My computer was having intermittent hard drive problems, and last week they got bad enough that I sent the Macbook Pro off for repair (free under warranty). The good news is they fixed it, as far as I can see; the bad news is they dropped in a new hard drive, so I’m starting from scratch.

I’m pretty paranoid about backups (four times a day, to external drives in two different locations) so I didn’t lose any significant dat. The problem when this happens (the second time in a couple years) or when I get a new computer, is that I have to reload all the third-party applications I use; and that means figuring out what I need, finding them on the net, reinstalling, finding registration numbers in my saved mail, and so forth.

To save myself some time next time this happens, I’m noting down the apps I’ve reinstalled this time. And in case anyone else cares, here they are.

Commercial apps.

Commercial
Comments
Photoshop I hardly ever use this, but it’s nice to have on hand
BookEnds Reference and bibliography software. Much better than EndNote
DNA Strider DNA/protein analysis and enzyme mapping. There are probably better free products out there, but 17 years of finger memory is hard to quit
Flowjo Flow cytometry analysis. Registration is tied to the computer, need to update via the company
iWorks Pages and Keynote from Apple. I don’t know if I’m actually going to reinstall this, I hardly ever use it
MS Office Word,Excel, PowerPoint. Yes, I’ve tried the free alternatives. No, I don’t like them.

Freeware, donationware, and shareware.

Free- & shareware
Comments
4Peaks DNA Sequencing reader
Adium Instant messaging client for AIM, Jabber, MSN, Yahoo
Adium themes “Old Phone” dock icon
“A Little Less Than Minimal” contact list
“Good Grey” message style
Big Cat Scripts Contextual menu applescripts. Very useful and customizable
AppleWorks I still have one legacy database in this that I haven’t transfered to SQLite
CyberDuck FTP/sFTP
EnzymeX DNA/Protein analysis. I should probably use this instead of Strider, but old habits die hard
FastScripts Lite Menubar access to Applescripts. Not much difference from the builtin scripts folder
Firefox Not my default browser right now, but useful for some things
Firefox extensions Adblock Plus
Adblock Filterset
Quick Proxy
Download Statusbar
Gleam Flickr uploader
Google Earth  
Google Hosted Mail Notifier Menubar notice when I get new mail in my hosted gmail
Growl System notifications, integrated with several other apps. Also remember to install growlnotify
Journler I haven’t paid for this yet but probably will soon. Flawed, but better than the other organizers/notebooks I’ve tried.
JungleDiskMonitor For my Amazon S3 account. Still in beta. I will probably pay for it when it’s out of beta, but haven’t decided for sure yet
Magic Number Machine Stupid name and dock icon, but a good scientific calculator
MagiCal Customize menu time and date display
MenuMeters Menubar CPU use, also quick access to the Console
PandoraMan For the Pandora Streaming Radio service, which kicks ass
Safari 3 My default browser on Intel Macs, though it was less stable on PowerPC macs. Faster and smoother than Safari 2
ServiceScrubber Eliminate crap from the Service menu, so you can find the few services that are actually useful
SlimBatteryMonitor Uses less space in the menubar than the builtin battery monitor
Stuffit Horrible company, but I still need the expander occasionally
Synergy iTunes monitor and controller. I got a license for this years ago when it was by far the best controller, now competitors (including freeware) are catching up
Synk 5 Backup software. I use it a lot. (The latest version is 6, but I wasn’t impressed by it and already have a licence for the previous version so stuck with v.5)
TextWrangler Programming editor. Nothing else I’ve tried has been as versatile.
Vienna RSS reader
VLC Video viewer
WeatherMenu Weather in the menubar. Now freeware, but I got a licence many years ago when it was by far the best available – now there are competitors that are close
Windows Media Player I used to need this for baseball highlights and listening to games on MLB’s stream. Don’t know if I still need it, but hey.
X11 Apple’s verions of the X window system
XJournal Livejournal blogging client
XCode Apple Developer Tools
XMenu Menubar access to apps. There are a million different apps for this, this is just as far as I got before I found one I was comfortable with

Programming in Python. Apple includes Python2.3 and wxPython2.6 (or so), which are a few versions back of the latest. I update to Python2.4 (the latest is 2.5, which I haven’t moved to yet) and the latest wxPython (2.8.4 as of now).

Python/modules Comments
Python2.4 Programming language. Packaged for OSX here
wxPython2.8.4 For GUI integration
NumPy Numeric modules. OSX package
PySQLite SQLite database API. OSX package
Python Imaging Library (PIL) OSX package
ElementTree XML parsing
mxBase tools Required for BioPython
py2app Turn Python scripts into standalone apps
PyObjC Python/Objective C bridge
appscript Manage apple events with Python (just like Applescripts)
BioPython Many bioscience-related modules
DarwinPorts Unix-type apps ported to Darwin. I don’t use this just for Python, but it fits here better than elsewhere, I guess.

Dashboard widgets. I used to use widgets a lot, but have gradually moved away. I still use some of these regularly, though.

Widgets Comments
Reminder Widget Minimalist reminders (uses growlnotify). I wrote this one
Translate Widget DNA formating, translation, analysis. I wrote this one too
Digital World Clock Know the time for my sister in Switzerland and my brother in Beijing
Flip Clock Widget A clock for local time
iCal Events Widget Upcoming events from iCal
Scoreboard Widget Red Sox game tracking. Like I don’t already have it on the radio
AlbumArt Widget iTunes track indicator, with album art
PEMDAS Widget Calculator widget
Package Tracker Track FedEx, UPS, DHL pacakges

Applescripts for /Library/Scripts. These are just things I slapped together myself; here to remind myself to migrate them over. If anyone cares I can make them available, but they’d likely need tweaking for general use.

Applescripts Comments
File from Safari URLs Save the URLs from all open tabs into a text file
File to Safari URLs Open URLs from a text file into Safari
URLs -> Journler Save URLs from all opens tabs into Journler
Journler URLS -> Safari Open all URLs from a Journler page in Safari
Format Excel Chart Why doesn’t Excel let you save a default chart format? This makes the half-dozen formating changes I invariably set
Format sequence Take a DNA orprotein sequence, make a tidy numbered output
Images size adjust Quickly adjust the size of selected images
Strip sequence Remove all non-DNA characters (including spaces and newlines) from a DNA sequence
Track -> XJournal XJournal reads iTunes tracks, but doesn’t format classical properly. This is a fix for classical tracks

Finally, remember to copy back:

Files Comments
~/Library/Keychains/login.keychain Don’t lose your passwords
~/.bash_profile Terminal shortcuts and formats
~/.pythonstartup Python preferences