocols. So each of these components can have different privacy settings. So maybe I want others to be able to discover that I am working on hydroxy methylpheryl oxidation, but I don't necessarily want to share my reaction data just yet. So I can leave my top level public so it's discoverable, but keep my data private until I'm ready to share it. I can store all kinds of different file types in my project, and many of them will render right in the browser. I can store them natively on OSF storage, or I can connect a number of different add-ons. So for example, maybe I'm collecting reaction data on an instrument that is connected to a computer, and it dumps all of the data directly into a Dropbox folder for me. I can go into this reaction data component and go to the add-ons tab and connect my Dropbox folder. So it's a couple clicks of a button. You provide your authentication token to Dropbox, and you connect a particular folder, and then you'll see all that data directly in the files browser. And it just pulls that right in for you. There's a number of different add-ons. The most popular ones are Dropbox, Google Drive, or Fox. It's also worth noting I'm a collaborator with Sarah, but it's not my Dropbox folder. But because I'm a contributor on this project, even though I don't have access to that specific Dropbox folder, because she's provided the token, I can see all of those files here, and she doesn't have to add them to her Dropbox just for that. So let's pop into the lab notebook component. And here I'm using the wiki as my lab notebook. So do you want to talk about... Sure. So where we thought we'd jump in is in a use case where perhaps I'm a PI running a lab, and I've got several grad or postdoc students that are going to be working with me for the next few months, and I want to make sure that I have good visibility into their day-to-day and make sure that everything that they work on is captured here so that the next students that I bring in can pick up this work and continue on. So what I've done is simulated a situation where the notebook is a component that then I would add these various students to. I could also have multiple components within this lab notebook component for each of those students. It's flexible to work with whatever the situation may be, but in this case I've just provided the daily lab entries for these staff to sort of look, and this is very basic, but you could imagine much more elaborate if needed. But basically here I can describe what I want to see in every entry from this point forward. So I want them to give me some description, some experimental setup and design information. I want any data collected here either in a table, which I've sort of simulated a table where they could list out some characteristics that we saw. We'll get into a little more depth in ways in which you could provide data here in context and annotate that data. And finally, I just want basic conclusions. So that's sort of the template for working, and this is something you can make as sort of a home wiki so that everyone coming from here can just copy and paste this into each wiki entry to make sure that it follows the necessary information that everybody expects to see. A question, can the wiki content be duplicated to work like a template as in for my next project? You can duplicate an entire project which would template everything within it. So you could set up basically a component that you want everyone to copy. Or I think it's, yeah, it's not built yet. That's not doing specifically what you're asking for is not possible, but that is a great feature. Yeah, I will make note. Thank you. Okay, a couple details just to talk through about how the wiki functions. Right now you're just looking at the view of what I've already entered, but what you can see is that I obviously started working on this and made several different iterations. And so if you wanted to go back and see the first version of this and that was a version you wanted to go back to, then that's simple to do. You can also compare versions where we can see what's changed from one point to another. This might be useful if one person who started this research project sets a template and then down the road somebody has iterated on that. It's easy to kind of follow that track and know what's changed when and by whom. If I wanted to go in and edit this, this is where we can get into very simple understanding of how the wiki functions. It is using markdown language as the syntax, which is really simple to understand. But if in case that's not something that's needed to your workflow, there are buttons in the UI that allow you to quickly sort of drop things in. So if you wanted to interpolate the list for your report findings, you can just start working that as you'll see on the left side, it's in real time. So things that you want to put in here, you can just add an item or discussion, and you can keep adding more and more. And then you can quickly see those reflected and save that version. So that's a quick understanding of how you might be able to work with a template for setting the stage for the entries that you want to see. If that's applicable, that's how you would go about it. If not, we've kind of carried that theme throughout. So all of the entries in this particular lab scenario are using the prescribed template that we came up with, which is very basic. But here's an example of day one, October 1, 2019, where there's some initial work done to describe what the protocol is that's going to be used and some specifics about the experiment. Yeah, we just used a template from the other page. And then I think here we have linked to this protocol that is stored in another component, but we'll show you in a few minutes how you can actually embed files in the Wiki as well. And we've used the numbered list and the bulleted list and markdown to describe each of the steps that we took to produce this solution and then also dropped in an image that renders right in the right in the Wiki. If that's part of your workflow, it's easy to put those things in along the way. Yeah, and real quick, let's open up the edit page. You kind of see how this is constructed and you go. Obviously the markdown headings and the numbered lists are here. I don't know if you want to talk about how the image was actually put into the Wiki, but I think people would want to see that. Yeah, I actually just dragged and dropped that from my desktop right into the Wiki and then it uploads that file into a folder on this component called Wiki Images and renders the image right there on the screen. Okay, I'm wondering if I might have something quickly. This is nice, I think, because like in this example, if I were in my lab making this solution, I'm just taking a picture of what it looks like. It's not something that I'm going to take lots of images. It's not microscopy images. It's just something to say like, this is what it looked like at this point in time. It's easy to just drag and drop in the Wiki. I'm not really going to do a whole lot more with it and organize it in any other way. Okay, let's jump into a little bit more of the details that we were sort of living to earlier, which are ways in which you can describe more specific things that are happening in other places in your project and bring them right in here so that you don't have to bounce around. One item might be that your experimental setup is actually easier to describe by just providing the video. So the Wiki supports video embeds of multiple video types. I chose to just drop in a YouTube video, but it's a very simple syntax. You just, here it is right here, use the at symbol YouTube and drop in the URL. Then you can describe different pieces of that. You could pull out screenshots, still images from specific stages that are happening in that experimental setup and drop them right in and actually describe them for anyone else who needs to come in here and understand exactly what was done at that time. If we move on to the next iteration that we wanted to show you is around the ease of just sort of embedding files directly into the Wiki space. So this is going to show you a protocol file that was embedded directly here and it's rendering as just as it would in the iFrame in the browser. So you can scroll if there are multiple pages you'd be able to scroll. You have all the functionality that you have here where if there's any more pages, I mean everything is easy to sort of see in one place right here. So the way that you would do this, it's a very easy syntax. You just use the at symbol, the osf, and then you put the GUID for the file. And then you can carry on with describing and annotating. You could do multiple files. You can make this as long as you need to or you could break it apart into multiple Wiki's. Another aspect that is pretty neat is that if there is another project that you want to reference in your specific research project, you can do that just as I did previously, which is to take the GUID of a file from another project and drop it in. This is what I have done here. This is another project public on the osf that has to do with tumor cell images. And I have used the same mechanism to just use the GUID of this particular file and embed it right here into the Wiki. And one of the features that you can use on just regular file rendering within the osf that also actually carries over into the Wiki is for these really high res images, you can zoom in and pan across the image to see specific areas. So I'm going to try to demo that for you real fast. What you need to do, one, there's this really handy helper function here, but you can zoom in by clicking on the image and scrolling. And then you can move your mouse left or right to pan. I think there's a lag. I think you're seeing this. Hopefully you are. But I encourage you to go try it out too. This is really nice because a lot of times these images are really difficult to bring into an interface when there's so much high resolution data there. And just to clarify one point, Nikki kept mentioning the GUIDs for files. Those are those five character IDs at the end of the URL. So that's all you need to know to be able to embed these images. So this is the file that I pulled in in the project. And I just captured this five character GUID that references the file to persistent identifier OSF. So I'm able to drop that in. And it recognizes that. Let's see. What else? So a couple more details that I don't think we gave a whole lot of context to, but I'm happy to do that. Is that files support tags? So you can tag those files if they're probably for easy discovery. The recent activity logs on this project specifically that Sarah and I are collaborating on shows what actions I've taken and when I did them and what general updates I've made. So that's really helpful if you've got a multi multi collaborative project where you've got different people engaging. If you want to just if you're not necessarily part of the day-to-day but you want to come in periodically and check the activities that are happening. It's really easy to scroll through the daily entries to see who made changes to what and when they did them. I think that is a good introduction. I can switch back to the slides. There's a couple more examples besides the live demo, but before I do that I actually want to pause and give an opportunity for any questions that you might have in mind that we didn't show or you want to see again or that we didn't give all the answers to your questions. In the live sort of demo before I give you some references and look at those together. So does this mock-up have a dmp or remade.txt to describe how to name the files, file formats for the data in this demo? That's a really good question. We actually do not have in the example project, but that's a really good suggestion. I think a really good thing, probably at the top level project would be to add a file that would be a data dictionary that might describe what the columns are in all of your files, a data management plan that describes. You generally produce these when you're applying for funding, how you're going to manage the data, and so certainly including a copy of that in your project would be a good suggestion. And then file formats for the data. I'm not sure if you're asking the OTSS supports any file format and then it will render all of the most common file formats in the browser and they can't be rendered in the browser then you'll just see a message that says you can download the file format. And then with another question, could you show again the way to add the high resolution image to the wiki? Sure can. So if I go over here to the project where I pulled the first image, I will actually choose a new image to embed and I'm going to click on it so you can see it here, which will also give me the GUID so that I can take this and I'm just going to copy it right out of the URL. And I'm going to go back to the, let's see, pick a wiki and go into the edit page for the wiki and show you how. So here, this is how I did the first one, that's the first image you saw. So if I did this again, I would take at a US square bracket, OSF, and then put in parentheses and I just paste it in the GUID for that second image. And it should start to show up, yep, there it is. So it's the second image that we pulled off of that other public project that had some prostate tumor cells I think. And then I can save that and in the same way you can zoom in pan for high-res feed. We have other questions coming in yet. Do you know if OSFDLN is comply with US government FDA regulations? I do not know the answer, but I might be happy to follow up. I would be happy to sort of explore that and follow up. I'm not sure that we have your information, but if you could provide that, we'll certainly look into that. Okay. Is that all the questions we have for right now on the live demo? Thanks, Aspect. Anything else to show? Okay. There's a couple more that I wanted to point out. So this is a project also public on the OSF where someone has actually been using the OSF as an ELN. And these are examples from their entries within this lab group. So their taxonomy for naming within this sort of ELN component was each person in the lab puts their last name and then the entry for their lab notebook for the day. And so it looks like they've certainly got a lot more code-specific things that they're putting in. They seem to be having the same sort of template that we were using or something similar. And so you can see how that is applied sort of across the team for each person. Took the template, copied it into their entry, and then filled it in. So here's a really good example to sort of complete your awareness of opportunities that exist out there. There's also another project on the OSF that's public or Cambridge did in the ELN pilot. And so there's a lot of examples in this and also I think a video that demonstrates a lot of what we show today. So we will certainly are recording available so you can do that. But if you want a second recording that you could take and show to others or make part of your resources if you're within an institution or a lab that you want to share with others that may want to see some examples. Okay, but we're happy to continue to follow up our questions that come to mind after we finish today. There's also a really good there's also a really good help guide that breaks down with pictures and a lot of great text of how to use the wiki in those special syntaxes that we showed you today. And obviously we're always available if you have questions just reach out to us at contact at www.seagulls.com. Okay, thank you very much. We appreciate it.