Ian's Software

Me

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Them

I've written a few small programs for my own use. If you find them useful, they're freely available.

Problems, comments, or suggestions? My email address is iayork, and I'm at iayork.com.

"XPlasMap": Plasmid maps for OSX (Beta)
"Translate Widget": DNA/Protein manipulation Dashboard widget for MacOS10.4 ("Tiger")
"Reminder widget": Reminders widget
"Top widget": CPU usage widget

I make no promises or warranties of any kind. They work for me, and I haven't heard of any problems from others who have tried them, but I won't guarantee that they will work for you. Use at your own risk.

XPlasMap

Plasmid maps for MacOSX.

XPlasMap draws plasmid or genomic maps, showing features such as genes, promoters, multiple cloning sites, and restriction enzymes. The maps are fairly customizable, and can be generated directly from GenBank, FastA, or text sequence files as well as de novo.

XPlasMap requires MacOS10.5 or newer. (Older OSes may work, or I may have old versions of XPlasMap around that work with them, if you're desperate.)

XPlasMap is free (as in no cost) and can be redistributed as a complete package. I make no guarantees or warranties of any kind.

More info/Download

User's Guide

Translate.wdgt (Download here)

DNA/Protein conversions

Manipulates DNA or protein sequences.

Translate DNA to protein, 3 frames
Reverse translate protein to DNA, using human-optimized codons
Format (60 characters per line in groups of 10, numbered at line breaks)
Scramble
Make antiparallel (complementary) strand

Input is taken from the clipboard (copy the sequence, there's no need to paste it into the Widget).
Output is put back on the clipboard to be pasted as you want.

Reminder.wdgt (Download here)

Quick reminders in 'X' minutes (Requires Growl)

There are several countdown and stopwatch widgets out there, but none did exactly what I wanted. This takes short messages and floats reminders after a certain number of minutes. Requires Growl -- specifically, growlnotify.

Obsolete and no longer available

Top.wdgt

Top four CPU-using processes not in the Dashboard, + top four in the Dashboard

The output from "/bin/ps -arxwwo %cpu,command| head -20", sorted into Dashboard and non-Dashboard because when Dashboard is opened, Widgets dominate the CPU usage.

This widget still works, but there are now far more functional pieces of freeware available, so it's pretty pointless. Let me know if you have any particular need for it.

Savage Plasmids

Web-based plasmid maps; view on web browser, or download printable version

Draw genes, multiple cloning sites, restriction sites

Plasmids can be saved for later editing

(Experimental) Virtual cloning -- copy, insert, and delete fragments

Viewing with web browser requires SVG capability: Adobe's free SVG plug-in for most browsers is here. Built in SVG support in Firefox and Camino is incomplete; on these browsers the postscript map should be more accurate.
Downloadable version is Postscript format; at least in MacOS10.4 or higher this is readily converted to other formats (PDF, TIFF, PNG, JPEG) using Preview.app.