Life of a Lab Rat

Back in the glory days of System 7 it seemed that everybody had a plasmid-drawing tool (I was originally going to say 'widget', but you'll see why I changed my mind in a minute). Then something went horribly wrong and all these useful little programs broke or went outrageously commercial (you know who you are) and consequently out of the reach of many of us.

So for a while there we were using Illustrator or similar to draw plasmid maps, which is a little bit like using a howitzer to take out a cockroach — it's expensive, there's a lot of collateral damage and you're never quite sure if you actually got it.

OK, so maybe that analogy is flawed. Never mind. Where was I? Oh, yes. Plasmid maps.

The incomparable but fairly well-hidden Ian York not only writes intelligently about immunology, thereby demonstrating that he is much, much smarter than I am, but I am reminded (because I promised to do this months ago) that he's written a little DNA-mapping program, XPlasMap, which as far as I'm concerned proves that he's superhuman.

I heartily endorse this product or service

This gadget (which would, I'm convinced, make an excellent OS X widget) slurps a sequence, finds the open reading frames and restriction sites, and makes a quickndirty plasmid (or linear) map in a mere couple of clicks. It is dead easy to insert fragments and to change the labels and colours, although removing sites you don't want to see is a little tiresome, and it would be nice to be able to zoom into crowded bits of the map. It also would be handy to be able to insert fragments by restriction site rather than base number, and to export the entire sequence (making the save file a package, as does EnzymeX, would help here), but for a simple to learn, easy to use tool for making records of all your plasmids, you can't really go wrong with XPlasMap.

Oh, and it outputs JPEG and PNG files for further furtling, although the reason for the JPEGs being 4,000 pixels wide is probably merely further proof of Ian's superiority.

Comments

Thanks for the endorsement.

removing sites you don't want to see is a little tiresome You can batch-remove sites in the List View, using the standard select-many keys (click with shift down to select a contiguous series, or select with command down to select a non-contiguous series) followed by the delete key. (Some List View operations are still running rather slowly, though, and this is one of them. That's something I hope to get fixed soon.) You can also just hide the sites ("Hide text" in List View), so they don't clutter your map but are available in case you want to check them later.

it would be nice to be able to zoom into crowded bits of the map There is a zoom (in the status bar or the toolbar if that's turned on). But you probably mean something like a magnifying glass that can both zoom and move you to the site. That's a good idea.

It also would be handy to be able to insert fragments by restriction site rather than base number Not quite sure what you mean here. The new-site dialog needs both name and position, but doesn't care what order. Do you mean something like a batch input? That would be easy enough to put in, if there's interest.

the reason for the JPEGs being 4,000 pixels wide That should be fixed in the latest release. Please let me know if it's still misbehaving.

When I planned this I deliberately decided not to get much into sequence-based analysis because I didn't want to compete with high-quality freeware like EnzymeX. The goalposts on that decision have kind of crept a bit, so I may think more about exporting the sequence and so on. I worry about the file size -- I'm usually using the program to map genomic maps now, for many millions of bases, and if I carry that sequence along it would obviously make the files huge (and slow) as well.

Thanks for the feedback.

By the way: Your spamguard feature .... In an effort to curb malicious comment posting by abusive users, I've enabled a feature that requires a weblog commenter to wait a short amount of time before being able to post again. Please try to post your comment again in a short while. Thanks for your patience.
... seems to count "Previews" as "Post" attempts.

Posted by: Ian | October 6, 2007 10:02 PM

I have version 0.96 - which I downloaded this afternoon, so I'm a little confused about points 3 and 4. When I went to 'I'nsert a sequence I only appeared to have the option of choosing by position. Unless I missed something of course ;)

I understand about not wanting to increase the file size. Pages, I think, saves the text in its packages gzipped, so there's that possibility.

Yah the preview thing bugs me, too. I'll have a word with the admins (it lies, by the way - "I" did nothing of the sort!) if the activation energy is exceeded.

Posted by: BK | October 6, 2007 10:58 PM

I'm sorry, I misunderstood your point about inserting fragments. That's a good suggestion and I'll see if I can add it in.

Question about the JPEGs: Is the canvas huge with a small image in the corner? If so that's the bug I thought I had fixed, and if you can send more info about the appearance and your system I'd appreciate it.

If the whole JPEG is huge including the image, have you changed the export resolution in the Preferences? If you have, and the images don't change size appropriately, could you again file a report?

Thanks

Posted by: Ian | October 7, 2007 12:22 AM

Ah, yes - the image is huge. You see, I'd have thought the preferences would refer to JPEG *compression* quality. Selecting 'low' gives a 800 px image at 72 dpi (versus your 'high' of 4k at 72 dpi).

You'd have to talk to a proper graphics person to see if that's appropriate, not me. But PNG is a better bet than JPEGs for computer graphics anyway. . . transparent backgrounds and everything. Nice.

Posted by: BK | October 7, 2007 08:51 AM

Hello. Nice blog here. Just thought I would throw in my 2 cents as well... Now that i'm a the NCI we have tons of cash for all kinds of software that nobody uses =D , but aside from that there are two VERY good options that are free - 1) Invitrogen now owns VectorNTI and I recently discovered that it is now FREE to download. This is quite amazing becuase while I was in grad' school it was something $5000 US per license. 2) There's another excellent (if a bit "crunchy") plasmid editor which I just love to use and did so the entire time I was in grad school. Its called "ApE - A plasmid editor" and it uses the Tcl/Tk toolset so it runs on MacOSX, UN*X and WindowsXP. Free, simple to use, and actively developed by a real-biologist. I dont have a link atm, but i think a quick google will bring it up.

Posted by: Jonathan | October 10, 2007 10:51 PM

Hi Jonathan,

thanks for the comments.

VectorNTI appears to be free to download, but it looks like a trial version, not free to run. It also doesn't work on Tiger, according to the IVGN website.

I tried ApE last year, and didn't like it much. I also heard bad things about the extension it relies on, so was wary about pushing too far.

CLC do a free version of their workbench, which isn't bad, although it feels 'wrong' to me. But then I still run EMBOSS as my primary sequence mangler, so you probably don't want to believe anything I say ;)

Posted by: BK | October 11, 2007 09:35 AM

If 4,000 px wide is too wide, clearly you need a larger monitor.

Well done Ian. Good stuff. And look, he's responsive too!

Posted by: El Whiffleroon | October 12, 2007 02:09 AM