BioRender 101 Webinar

Overview

Welcome to the BioRender 101 webinar. My name is Shiz. I'm one of the co-founders and in my previous life, I was a medical illustrator. I’ll be going through some basic tips on how to use BioRender specifically, but along the way, naturally, we're going to cover some design tips. So hopefully, you'll walk away from this webinar with some new tricks in your back pocket.

If you can see my screen, I am on a Chrome browser and I'm on the BioRender login page. Now this is a little bit different from the BioRender website home page. But you can navigate to this sign-in page through the BioRender.com website. So just to differentiate those two, sometimes people get confused, you can click here to sign in. And then it'll take you to this exact same sign in page. So if you already have an account, go ahead and log in with your credentials, but I'm going to use my demo account.

We recommend using Chrome just because it's the best browser we find for these sorts of graphics heavy apps like BioRinder. But we do support other browsers like Firefox, Safari, Edge, etc.

So here's the BioRender interface. Some of the feedback we've gotten is it kind of reminds them of a visual version of Google Docs.

And it'll obviously look different depending on everybody's accounts. Mine is a little messy right now because I've been really busy in this app, but I've got lots of different types of figures and different formats. So we've got slide presentations, posters, cell-to-cell interactions and I even have my own little activity sheets and design tips as I'm doing webinars myself.

So just getting a little bit acquainted with the user interface here. These are all my figures in this section below. On the left hand panel, you've got a folder system. There are images and folders shared with me. For example, maybe a teammate has made a bunch of figures and they've thrown it into a folder, and they've shared that with me. That's showing up here in my left hand panel. This drop down is all the figures and folders created by me, and I haven't shared it yet.

So it's not showing up in a shared context at all. It's just me privately. If I navigate up here, we've got our BioRender templates tab with all of our beautiful pre-made templates. A template is just a pre-made figure. Basically, it could be anything from a simple, you know, 4 step sequence all the way to a nearly finished figure. So sometimes people like to start here if you want to type in something specific ex. PCR. If you want to get more specific, like a machine that you're using in a PCR process, you can also search by category or search term. 

I'm not going to go too much into detail of this, but just know that we do have a really snazzy poster maker in BioRender with columns and rows that format when you stretch and skew them, which is really cool.

Let's go back to the homepage here.

I'm gonna go ahead and start with a brand new figure. Going to go here to create a new illustration. And I'm presented with this blank canvas and let’s just get a little bit acquainted with this interface. We've got a lot of options here on the left hand panel for icons. We've got templates, brushes, favorites, uploads, all of that. What happens up here in the navigation bar are more options that will pop up as you add icons.

So for example, if I add in, say, a cancer cell to my canvas, I'm going to drag and drop. You see that when I've added that, I've got a whole bunch of new options that pop up here as well as new options that pop up on the left.

I'm using a paid version of BioRender right now, but for the most part, a lot of the features are the same. I'd see a few key features you get access to when you unlock and use the upgraded version of Biorender. Lots of cool features like slides. For example, I can make an entire slide deck in BioRender. So that my next presentation is very visual. And a couple of other things, like layered icons, gradients, higher resolution export, things like that. So I'll call those out as I go along, whether it's available on the free version or not. I'll try my best to differentiate. 

So here's my cancer cell. Obviously, there are lots of options here to change the color of that icon. A lot of preset colors. You can also change the cell to pretty much any color under the rainbow and any saturation or dullness which is really cool. We can apply that. And that's really getting started. A blank canvas. You can drag an icon and edit that icon. And then what you do is you just sort of build upon that, add more icons and more elements. 

I'm going to go back to my home page though because I've got a couple of style tips here that I’d love to share with you. I’ve got my little header slide to kick off our demo. And again, this is using the upgraded version of BioRender. You can see that I can hide and show my slides here on the right hand panel.

I know a lot of us are coming in with ideas of how you want to use BioRender. Probably a certain use case in mind, like a presentation you have coming up. Maybe it's a lab meeting, or a big presentation you're giving, or just one that you're giving in a small meeting with a couple of colleagues. Always good to have some visuals to back up your stories. You might be preparing for a publication. In which case, you might be making a graphical abstract, or any of the figures within the body of the text.

We're all going back to conferences now. So again, you can make the entire poster in BioRender or just the figure.

But I did want to highlight a couple of use cases that might not be immediately evident that you can use Biorender for and that we're hearing more and more feedback that It's becoming really critical in scientists or teammates day to day.

Whiteboarding, lab meetings, grant proposals, etc. You can use the free version for grant proposals. Obviously, I'd recommend upgrading for the high resolution export. So you can have a high res, crisp export to include into your grant. Process diagram, experimental protocols and guides, Even social media, onboarding materials, and many, many more.

I'm sure many of you can come up with your own ways to use more visuals in your day to day, but these are the common ones that we hear feedback about. 

So just to get comfortable and acquainted with the different types of icons in BioRender, sometimes that feedback we get as well is that there's a lot of different things you could build in BioRender and many different ways to do it.

So I thought I had shown you different types of icons. You don't have to memorize this, but just to get acquainted with the types of icons we have. If I type in antibodies here into the search bar, you can see all the different types of antibodies that show up in the search results. Some are a little more complex than others.

I'm going to just drag out this simple antibody or representation of an antibody. It's blue. If I zoom in, you can see a slight outline around it - very clean representation. Awesome. So this was what I would call a regular icon.

Regular as in it's sort of static. You can change the color of it. So the original was blue, but maybe I want a red one or maybe a fluorescent glowing antibody. So there you go, you can make that regular icon glow.

But most “regular icons” behave like this. Now a regular icon with layers, I would say maybe something like a cell. The reason being is we've actually extracted the layers of this icon for you to be able to independently edit. So say you want the nucleus to be lighter or darker or maybe you want it to have a corrugated edge around the nucleus if it's sort of degrading during apoptosis. You can actually do that now in BioRender. So I've got my green cell, and I'm going to come up here to layers. 

Now, not every regular icon has layers, but some do. And you'll know if it does or not just by clicking on it and expanding this layers panel. So here I'm on the cell layer/membrane or the nucleus layer.

Let's click on the nucleus layer and see what we can do with it. You can change the transparency so make it disappear completely or, you know, make it invisible or make it a little bit more transparent. This is actually really helpful if, say, you're adding a label like T-cell, and the presence of the nucleus is a little bit distracting. But you don't want to remove the nucleus completely. You can actually make the nucleus a little bit more transparent so that the T cell label shows up a little bit better.

That would be one use case for making this more transparent. Saturation if you want it to glow or maybe you're staining the nucleus with a certain color.

Can do that as well. You may want to then make that fill color a little more fluorescent. So you can see here I've made the nucleus glow.

I can also make the borders of that nucleus dashed. Now again, this is a cell, but you can see how you can use this as a mouse tumor or a protein. So now this looks like a T cell with a nucleus that's glowing where the nuclear membrane is sort of degrading or maybe porous.

That's important for you to show things entering and leaving the cell. Okay. So that's a regular icon with layers, grouped icons. Probably self explanatory, but just in case we're not on the same page, I'm going to type in antibody again. 

Then you can see that some of the icons that show up have a little purple bounding box that shows up if I scroll over. Those mean that it is a grouped icon here. Basically, what that means is our design team has gone through and sort of layered and grouped regular icons into a grouped icon, so it's easier for all of you to have another starting point. Maybe it's a cluster of icons like this.

So you can imagine if I double click, I'll probably be able to independently manipulate some of these icons within the group and then go ahead and edit that single icon as if it was a regular icon. But if I double click out of that, I'll have that group to manipulate again. If you use Illustrator or Photoshop, it sort of works the same way. But that's an example of a grouped icon.

Another reason why you'd want a grouped icon is maybe our artist has put together an icon that is even more manipulatable, for example, this antibody with these sort of markers on specific domains here on this region of the antibody. Those can be removed. So if I click in, these could be like I did it or manipulated even further, and these aren't actually made of regular icons, they are made up of shapes. See my options have changed here. It looks a little bit different.

It's because these are BioRender shapes, sort of like in PowerPoint or Illustrator when you make objects with shapes. It's not a flattened icon. It's more of a circle, square, star sort of shape. And then obviously, you can edit those individual parts as you see fit. Maybe you want to highlight the foremost domains like this. Anyway, that is an example of a grouped icon.

Everything looks a little bit hazy here and light gray. Because I'm still in what's called an editing mode of this grouped icon. So if I click out, you'll see everything comes back to full opacity. And then you can have groups within groups within groups. So just be careful if you end up in an infinite spiral of grouped icons. You can usually avoid that by going into the layers of groups and ungrouping them.

Now brush icons are also pretty straightforward. I don't think we have any antibody brush icons, but likely you might need a brush icon when you're dealing with DNA. So I just typed in DNA into the search bar, and then I had some icons show up that were regular icons. Some that are grouped icons like this one here, and some that have this little brush icon and that's telling me that this is editable like a brush. So basically, a sort of flexible bendy pattern. This has been important for a lot of scientific concepts that have long strings of patterns, like maybe a membrane. If you're talking about the surface of a cell, you might need to show waves in the phospholipid bilayer.

So this is when a brush might be helpful. Now if you're interested, I'm going to get a little bit technical here, but if you want, you can even expand this brush so that each little piece of this membrane is editable in and of itself. You can separate the brush into editable icons on the left hand panel. Doing this is not reversible and you're going to be able to edit each little piece. 

So I'm going to double click into this newly made grouped icon, and you can see here that now the phospholipid bilayer is editable independently. Again, this is not a reversible action, so now this is permanently going to be piecemeal like this, but you can always redraw it and very quickly edit those yourself.

Last but not least here is a PDB icon. Now if you need a little bit more detail in this antibody, maybe you are a structural biologist or you have a favorite protein with the exact PDB ID. You can actually upload your PDD file or retrieve it from the PDB library. So I'm going to click this PDB retrieve and this just pulled right in from the protein data bank. And I can manipulate this to whatever view or vantage point I like. Why would I use this? Sometimes you just want a bit of a pop of 3D or some ribbon or quick surface view of the protein just to bring focus to your graphic. Shading style and I know this cartoon style is very popular versus tune flat.

So I just wanted to highlight a few different types of icons in BioRender and there are a few more, but they're not really icons. I'd say they're, you know, picture types. And that is uploads. You can upload anything into BioRender as long as it's sort of a JPEG or a PNG or an SVG file. Maybe you made your own icon in Adobe Illustrator, and you want to bring that into BioRender to use. Some of you are very crafty. So you have your own icon set already. You can actually upload those into BioRender and then add it to your icon set as you're making a figure. 

I don't know if this just is something in the science world where everyone loves to make sure everything's really aligned and straight. I'm definitely in that camp as a medical illustrator. I like things to be nice and neat. But I guess it’s particularly helpful when you're trying to align panels and such for publication diagrams, or if you have objects like this that you want to have in a straight line, and it's a little bit tricky unless you have the right tools.

So say you have a bunch of stuff like this, maybe four antibodies in a row. There's different ways you can align in BioRender. One is grid lines. Grid lines are sort of like using graph paper, so I can turn it on and off here. If you can see, I just click this hide grid, show grid button. So you can use that just to eyeball it.

If you don't like things that snap in place, you can also put down your own lines by coming up to the ruler. You can see here I'm in the ruler area of BioRender. If you don't see this, it probably means your ruler is turned off. I'm just going to lay down a couple of guidelines. These are temporary little lines that you can put down yourself. I'd like to use guidelines to create a border around my entire figure like this.

So it's sort of a visual cue to avoid putting anything in that area of the figure because you likely don't want things to kind of butt up against the edge. And it really helps to kind of create a visual border or breathing room around figures when you have a really nice buffer. And of course, you can hide these by right clicking and hiding guidelines.

Another way to align objects is to enable alignment. So again, if you're the kind of person that likes when things snap into place, you can go to view and enable alignment, you'll see here then these objects will start to sort of snap into place. And my mouse is sort of forcing me to find these places where it'll lock into place like that and these purple little lines are telling me the distance between them.

Finally, you can actually just use the align feature, which a lot of people don't know we have. You can also distribute them evenly. If you really just want something to be in a row, numbering protocols, that's a good way to use this tool as well.

We're going to move on to one other use case, which is very common. And that is protocols or timelines. If you're writing an experiment, you want to show what you've done visually instead of just a bunch of text on your presentation slide or your protocol section or methods section of your manuscript.

I'm going to type in the protocol, and then you'll notice here that there are two little tabs when I use the search bar in BioRender, icons show up related to protocols. So, you know, machines, some vials, Not really sorted by relevance though. Just sort of a bunch of icons. In this case, because protocols are more of a concept than a specific icon, I'm going to navigate here to templates.

And now this templates tab is actually the exact same content you'll find if I go back to see my gallery and then BioRender templates. If I type in protocols here or protocol, the exact same search results will show up as if I was within that view. The only difference is it's just really teeny tiny when I'm working here in the search bar.

So if I type in protocol, hit enter and I go to templates. See, it's really small. Actually, if you roll over it like this, you get an expanded viewership, so that's really nice. I'm going to go ahead and select this template.

I just clicked it. And then I can either replace my current Canvas or add to it. I'm going to go ahead and just add to my illustration. Okay. So you see here it added as if I've done the figure, which is great.

Hopefully, we have something close enough to what you need that you actually won't need to make a figure in BioRender if we've got exactly what you need. Hopefully, in the best case scenario, we have what you need and you just kind of tweak it a little bit to your own liking. And you can export, throw it into your slide deck or use BIoRender to present whatever you need to do.

In this case, it was added to my Canvas, and you'll notice again that the purple box showed up. So it is actually imported as a grouped icon. We learned about grouped icons a minute ago. It's basically a glorified group icon.

So what I can do, if I don't like that it's moving all in one chunk, I can come down here and edit the group I'm actually going to click ungroup, up here ungroup, and this is going to expand this whole giant grouped icon into little pieces. So you see here it's now no longer a grouped icon.

And that's just easier for me to edit now. This looks great. I think maybe I don't like this machine, so I'm going to look for a different mass spec machine. Maybe it's this one that I actually use for my experiment, so I'm going to replace that icon. Sometimes you want to actually add real data or findings to your diagram. You can actually upload an exported diagram from graphpad Prism or any file as long as it's a PNG or a JPEG file or an SVG.

We are working on improving the graphs feature. So there might be a world where you might be able to actually create a graph environment or soon, but not yet. Currently, you'll have to just import a PNG file that you've exported from GraftPad, which I've done here. So I'm going to go ahead and use that as my last step.

There you go. Okay. So that's how I would manipulate a template that is preexisting to my own unique use case. And again, protocols or timelines are a very common way to do that. 

Sometimes what happens is we take graphics from Google, and they all come together looking a little bit like a Frankenstein figure. So to avoid that, we've made sure that all of our icons play really nicely together. And this is an example of that. Some of our icons are actually even more editable than you think. So something like a syringe. If you need to show parts of a syringe, you can actually look for the grouped icon label. So if you need to show something pulled back like this in the case of a syringe - maybe you want to hide part of the needle if it's sort of being injected like that - lots of ways to get creative with showing action in your protocols or experiments. So that's protocols and experiments. 

I wanted to leave you with a few last tips here because I think the power of BioRender is definitely in its illustration capabilities and fast figure making capabilities, but it's also more recently, what I'm hearing is in its ability to collaborate with your teammates so you can share the wealth and also share the burden a little bit.

So if you want help in making your figure or if you want feedback on how your figure is looking or “Is this protocol ready to export? Can you come in here and add comments?”. Instead of your usual, you know, printing it out or emailing, sending it to your PI or your student, having them print it out, mark it up at the marker, scan it, attach it, send it back and forth, back and forth, you can actually just share this as if it was a Google doc.

It is very secure. So you could only share it with people that you specify. So you could add your teammates. Maybe I'll add myself, but imagine that this is somebody else. I've sent the invite. So now there are two people on this document. And close it up. And you can see here now the other Shiz Aoki has access to this file. And what will happen is you can kind of come in here change this to a purple fluid or something like that.

And now I'm going to get a notification that there is a comment. If you're using slides, actually it'll show the exact slide that the comment is on, so that's really neat as well.

And eventually, you'll have a diagram full of comments with really good feedback from your colleagues.

And you can write “done”, post that and you can resolve the comment. This really improves the efficiency of your workflow if you don't have to export, attach to an email, send it back and forth. If one person that you're tagging doesn't have a BioRender account yet, they can actually create one for free and start to contribute to your doc that way as well.

So that's a really important feature that I think is definitely worth noting. It's a little bit of an unknown feature that I think is quickly becoming a popular one. Another really helpful feature is this help button and that is if you're in a jam and you can't find how to change colors in BioRender or maybe how to upgrade your subscription, how to request a custom icon, things like that. This is like your go-to search tab. So if I type in “changing colors” or “how do I use a color picker tool?” Lots of different ways to get your answer. “How do I change the canvas color?” And what will pop up is sort of a little tutorial on how to change the canvas color, which is what I picked here. And a little gif on how to do that. Okay? So that's there for your resource. 

If you are stuck on how to use certain features in BioRender. Sometimes if you really can't find what you're looking for, you can actually send us a message and start to chat live with our very knowledgeable customer experience team. Usually between the hours 9AM to 6PM ET, Monday to Friday. Sometimes on weekends. But, usually, we'll have your answers sort of in a prewritten article. 

Alright, we covered a lot, but still had so much to go through because there are a lot more use cases in BioRender. We hope that you Have fun making your first figures, your first posters, your first slide decks within the app!