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BioRender Special 101 - Sliding into BioRender’s newest features!

Description: Jacqueline McCoskey (Account Executive, BioRender) gives a basics course on BioRender and all of its exciting new features including including slides, PDB upload, gradients, RTC and commenting!

This webinar was recorded at VISUALIZE 2021, a virtual BioRender event dedicated to advancing communication in science.

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https://biorender.com

Overview

I hope you're ready for an amazing day of design tips and demos with new and exciting features here at BioRender. Jacqueline McCoskey kicks us off with a special edition of BioRender 101. I have the fortunate pleasure of working with Jacqueline day in and day out. She's an account executive here in the business development team at BioRender. She always brings her A-game and infectious energy to the webinar. Prior to BioRender, she was part of a lab at the University of Toronto where she studied a wide range of outcomes associated with sport-related concussions. So without further ado, Jacqueline, I'll pass it over to you.

Awesome, thanks Jeff. Everyone can hear me okay? Thanks so much for joining today and thanks for that great intro. Just to give you a little bit of an overview of what we're going to be covering today, the plan is the basics and then a little bit more of some advanced features. Again, to kind of give you, depending if you're new to BioRender or if you're a pro, we'll make sure you leave with something cool and fun today.

Again, overview of what we'll be covering today: so we'll just do a little bit of an overview of the platform itself, make sure you know what you're looking at, what you're working with. We'll search the icon library. This is always really fun because there are so many different icons. I always have a really fun time doing this. We'll go through our icon types because we do have a few different types. And then we'll go through our newly launched slides feature as well as our highly requested new PDB upload. And then lastly, we'll get into some fun little design tips on how to use gradients to make your story a little bit more impactful.

Alright, and now we can get started. So, the cool part about our slides feature is that the intro was actually done within it. So this really allows you to do everything that you need to do with BioRender, you can present on-screen all within the app.

I'm going to go back to my gallery view here and just to give you again a little bit of the lay of the land here. So this is going to be your home page when you log into BioRender. All the images that you create are going to be saved down here at the bottom in your gallery. You can see I've got a whole lot of everything going on here, different types of images. I wouldn't say I am necessarily that organized, but luckily our team has made it very easy if you are more of an organized person by creating these different types of folders on the left-hand side here. So you know any image or any of the images that have been created by you are going to be saved up on the top here, and then any of the files that have been shared with you will be shared on the bottom here.

This is going to be covered in-depth in a later tutorial at 1 PM, I believe by Polly, but this is just to keep in mind.

These things are here to keep you organized and depending on what project you're working on, there are essentially two different ways that you can start a figure. I'm going to walk you through both, but I like to start off with our templates. So I'm just going to click on our template gallery, and as you can see, we have tons and tons of different types of templates. They're constantly being added to every single day, and they are fully editable and customizable because they are made out of 100’s of BioRender icons. The really neat part about this is these are all created by our in-house science design team. So pretty much, these are all people who almost all of them have backgrounds in science or PhDs, and what they do is they put all these icons together and make sure that they not only look beautiful, but that they are scientifically accurate. It goes through a rigorous process, and if you're interested, I highly encourage you to come to the session by Jerry and Vikki at 2 o'clock to learn how all of these get published.

As you can see, we have a wide range of different types of templates. They are all categorized, so if you're working on some pathways, some more intracellular cell-to-cell interactions, you'll be able to find all of these. And then, on a larger scale, if you click on our anatomy and clinical, you can see we have more of the organs, the humans, things on a little bit of a larger scale. They are also searchable. So if you search up a specific topic like Immunology, we're going to have all of our templates that have been tagged within Immunology.

Going back to our home gallery, I'm just going to show you kind of the basics of how you can walk through creating a figure from scratch. So what we're going to do is just click this big blue button, and it's going to take us to our canvas view.

Here is our canvas. Basically, anything that you bring onto your canvas is going to be on your final figure. This gray space is a little bit more of a working area, but just allows you to have some things hanging off the canvas. It's all going to be within your final figure, which is going to be in this white space here.

On the bottom right-hand corner, we have this little keyboard button. If you click this in, you'll see we have all of our specific keyboard shortcuts. I will try to keep those to a minimum today, but they are a good resource if you want to become a BioRender pro. They make you become super fast and super speedy. They're quite common to other types of software. So like control V, control C for copy-paste on a Mac, those types of things, but we do have some special ones if you want to check those out.

We also have this help button here, so if you're ever in the app and you have any questions, feel free to click on that, and it will take you to our help center.

Any specific questions or issues? We do have a live support team that is awesome. They will get back to you within a minute or two, depending on where you're located. We have agents all over the world, but they will get back to you in a timely fashion. They are amazing problem solvers, so if you ever need anything, I encourage you to use this resource here.

On the right-hand side, we have more of our basic features. If you want to zoom in and zoom out, you can add and remove rulers, add and remove grid lines if alignment is something that's important to you or if that really helps you with your figures. Then, on the top, we have our slides feature. That's what I was talking about before. This is how you present within BioRender. It's also a really great way to, personally, work on a multi-canvas sort of view. So you don't always have to go back and create a new image if you're working on something that works, you know, similar to the previous image. Here's our comment button. This is part of our new real-time collaboration feature. So if you're working live with someone, they can add comments to it. This is going to be touched on again at 1 PM in the session with Polly. I encourage you to come to that one as well.

Then, over on the left-hand side, we have more of our contextual toolbar. These again are more of our basic PowerPoint types of features. If you want to change the color or the size of your canvas, if you want to add some lines or shapes or text, this is where you're going to do this. Additionally, depending on what you have highlighted on your canvas, there's going to be another sort of set of buttons that appear right here, and I'll show you that in just a minute. But basically, what this does is it allows you to manipulate what you have on the canvas just to make it a little bit more custom and a little bit more specific to your work.

On the left-hand side is our content toolbar, and this is where you'll probably spend the majority of your time with BioRender. It has all the content from our icons to our brushes to our uploads, and it's really like the bread and butter of BioRender.

I'm just going to start off showing you our icon library. So we have thousands and thousands of different types of icons, but they are all categorized just like those templates. If I go into my cell types and I go to my immune and blood cells, here's an easy way to just search through and browse. I always find it's fun to see what's available, but you can search. So again, just to show you the range of different things that we have within the library, I'm going to start off on like a very micro scale here. Let's search up antibody.

You will see we have tons and tons of different antibodies – more than 100 of them – all specific, a little bit different from one another, but they are all there if you search that up. Or, if I search up something like neuron, you can see, like, who knew that there's been this many different types of neurons? We have all of these different types of neurons with different added abilities depending on what you're working on.

Or let's say if you were working on an animal model. I'm going to search up Mouse, so we have a ton of different animals, but if you are working on model organisms, our library is really extensive. You can see we have animals from all or Mice from all different orientations with different organs in them, just their head, the full body, so whichever sort of orientation you're looking for, we will probably hopefully have it.

And then again, on a larger scale, getting a little bit more macro here, let's go search up a liver. As you can see, we have some healthy livers, we have some disease state livers, we have livers with gallbladders. We also have patients with livers inside of them. So, I highly encourage people to just if there's anything that you're curious about, just search it and see if we have it. We've got a really, really extensive and fun library to look through.

So, you're probably wondering, we have these different types of icons here. You see these little blue, or sorry, purple, boxes with the purple box on the left-hand side. And that gets me to my next point. So, we have basically three different types of icons, and I'm going to start off. Let's just say, let's search up like cancer. So, I'm going to start off here with more of our simple type of an icon, and it'll be denoted within the icon library here as there being no sort of box on the outside. When you hover it over, it's just going to be plain and basic in that sense.

So, I'm going to drag this out. As you can see, it's that simple. All you have to do is just drag and drop it, and there you have it onto your canvas. Now, I'm going to go back here, search up our cancer cell again, and now you'll see this one, for instance, has that purple box on the bottom left-hand side. And when you hover over it, it also has another purple box. So, I'm going to drag and drop that on our canvas here, and this is what we call a grouped icon.

So, to provide some context, basically, we have simple icons with the blue on the outside, grouped icons with the purple on the outside. The blue simple bounding box is basically this is more like the Lego pieces of BioRender. These are like the foundation of it. You can change the color of it, so if I wanted to change the color of this, you can do this on the left-hand side, this little edit tab. And then you can also change the transparency of it. Those types of features are up at the top here, but for the most part, this is kind of set in stone as it is.

Lower level of editability but we still have a wide range of ways that you can customize it to yourself. Our grouped icons are actually an icon made up of these smaller sub-icons. So pretty much what it does is it puts icons that are typically used together so that you can actually click in and edit these individual pieces on its own. So if you want to cut, change the color of those specific pieces, or if you want to actually delete one of these cancer cells, you can do that. But pretty much the purpose of this is that we've tried to remove the leg work for you so you know things that are constantly being used together. We put them together first so you don't have to do it yourself. But again it still has that wide range of customizability in it.

We also have a third type of an icon. So I'm just gonna search up something like DNA and this will be denoted on the left-hand side here with this little brush option and this is our brushes. The brushes are really, really cool. I love them. They're so much fun to play with. But I'm just gonna drag and drop it onto your canvas on my canvas and as you can see, they act as if it's like a paintbrush. So if I drag it from this side here, it's just gonna add helices, rather than stretching out the helixes that were already there so you can make it as big or as long as you want. And then if you click it, you see these little nodes. These nodes make it even more customizable so I can make a really custom and cool shape here depending on what I am working on. Everything is going to be adjusted as is.

You can also change the color of the icon within the brushes as well. So if you wanted to click this here it is, it'll change the color there. I'm just gonna actually, we'll just drag this up to the top so we have a wide range of different brushes as well. So if I go to my brush tab on the left-hand side here, here are going to be all of the different brushes that you can use and edit and modify depending on what you're working on. Let's see here, I'll kind of show a few of these. I know I personally have spent.

A lot of time in the past was spent doing some copy paste so sticks and circles in PowerPoint to create a phospholipid bilayer. But here it is, it's that simple. All I have to do is just drag it out. Again, you can make a super fun and custom shape. And it's that simple to do. Let's move this up here.

If I go back to my brushes, you can also see we have these circular brushes, so these ones that look like circles. Let's use this one right here. We'll drag and drop this one, actually maybe we'll delete these guys as well. So these ones, how they work is the same thing as the nodes. All you have to do is actually click into these little nodes and it's going to be specific to each. It'll make these little cuts into it so that you can, you know, change the actual color of this portion right here, but still keep that 360 degrees. That's super important for these cyclical types of figures.

The brushes are even more editable, so I'm going to go up and bring in this enterocyte brush here. This one, oh actually, let's bring this one. I like working on this one. We'll drag and drop it, and this is a really fun way to use the slides feature. So I'm going to show you how you can actually sort of make some movement with the size features. So what you can do is, I am going to drag this out here and make this a little bit bigger. You can actually change the size of these little cells as well. If I go, oh I didn't mean to do that, that's control Z. We'll drag this down and I go up to the top of my brush options. You can click this little separate brush into editable icons. Let's click this here. We can separate it, and now what happens is it's actually made into that grouped icon that I showed you previously where you can actually click in and change each of the individual pieces. So if I wanted to change the full color of what's on my brush, I can do that but I'm just going to keep this as is for right now.

Oh, let's go back here. Okay let's keep it this brown color if it works. I'm going to add a slide here, so what you can do if you click your slides section and I just click a duplicate slide. Now, if I work off this second slide here what I can do is I can actually go in and change these individual pieces. So, I can highlight a few of these and now let's make these ones a red color. So, if I wanted to show some sort of damage that's going on within myself. Now, I'm going to copy this one again and work off of my third slide, and we're going to show some more damage.

So I'm going to pull this piece out here. Let's pull this one out here, and we'll just highlight these ones. If I click more, I have all these different options, so I can show something that's really good. Something is not going on here.

Now, if I go back to my initial slide and I click present, I can actually just click through here and it shows the progression of the damage as you're going through it. So, it's a great way, it's super easy to present with BioRender, but it is really awesome to be able to use multi-sort of level canvases as well.

If I wanted to, you know, I don't want to go back to my home page here, but I want to add another slide, I can do that, and I can show you some other features here. And one of the other things I did want to show you is actually our pdb extension. So, if I click this pdb file, previously anything that was in the protein data bank, you could have access to within BioRender. So, if I just click pdb retrieve and I add my pdb ID, so say if it's one that's one that I know, it's 1HZH I'm going to load up my protein. It's going to take me to this other view here. Sometimes it just takes a second to load, and here you can see you actually have your full protein structure on your canvas. You can also change the structure of it. So, let's say if I wanted to change it to this little quick surface one, sometimes it takes just a second or even Van der Waals. I know that this one looks pretty cool. You can also change the color of it. So, let's go to hydrophobicity. And again, you can change a number of different features, but I like this little tune feature here and it makes it look really nice. So, what happens is I just save it as a new icon, and now it's going to be saved into my BioRender pdb library. So, I'm just going to drag and drop this out to my canvas, and it works just like all of the other icons as well.

That's how it worked previously, but a really new and exciting feature, which is something that we had requests for constantly, was to be able to actually upload your own file. So, if the protein hasn't been actually published within the protein data bank yet, I'm just going to click pdb here. You can upload your own file to it. So, if I click pdb upload, as long as it's one of these files, these are the different files it supports, and you can either drag it or you can download it. So, I'm going to download this pdb file that I have saved. We'll open it up, let's give it its proper name here, and I'm going to load up my protein. It takes a second sometimes, and there it is. So, it's super simple, so easy. You can create your own, and if it's not in the protein data bank, you now have the ability to upload these functions.

Or these specific proteins work in the same sense where you can change the structure of it; you can change the color of it. Let's just save it! Let's use a different tip of the style here. I think this one's cool, we'll save that as a new icon, and again, it just works like all the other icons where you drag and drop it and there it is. So that's one of our new and exciting features.

Um, one other thing I did want to show you: I'm just going to go back to my gallery here. I wanted to walk you through gradients because it's a really cool way to show, you know, if you wanted to convey some sort of a spectrum. I don't think a lot of people know exactly how you can use them with BioRender, but it is quite simple actually. So I'm just going to click my visualize folder here - that's me trying to be organized - let's open up our gradients here.

This is a really great way if you know you're trying to show some sort of a spectrum in terms of like, I don't know, a pH scale or like visible light or something along those lines - some sort of a diffusion pattern in this sense. And as you can see, we have a high concentration on the left-hand side and a low concentration on the right-hand side. But I think it would just look a lot nicer if you can actually show it being a little bit darker here as well and then a little bit lighter on the right-hand side.

So how you can do this is I'm just going to click into my image here - so I'm going to click into this box - and it's going to highlight the shape here. And I'm going to go up to my fill color options. And as you can see, it's filled with a solid color right now. So what I'm going to do is I'm going to click my gradient here. And you can see this is the solid color that's within my box. Now I want it to blend with some sort of a white, so I'm going to click this down here, and as you can see, it already added that gradient.

But this isn't the way I want it to look like. This has the gradient as if it was a higher concentration at the top and a lower concentration at the bottom. So the way that you fix that is if you go up to your little angle button on the top right corner here, I press this down - um, and in this sense, I'm going to do 270 - and now we have the proper gradient going from darker to lighter on the right-hand side.

That's if you want to do it manually. We also have a number of different presets at the bottom which is really cool. I could have done it quite simply just like this and there it is.

Other things that people like to show gradients on, let's say I want to look for a falcon tube and I want to show a change in concentration of some sort. Let's use this one right here, I know this one has high editability. I'm going to click in here, let's delete this red part but I want to show it going from lighter to darker to show the concentration is stronger at the bottom. Again, we have our solid fill color up at the top. I'm going to click my gradient, we'll add the white and that's not the way that I want it so we're going to switch it and go 180 and there it is. It is quite simple, it's really fun, it makes things look really really professional.

One last way that people typically, well there's a number of different ways that people use these, but one other easy sort of way to use these in your figures to add some depth. Let's show my slides here. I'm going to go to slide two. If you want to show some depth within your well plates of something that you're pipetting you can also do that. Oh, so I want to lock this in place, block objects and then I'm going to highlight my wells here. Let me see here, unlock, sometimes these goof a little bit of trouble. There we go, so now I have all of my wells highlighted and you can see that they are the solid color. I'm going to go up to the top here it says, fill color again click my gradient, we'll change and add this little white feature on the bottom but this isn't the gradient I want and I can click this little circular gradient and it's cool, it'll show this like specific depth within my well plate. So a really easy and fun way to make things look really really professional.

This is kind of the section of the basics of BioRender as well as more of a tip, a little a few of the advanced features. But if you do want to stick around in the following session that starts in about five minutes, Francesca is going to go through some really really cool tips and tricks, some of our new features as well and make sure that you're all biorender pros by the end of it.

All right and I'll pass things back up to Jeff whenever he's ready. Thanks again everyone for joining, really appreciate it. 

Due to continuous improvements in BioRender, the application may appear slightly different in some of our videos.
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