Drawing software for biology

September 30, 2005 6:06 PM

Drawing program: Can anyone recommend a drawing program, not Photoshop, for manipulating and editing figures?

I work in a biology lab. My PI wants a program to draw figures, such as cartoons of genes, cells, including their receptors and internal biochemical pathways, interactions with other cells, nothing too fancy. Also to put pictures, titles, captions on graphs imported from a program that's not Excel. Etc.

Sorry, I know the wording is really ambiguous. I'm trying to not get into the technicals. She just wants a basic text and figures editor and creator. Photoshop doesn't work for her because it's more of a manipulation of photographs (which we don't have) and I think it's also a bit too fancy (I've personally never really worked with Photoshop...*gasp* I know I know). She currently uses Powerpoint, but that doesn't really suit her needs either. It's too simple. A lot of times, when she pastes several figures together from another program (FlowJo, if it means anything), she tries deleting some parts of the graphs, like axis labels and legends to create a collective one, PowerPoint still retains the old stuff.

I've heard that there's something called ChemDraw for chemistry presentations. Is there anything like that for biology?

Any suggestions will be much appreciated. And if anyone needs clarification, I'll try to answer the best I can.

posted by state fxn to technology (20 comments total)

One more thing: I think the software should be compatible with Macs and PCs. But suggestions for either are welcome.
posted by state fxn at 6:07 PM on September 30, 2005

The obvious answer is Adobe Illustrator, which is basically Photoshop for diagrams and logos.
posted by cillit bang at 6:15 PM on September 30, 2005

In the adobe world, you want Illustrator rather than Photoshop. Illustrator is for manipulating lines, shapes and curves. It natively creates PostScript, but can output in many other formats (including bitmap, IIRC).

However, if you need to extend PPT's drawing capabilities, you might want Visio on Windows or OmniGraffle on the Mac. These programs are for drawing flowcharts and other diagrams that involve connected shapes.

The primary difference between programs like Visio and Illustrator is that Visio is designed to manipulate the interactions betwee shapes. Illustrator is designed to create the shapes themselves, and does not support "rubber band" linking between objects.
posted by b1tr0t at 6:18 PM on September 30, 2005

Illustrator is, if anything, harder to pick up than Photoshop. They are both from Adobe but are fundamentally different: Illustrator is vector-based and Photoshop is pixel-based. Using Illustrator means wrestling with Bezier curves, which are such a delight to a designer's heart.

Apple's AppleWorks might be all right for your purposes, but it's Mac-only, of course. Luckily there are file formats that allow for a good deal of transferability between drawing and painting apps.
posted by zadcat at 6:22 PM on September 30, 2005

b1tr0t or anyone else: Can you clarify the "rubber band" linking part?

I don't think we want to animate the shapes. And for linking objects, can't we just put one next to the other and call them connected? (This is just from my basic experience with working with the Drawing Toolbar in MS Word)
posted by state fxn at 6:33 PM on September 30, 2005

Adobe Illustrator is the standard vector drawing program, but I don't think many working scientists actually use it. Too complicated (learning Illustrator has been on my to-do list for the better part of a decade). I've gotten a lot of mileage out of the OpenOffice drawing program. If you're going to be drawing chemical structures or equations, you'll probably want ChemDraw, but there's a freely available program called Isis/Draw (warning: awful website, registration required) that does just as well, if not better. For doing charts and plots, Origin is nice. It's a lot more flexible (and more powerful) than Excel. All of these programs have learning curves, of course. As a result, the vast majority of scientific presentations I see consist of figures that are cobbled together from Powerpoint drawings and Excel charts. Yeah, it's shameful. Good design, unfortunately, takes too long....

I don't think you want Visio; it's not very appropriate for drawing funky-shaped biomolecules and whatnot.

It's nice to have some rudimentary Photoshop knowledge for getting your art into its final form. I prefer to submit high-resolution TIFFs for publication; you don't have to worry about anything getting fucked up in translation or rendering. Photoshop is good for getting those TIFFs just right on a pixel-by-pixel basis.

I've never heard of software specifically designed for illustrations in biology or biochemistry. If one exists, I, too, would be interested to know about it.
posted by mr_roboto at 6:37 PM on September 30, 2005

Illustrator is Hard to get the hang of. The MS equivalent, Publisher, is much easier to use, but it is equivalently less powerful. FWIW, my local bio grad student uses Photoshop for about the same things you are talking about, he also learned it on the job.
posted by whatzit at 6:40 PM on September 30, 2005

An old version of Corel Draw, like Corel 3 would work.
Cheap/free, and easy to learn.
posted by weapons-grade pandemonium at 6:49 PM on September 30, 2005

If you're going to be doing a significant amount of drawing, you might want to look into getting a tablet as well. Many people find it much easier to draw with a stylus than with a bar of soap (aka mouse).
posted by alms at 6:57 PM on September 30, 2005

You can put several things together and call them linked. The problem is when you have a lot of connected objects, and deicde to move some of them in order to add a new object, like this:

a----b
|     |
|     |
c----d
|     |
|     |
e----f

and you want to move node D out:
a----b
|      \
|       \
c------d
|       /
|      /
e----f

With Illustrator, you have to adjust the shapes, then adjust the connections. With Omni Graffle or Visio, you just drag D and the lines follow along. Obviously this feature becomes more important with more complicated graphs.
posted by b1tr0t at 7:35 PM on September 30, 2005

[btw, that was rubber banding]
posted by b1tr0t at 7:35 PM on September 30, 2005

I'm finishing a graduate degree in biology (immunology) so I've had to draw lots of cells, receptors, signalling molecules, &c&c&c.

I've been able to generate a lot of really good looking (sometimes as good as the stuff that shows up in, say, Nature Medicine and almost always better by far than most of the stuff that people show at conferences) using Macromedia Freehand. I've been wanting to learn Illustrator, but haven't had the time nor the software.

I actually use Flowjo (and Cellquest) - I export the plots and manipulate them using PaintShop Pro. Quick and fast.

If you want, my email is in my profile.
posted by PurplePorpoise at 7:46 PM on September 30, 2005

Oh, for graphs (I hate excel graphs), I love Prizm. It's fast, powerful, easy-to-use, flexible, and it can export graphs from 72 dpi ("screen rez") all the way up toe 1200 (which is overkill even for publishing). Absolutely the best compromise stats program (power & ease of use & flexibility) that I've run into.
posted by PurplePorpoise at 7:48 PM on September 30, 2005

i suggest using Alias Sketch Book Pro 2... works really well w/ tablet PCs or wacom tablets. its JUST like drawing/sketching on a notepad... its a very nice program.


.//chris
posted by hummercash at 7:55 PM on September 30, 2005

I work in a biology lab, and have done many figures for papers and posters, etc. I use Canvas, and think pretty highly of it. However, I think any application with fairly sophisticated vector tools will work for you just fine. In my experience, vector drawing has a steep initial learning curve, but once your PI gets the hang of it, a good vector program is very powerful.
posted by statolith at 8:03 PM on September 30, 2005

The lab I'm in uses Illustrator for all those purposes. Yes, it's a bit more difficult than photoshop, BUT your final images are so much better/sharper, and you can export it to pdf right away.
Also, because it's vector based, you can resize images for different purposes (presentation, article, grant application, random meeting) without losing quality. And you can draw cool cartoony sciency things with it that look professional even if you can't draw to save your life =)

Previous labs I've worked in years ago (1999, 2000) used CorelDraw, but I get the impression that a lot of people nowadays are using Illustrator for the purposes.

What's hard about it are the drawing tools, but since you'll mostly be editing existing images, adding things to it, it's very suitable for biology figures. It took me an afternoon to figure out how to make the figures for my paper/presentations, and that included time just randomly drawing trees and flowers and balloons and other non-scientific doodles.

I've also used ChemDraw (because I started out in Chemsitry and slowly moved to Biochemistry and cell biology) and that is not at all like anything you'd want. It draws molecules.

There are also some professional programs available from bio-companies with which you can draw cellular pathways specifically, like this program, but that is only for one specific purpose (and ChemDraw is like that too, but for a different purpose). You don't want to spend money on that. (Your PI doesn't, either =P)

So, what you probably want is Illustrator: sharp images, can edit imported other images by adding text, remove graph axes etc., multiple export formats, and journals love images prepared in Illustrator too.
posted by easternblot at 8:11 PM on September 30, 2005

Inkscape is a free, simple vector drawing application. Illustrator or Freehand are probably overkill if your Pl has a hard time with photoshop.
posted by signal at 8:37 PM on September 30, 2005

Simple as in easy to learn not as in limited. It imports / exports all kinds of formats, has lots of cheesy effects, type on path, can be scripted in Python, etc.
posted by signal at 8:44 PM on September 30, 2005

Thank you everybody for your responses! I'll check out each one and see what happens.
posted by state fxn at 8:48 AM on October 1, 2005

If you want a really easy-to-use program for simple figures or line drawings, try Macromedia Flash. Anything you create can export directly to Illustrator, and it's dead-simple to use.
posted by Civil_Disobedient at 11:01 AM on October 1, 2005