BioRender 201 for Biotech and Pharma
Learn design techniques and how to use our most powerful figure-making tools to help you:
- Easily create a clear and compelling figure layout that guides your reader
- Better customize icons and templates to accurately visualize your experimental protocol figures
- Speed up your figure-making with easy-to-learn design tricks and shortcuts
... and more!
Welcome everyone to the BioRender 201 session today, which is designed specifically for new and advanced features. The goal for today's session is to build on some of the basic tools that have been previously covered in the BioRender 101 introductory session. But don't worry if you haven't had a chance to attend that before, we will do a quick review of the basics just to make sure that all of us are on the same page before we start going deeper into the platform.
For those of you who I haven't gotten a chance to meet yet, I thought it'd be nice to introduce myself and not just be a floating voice here. My name's Tim, and I'm a science communication and customer success manager here at BioRender. I'm actually a scientist by training. I did my undergrad in Biochemistry before getting a PhD in Pharmacology and Therapeutics. It was really during my time in grad school where I began to realize just how difficult it was to create figures for my papers and for lab meetings. I just remember always having to fight with PowerPoint to create timelines, trying to align each of those notches, making sure my labels were centered and properly lined up. It was a real struggle, and on one occasion, I remember this very vividly, I had to piece together some images that I found on Google along with some pictures that I took on my phone to create this Frankenstein figure that I had to present during a committee meeting. You can probably all imagine exactly what that turned out to look like. That was a really common theme during grad school for me. The quality of my end result never seemed to be positively correlated with the amount of effort that I had to put in. That's why I joined BioRender because I wanted to help scientists avoid the same problems and struggles that I had to go through and show them that there's an easier way to create figures that accurately represent their work.
Here's just an agenda of what we're going to cover. First, we'll do a quick recap of the basics just to make sure that we're all on the same page. This will be a bit of a refresher for the veterans in the room and also to make sure that newer folks can also find their footing before we can jump in.
Little bit further and then afterwards I'm going to dive into our five advanced tips and tools. These are the multi-select functions, alignment tools, customizing shapes and lines, looking at connector lines, and custom colors. If we have time at the end, we're also going to talk a little bit about collaboration as well. Now all of these will provide different examples as well so as you can kind of see the different tips in action. At the end, we do have a small time dedicated to questions and answers but if you do have any questions throughout, you don't have to wait until the end. Feel free to throw them into the chat and Q&A. We'll be sure to dive into anything that you want to see more of or anything that's unclear.
Awesome, so let's get started here with a quick recap of the basics. I'm actually going to start from the very beginning here just so that everyone can follow. When you first sign into your account, you're going to land in your gallery page here. This is basically where you're going to see all the illustrations that are available to you. These are all of your unsorted files and then you can also create folders for yourself as well if you want it to be a little bit more organized. Then there's a group together with different figures that might pertain to a specific project. Up top, these are all the files and folders that are going to be private to you unless you decide to share them. Down below, these are all the files and folders that have been shared with you. I'm going to talk a little bit more about this a little bit later on in the session but for now basically on this Gallery page everything that you have access to that's where you're going to find it.
In terms of using the platform to get back into the editor, just open up any of the files that you have access to and then it will take you into the editor. The analogy that I always like to use to describe BioRender is that it's very similar to Lego. For those of you who have played with Legos before or if you have some kids that play with Lego or if you're planning to buy some sets for your kids as well, for those of you who are unfamiliar, Lego's basically building blocks, pre-made building blocks that are given to you and then you can assemble different structures. BioRender works in the exact same way. We provide you with building blocks such as icons and brushes to allow you to easily construct your illustration.
I'm going to quickly walk through some of the major building blocks that you're going to encounter as you go through the platform. First up are what we call the icons. All the icons can be found in the left-hand tab here and all in all, I think the icon library represents over 50,000 different scientific entities. Here you'll see some of those major categories of icons that we have. Feel free to just browse through to see what's available. You can see that it won't go into cell types, we can go even deeper actually into subtypes of different cells and then here you can browse through all of them. What you'll notice as you're browsing through the icon library is that they sort of fall into two groups. You're going to have those that have just the standard thumbnail like this one here as well as some that have a little thumbnail or a little symbol in the bottom left of the thumbnail like this grouped icon here. Those represent our two different classes.
So we have our regular icons and we have our grouped icons and although they look quite similar on the surface, they're actually quite different. In this case, like on the left-hand side with this regular icon, this essentially functions as a single piece so you can do things like change the size, you can change its orientation, but you can also do things like change the color of that entire piece as a whole and you can also play around with some of the other properties such as the transparency, the saturation of the icon as well as the glow that exists behind it. What I wanted to highlight is that almost all of the edits that you make to it will affect the icon as a whole because this is essentially one single unit that you're working with.
To contrast this with the grouped icons, grouped icons while on the surface they look the same, what you can do with the grouped icon is actually double click into it and here you can see all the different pieces that went into creating this car and here what you can do is actually edit these pieces individually. For example, if I made a mutation into one of these domains, I can select that domain and then maybe change the color to indicate that. If I deleted certain domains, I could do that as well. I could
Just remove it. I can move things around. I know this is nonsensical; it's just really to highlight what is possible with the grouped icon. You can move things around, even after you click out of editing mode, when you move this around, you can see that all the elements within that group will move with you. This is a really cool way to customize the icons within the library to suit your needs exactly. And not have to worry about needing to move each of those components. So a really cool way to batch things together.
The next type of building block that we're going to talk about here are the brushes. Whereas the regular and the grouped icons are relatively static, it's going to be like the overall structure of that icon is going to stay relatively fixed. But with the brushes, it allows you to create these very dynamic structures on your page. What I mean by that here, I have a couple of examples. So here, let's say that with my regular icon for my DNA, if I wanted to make it longer, I can always grab the ends and drag it. It's going to look a little bit weird, or if I wanted to expand it, what I'd have to do is actually make duplicates of each of those pieces and just kind of stack them end to end. If anyone's ever created a phospholipid bilayer before, this might bring back some unfortunate memories.
Now what you can do with a brush instead of having to copy and paste multiple subunits together, you can work with a brush. You'll notice that we have this blue line that runs through this strand of DNA. If I needed to make it longer, I can just grab the ends and then pull it along. Right away, you'll see that all those subunits are added in automatically for me. This way, I can just focus on making this brush bend and shape it the way that I want without having to go through a lot of tedious copy and pasting. And this is true for any object that you see with this blue line, not just with brushes, but even with things like this line here. You'll see that we have those nodes again. Whenever you see those, this means that we can actually alter that shape, and so it gives you a lot of flexibility into how you want to portray different elements and ideas on your illustration. And of course, because the brushes are actually made up of individual pieces, it allows us to go in and make edits to those individual icons separately as well.
For example, I have my bio brush on the right here. You'll see that right now, we have that blue line, and we have those nodes. This means that we're able to bend things, move it around a little bit. But let's say that a portion of our membrane is damaged, and I want to show that visually. What I could do, I'm just going to make a copy to highlight the differences. I can go in and edit a few of those icons separately, and to do that, I can just click on the brush itself, go over to separate the brush into editable icons, and once I select that button, it's going to be a pop-up that'll let me know that, "Hey, this is going to be a one-way street. I can go from a brush over to a grouped icon, but I'm not able to go back." What that means is that I'm going to lose that flexibility, and if this is a structure that you know you're going to need later on for another figure, just remember to add it to your favorites before you hit confirm.
Once I do that, you'll see that we've turned it into a grouped icon now, and what I can do is double click in, and if there's certain portions that there's certain portions that there's certain portions that I want to maybe change the color to, I can just drag a box over that section, and then maybe change the color a little bit here. Now visually, when my audience goes to look at my figure, their eyes are instantly drawn to this darkened region. So it's a really easy way to kind of redirect your audience's attention and have them focus on things that you want them to.
We're actually going to talk about that a little bit later where you can leverage color to actually focus and guide your reader through your illustration. It's a really cool way to do things, and you don't have to actually change the composition of your figure at all.
So if we continue on with that Lego analogy, whereas the icons and the brushes are sort of those individual building blocks, what BioRender also provides are templates, which you can think of as fully formed structures. This is very similar to let's say you have a Lego car. It's constructed all from Lego pieces, and then you have the full car built. But even with those with that car, you can still swap out different pieces, you can change its appearance, and you can do the same thing with the BioRender templates as well. The templates can all be found under the templates tab on the left-hand side here. And again, we will split those into different categories. You can see all the major categories of templates that we have. And if you don't see your research field listed specifically in this category, what I'd also recommend is just kind of searching through the template library. There's a lot of different templates to choose from.
For example, for the microbiologists in the room today, let's look up microbiology. You can see that we have icon packs, we have different templates that you can use. So feel free to browse through and use any one of these in your illustrations. And to do that, just click on the template that you want to work with. You can either choose to add it to your illustration or replace the entire thing altogether. I'm going to go ahead and do that, so my slide now will just be replaced by this template here now just like with those Lego structures, these templates are again made up of all elements that are available within BioRender and you can actually see all the different pieces that went into creating this figure. What this means is that I can make a lot of edits to it. So if I needed to remove labels I could do that, or if I needed to move things around. Really, all these templates are here to serve as that foundation for you to start building your figure off of. It really helps you get a jump start on that figure making process.
Now that we've covered some of those foundational skills for BioRender, what I want to do is actually pivot now and talk about the things that everyone here is hopefully excited to learn about. These are some of the more advanced tools that you might not have gotten a chance to use just yet. These would be the multi-select, the alignment tools, custom shapes and lines, as well as connector lines and custom icon colors. The reason why we chose these features in particular is because they either one, allow you to save time, or two, allow you to really customize your illustration to represent exactly what you want to show.
So let's dive into some of these features here. First up, the two tools I want to talk about here are the multi-select and the alignment tools. These are very handy for helping you save time while you're creating your figure. First up, with the "Select all same icons" tool, this is actually really cool. Let's say that you have the smattering of antibodies on your canvas and what you want to do is maybe change the color of it. You could either click on a single icon, change the color, select the next one, change the color, and so on and so forth. That's pretty tedious and would take a very long time, especially with more icons. Instead, you can click on one of those icons, go up top to the toolbar where there's a button that says "Select same icons", click on that, and now all those matching antibodies have been selected. What you can do is change their color in bulk, and you don't have to worry about finding each one and changing that color. You can almost do that instantaneously, so it really helps to save a lot of time.
There might be times when dragging a box over all of your icons isn't going to be a feasible action. For example, if you want to change the color of your immune cells in a tight microenvironment of different immune and cancer cells. With the "Select same icon" tool, you can select your dendritic cell, select all the same icons, and change their color as a group. This makes sure that all the icons were changed and you didn't miss anything. Same thing with your activated macrophages, where you can select all the same icons here and maybe change it to a lighter blue. With your cancer cells, you can select all the same icons and make it stand out to be a little bit darker red. This way, all the icons were changed and you didn't miss anything. Rather than having to go in and click through trying to find each of those icons, or trying to creatively drag a box, all you needed to do was click on your reference icon, select all the same ones, and change all those at the same time.
Now, I want to take a little segue here. I know we're talking about changing colors and it was the colors that I chose to switch the immune and the cancer cells to were deliberate, and that's because it helps with the storytelling. Often, we can use color to help augment and help tell our story. If you remember reading story books or comic books when you were younger or even now, what you might notice is that villains or your antagonists are often shown in more reddish or warm tones, whereas your protagonists or your heroes are usually shown in green, blue, or cooler tones. The perfect example of this is Star Wars, where the Sith always used red lightsabers, whereas the Jedi, who are your heroes, will often use either a green or a blue lightsaber. This kind of storytelling can be applied to scientific images as well. By using blue/green to help depict my immune cells, who are going to be generally the heroes of your story, we can easily signify that. Similarly, by turning the cancer cell into a darker, warmer red, we can signify that it is going to be the villain of the story that we're telling with this tumor microenvironment here. We can do all that without changing the composition of this figure at all. All we did was just change the color, and you can easily see the impression that one is going to be your antagonist and the other one is going to be your protagonist. It's a cool way to change your story or add layers to your story without needing to change the components that go into it.
Additionally, what's really cool about color is that one can use it to create associations. Looking at heroes and villains, for example, but what one can also do is help guide the reader through the illustration as well. In the protocol, the protein of interest doesn't stand out from the rest of the illustration. The entire illustration is kind of a bluish tint, and the protein of interest is kind of a bluish tint. We can easily use the select same icons feature to accentuate that protein. To do that, we can click on the protein, select all the same icons, and then add a color overlay. We can match it against the Western plot and apply that as a color. You'll see instantly that the protein pops off the screen and really stands out against that background. This is an example of using color to help highlight elements that would be of interest. In this case, the protein of interest is in a bolder orange color versus the blue background, and you can really easily track where that goes throughout the figure. It starts off as a free protein, it's bound by some antibodies, which is then precipitated, and then we can purify that out before Western blotting. This really helps us to follow that story quite readily throughout the entire protocol.
The reason why the orange really stands out from the blue is because they are considered complementary colors, and complementary or opposite colors are essentially those that exist on different ends of a color wheel. These are pairs of colors that when they're combined or mixed, they cancel each other out. Examples of this would be your red/greens, your blue/oranges, your purple/yellows, and when placed next to each other they create the strongest contrast for those two colors and I have some examples down here of like complementary colors at work a lot of that goes into logo creation so for example you can kind of see like that blue orange or Fanta we have red green for our 7-up, etc. and what you'll notice that all these create these very sharp contrasts so things in your foreground can really stand out from your background and that's exactly the same sort of idea that we applied in our figure up top here to make that protein of interest stand out from the rest of my illustration um one thing to note though with the complementary colors is that red green might not be the most accessible color for people just because there are going to be folks that might be red green colorblind and so it's just something to keep in mind when you go to select your color pairing that red and green might not stand out as to everyone the same way that it might stand out to yourself so just something to keep in mind there and sort of building on that idea of as well about using Color to focus or guide people through your illustration I have a pathway here that kind of highlights that example and so right now here you'll see that this pathway highlights binding to my receptor it triggers a signaling Cascade leading to the eventual transcription of my of my protein and this is a relatively complex pathway right there's a lot of parts here that are happening and if I'm going to present this illustration it's going to be a little bit harder for my audience to follow along because when I'm discussing the receptor they might be looking at you know the the Cascade or the transcription factor or the transcription process sorry so instead by using color we can help focus our audience's attention I'm going to show you what I mean by that when I go into presenter mode here so what I'm going through to talk about this mechanism I can first have this top part colored where we talk about TGIF beta binding and then once we have that binding process we trigger the signaling Cascade that occurs after that signaling Cascade is done this results in transcription of my protein and from this by using sharp colors that stand out from the rest of my illustration this allows me to guide my audience through this talk and you'll see that even for yourselves when I'm just flipping through these slides what's likely happening is that your eyes are following where the color is so a kind of a cool way to use those colors to help with again guiding your audience through the illustration I think that's what's most important - the last thing you want to do is have your audience get lost in your illustration. You want to make sure that things are very easy for them to follow just because that you know everyone nowadays are doing way too much with way too little time and so the last thing you want to do is make it so when they're in a presentation or looking at a figure that they have to work extra hard to understand what's happening and so one of the ways to make it very easy for them to follow along is just to use color to just kind of guide their focus and orient them to where is most important at that moment.
So one thing, so up till now a lot of what we were talking about using the “select all the same icons” tool for was using it to change color. And that's not all the select same icons feature is useful for. There are going to be times that you're going to want to bring all these elements into a line to make sure that they're lined up properly. Here's an example of this: let's say we're in a capillary, we have our blood cells, and we want to show that they're actually going single file through this capillary. Rather than moving each one, we can rely on those guidelines to help us align everything. But that's going to be a really tedious process, and even with just five icons, that's still a lot of work. So, if you imagine having to do it with a whole bunch of text boxes and a protocol, it's going to be virtually impossible. What you can do is leverage that select feature. You can click on that first one, select all the same icons, and now you can go over to a line. We have different options of aligning our icons, whether it's against the left edge, through the central line, through the bottom, or we're able to make it fourth to align to different reference points. Just as a heads up for everyone, to explain the behavior of the alignment, essentially what we're doing is taking a look at those outer edges of the box that's created when I select all those same icons, and then we align it against that edge. For example, if I align it against the left, it'll actually push all the icons against this edge here, so I'm just going to move everything like that, and you'll see it kind of snap into place. If I go through the midline, it's just going to line up like the center of the box.
Additionally, once you have all those icons selected, if you want to make it more even as well, you can do the same thing. We have a set of distribute features as well. We have different ways that you could distribute, in this case, I just want them to be evenly spaced apart, and this way I can just click that and you'll see that all of the icons will then just be evenly spaced here. Of course, let's take this full circle. Right now, since we're all changing the color for everything, we can repeat the same thing since all of our icons are selected and make those icons uniform.
Lastly, I wanted to show here as well, like with selecting all the same icons, one of the easiest ways is for aligning all of your text boxes. That was something that was very difficult when I was creating timelines, but in this case, all we need to do is just select all the text boxes that we have of interest and then just force them to line down the midline, and we can snap them into place. It really saves us the time of trying to manually do it, making sure that it's not a pixel off. This just does it automatically, and I would personally have found it to be a huge time saver.
Oh yes, you can actually create a color gradient. I can show you how to do that right now, actually, since we're going into the custom blob tool. So what I want to talk about here right now is how to create custom shapes and lines. As a tangent to this, we can also talk about how we can change the colors to customize those icons as well. With the blob tool that's available, I know it's a little bit of a strange name, but it is a really cool feature. So we go into insert shape, and then we can go into custom shapes, and then we can grab one of these funky shaped shapes here, then we just pop it onto our canvas. Right away, the first thing that you'll notice is that we have those blue and white nodes. Again, just thinking back to our basics, those nodes mean that we can change the structure of this and change the structure of this element. If we want to create gradients or color, what we can do is go to fill, and then we right now it's just selected as solid, but we can also hop over to gradient as well to create a gradient for us.
If we wanted to depict changes in concentration or if we wanted to show that there's a progression from one state to another, we can go into that gradient mode and then play around with how we want that gradient to look like. We can even change the angle of how that's applied so you can really customize it as well. For folks that are maybe doing some developmental biology, it'd be a really fun way to show sort of like the concentration of your different developmental factors as they go from one side of your cell to the other to drive for the development of different features of your organism.
Going back to this custom blob tool here, you might be wondering what sort of instance you would actually need to create a custom shape, and something that's really cool that you can do with it is use it to highlight globular regions. An example of that is, let's say that there's a tumor in the brain, and I want to show not just that the tumor is there, but I want to highlight what regions of the brain are affected. Because it's such an irregular shape, it wouldn't be easy for us to put a circle or put a square to highlight it. In this case, we can create this custom shape.
Here and then sort of conform to our brain. And what I'm doing I'm just going to kind of pop that into position. I'm actually going to make the fill transparent so I can make this a red. Just to match the color of that tumor and then instead I'm going to turn up the transparency so it just kind of fades into the background a little bit more while still giving me like that reddish hue.What I can do actually is then just drag that custom that blob around and have it just highlight the regions of the brain that might be affected by my tumor. So you can you can then highlight some pretty fun regions of your brain here like so and so that's kind of one way to that's kind of like one way to leverage the blob tool and another way is to create like almost like custom proteins for yourself so on its own it might not be the most intuitive but once you start combining with different elements like this protein or this DNA here these nucleic acids you can kind of get more of a sense that this is a protein that might be doing something and because this is a custom shape if let's say there was a mutation that occurred which deepens the invagination on your protein you can just highlight that visually by dragging in and manipulating the blob a little bit to reflect that that mutation. And as you get better and better with the blob tool you can do some really cool things and so these are examples that are provided by our creative team so at first glance it actually might just look like there are these custom shapes that are scattered throughout or sorry not custom shapes but it just looks like you know it's one piece but if I click into this this is actually a grouped icon and all these shapes are just different blobs that were overlaid and you can even adjust your own as well if you wanted to just if you didn't like where the blob was in the first place you can play with it and tinker around with that to get that into the shape that you want and these are still relatively simple shapes but on the right hand side here with my brain slice you can see that this is much more complex so for example like something like this where I'm highlighting the insula you'll see that this was like essentially just a custom shape that was just manipulated to highlight that brain region so you can do some really fancy things with it and it just comes with some practice and as you get more familiar with using the custom blob tool all this will become a second nature to you.
Lines and Arrows
All right so let's take a look now about lines and arrows. We wanted to make sure that you know the lines that we have in BioRender kind of reflect that ability and so what I want to talk about here today are circular and plasmid arrows or circular arrows to kind of create them and to find those just go over the insert line and then you see that we have circular arrows that we can work with. Sorry about that so let's grab one of these circular arrows here and just drag it out onto our page and here you'll see that when I have it selected I have this editing panel that opens up for me and there I have all these different properties that I can work with and to address the question from earlier this is where you can actually change the color you can change a lot of the different settings of your arrow as well so whether you want it to be thicker whether it has a dashed line or not but the type of line that it is you could also play around with different effects so whether it has a line fade or maybe it's tapered where it starts like much thinner and it becomes larger at the end as well you can indicate whether the symbol that's on the start and the end point so whether it's an arrowhead or if you wanted to create neurons you can actually just flip between the different types you can and you can instantly flip between different styles of lines so whether it's just a standard line, an arrow inhibitor it's really just by changing the heads in the tail.
Now, the cool thing about circular arrows is that the main difference here is that with the blue and the white nodes, rather than being able to change the shape, the white note acts as a snipping point. So, if I needed to create a break in my arrow to insert some information or whatever it is, I just click that white node and I can create that break. Then from there, I can grab that blue node and then I can change the size of that break as well. This is a really cool way to kind of create like this circular flow of information where I have space to insert my own information.
In this example, it looks like on my right-hand side, I have this very fancy plasma that I've created. But actually, it's just two circles that are stacked on top of each other. You can easily make it for yourself as well, and I'm going to walk you through exactly how to do it. If you're designing a plasmid and you want to show what that looks like, this is how you can actually recreate this last bit here. Using the example on my left, I have a thin circle at the bottom. What I'm going to do is overlay it with another circle, so I'm just going to use maybe this one here that I was using earlier, and I'm just going to roughly match the size of my arrow against my previous point. You'll notice that as I move this circle around, I have this little tiny dot right in the center of that circle here, and this kind of acts as my reference point. I know that my two circles are stacked on top of each other and I can use that to help guide as I adjust the size of my arrow as well. Once I have it in place, I'll just crank up the thickness of this arrow here, maybe to about like so, and then use that snipping point to help me create breaks. This is going to be my Gene A, this is going to be my Gene B, and you'll see that those arrowheads will automatically reappear when I create those breaks as well. Another bit of color tip, you can use colors to help you match or pair ideas and associations together. In this case, this arrow refers to Gene A, so what I'm going to do is actually click on that arrow that segment, go to color, use the color picker, and then select Gene A here, same thing with B, and lastly with C. This is a cool example of using colors again to create associations. Color is very powerful and something everyone should really keep in mind as they design their illustrations.
Of course, with circular arrows, creating plasmids is one thing, but you can also create circular workflows like this one. While it might look kind of complex, really it's just two circles or one circle that was then broken up into many different parts. You can kind of show the different phases of your phase diagram or alternatively, you're creating like this set of arrows that exist between each of the different steps. The cool thing here is that all of them will always be a perfect circle, and so you don't have to worry about needing to readjust that afterwards. As you get more comfortable with the arrows, you can do some cool things like this biological pathway here. It looks really fancy, but again, three circles. There's one circle here, one circle here, and one circle here, and then the rest of it was just overlaying with different icons. There are a lot of things that you can do as you get more familiar. You can create illustrations that become increasingly powerful.
All right, as we continue on, like the topic of lines, one of the really cool things about lines is that it anchors to different elements. Previously, when we had to work with lines, what we'd have to do is try and line it up with our center points, but what happens is that if I needed to move protein A or the phosphorylated version, my arrow doesn't actually adjust with me. I have to manually then remove or move the arrow again and try and adjust that, and that's a really tedious process. In BioRender, a really cool thing that you can do is actually anchor that arrow to different ends. What I mean by that is that if I bring my cursor close to that first element, you'll see that there's a symbol that pops up with those two dots and a connecting line. This means that I'm anchoring to one side. Then I'm going to bring my cursor close to the other elements, and you'll see that the same symbol appears, letting me know that I can then anchor to this object as well. Now what happens is that if I were to move protein A, you'll see that that arrow automatically adjusts with me. So, all I need to do is focus on moving that label, and I don't have to worry about modifying that line afterward. It's not just with your text shapes as well. You can also anchor to entire icons. For example, in this case, I have anchored that arrow to my icon in the middle. You can move that center piece, and those arrows will automatically adjust with you. Would not recommend this, but it's to show you what you can do. You can actually just move that center piece, and you'll see that those arrows will automatically adjust with me um but would not recommend this as a composition for your protocol is designed in a linear fashion, but if you ever need to shift things around, the arrows will automatically adjust with you, so you don't have to worry about editing them afterwards. Anchored arrows are especially helpful when creating flow charts. If you need to move any of the labels around, the line will automatically adjust with you. When creating flow charts, it is recommended to limit the number of angles that appear. Focus on either perfect vertical or horizontal lines and minimize the number of off-angles that appear. When things are anchored, it becomes easy to make adjustments. For example, since it's anchored to the label on the right-hand side, if you move the label, the line will automatically snap into place. You can group text plus the hang above the arrow as well, so it stays centered when you move it. There are guidelines that will help ensure that the icon is centered above the text itself, which you can use as guideposts when adjusting those icons.
Limiting angles that come out of workflows applies to how pathways are created as well. It's important to make sure most of your angles are 90 degrees, so it's easier to manipulate your pathways that look cleaner with fewer angles. The color editor is really cool. Inside the color editor, there are color presets that you can work with to change the color of your icon as a whole. For a subset of icons, you can change the individual layers as well. There are different properties that you can work with, such as transparency, saturation, and glow. You can use the glow feature to create a really cool fluorescent effect. One application is for green fluorescent proteins. If you double click into it and apply glow to all of them, you get a really cool fluorescent effect.
For a lot of folks, they will also apply a red glow to their objects because what it does is it gives you that sense of inflammation of that redness the heat or damage even and this is a really cool way to kind of add again more context and more layers to your illustration without needing to add a lot more elements it's really just again leveraging color to help us create those sensations.
And so like what we have like this image you can do some cool things and one thing that I wanted to show everyone as well before we wrap up if you're someone that works with a lot of crystal structures or if you're a structural biologist you might be working with you know protein crystal structures quite a bit and you can create some cool effects like right now you can create like this almost x-ray view of your protein where you have like your surface and you have your protein underneath it and while it might look complex it's really just two proteins that are stacked on top of each other.
If I double click into it you can see that one is just my ribbon structure and one is just my surface and what I did was just stack it on top of each other and turn up the transparency of my bottom protein to almost create like this x-ray view for my illustrations. And to get to that essentially we're just working with the pdb file we just hop in here we can either retrieve something from our csb or upload it from your computer. I don't have any crystal structures. I'm very envious of people that have generated one before so I'm just going to use a sample protein from the literature and what we're doing is essentially creating one element that has our ribbon. I'm gonna save that. I'm going to repeat the same thing except this time I'm going to apply the surface to it and say Van Der waals we'll save that as well. Then now that I have my two proteins what I'm going to do is just stack them on top of each other or bring out my first protein here and then my next one on top of it line it up and I'm going to select that bottom one crank up the transparency a little and then turn this into a grouped icon and now I've almost created like that exact effect. Very straightforward, you're really just stacking the two things together and you can create some pretty powerful effects in your work.
Awesome, that's pretty much it for what I wanted to go over with everyone today. So I wanted to thank you all for taking the time to join me in this session. Hopefully, everyone learns some new tricks, maybe some learn about some features that you might not have discovered on your own yet.