Ploofle

Since I seem to be updating this list constantly, it’s going to become a page.  So there.

Slowly unsuckaging myself for the tentacles that are Microsoft…open source is finally fully working out for me! Except in the realm of modern games.

Work (office basics)
OpenOffice - Does word, powerpoint, excel-like things. Also has a better system for page layout and visio-like drawings in my opinion - except in page numbering and mixing landscape/portrait oriented pages.  Has awesome add-ons for spelling, such as a English (UK) OED spellchecker (which is what the UN uses) and a Mongolian(!!) spellchecker.  I find it hard to easily position graphics objects in Writer, though.
Firefox - You know what this is. While I don’t particularly like the new auto-popup as-you-type address bar, it’s become very useful when you remember a snippet of a page title and then can get back to it.
Free Download Manager - Very useful here in Mongolia. Supports download resuming without as far as I know putting crap on your computer. Its website is a bit tricky to find the actual download you want though, oddly enough.
CutePDF Writer - “Prints” files to PDF format. Have to download the ghostscript link mentioned on their site for it to work. I think it prints out with more accurate formatting than OpenOffice’s PDF export function.
Sumatra PDF - Simple PDF reader that will run off a USB drive - also saves/bookmarks the last page you had open of individual files if you do the ebook thing.  I’m moving away from this, due to the last version’s unforgivably slow initial loading/rendering of pdfs, the stupid issue with using “find” (sometime it won’t, and you sometimes get “stuck” in the find box when all you want to do is pgdn to the next page, and its lack of ability to select text in-pdf and copy to clipboard.  I’ve been using Adober Reader 9 (sigh) more lately.
Jarnal - Ignoring the painful misspelling of “journal” for this software as well as its less-than-attractive website, this is a really cool Java-based open source note-taking application similar to Microsoft Windows Journal (or the notetaking component of GoBinder and OneNote).  It doesn’t have many bells and whistles, but a very nice feature is the ability to import PDFs, write all over them (aka “annotating”) and export as PDF for others to view.  The other really cool thing is that you can collaborate on a single file across a network if others have this software, sort of like a digital whiteboard/scratch paper.  I haven’t tried this but it sounds intriguing for planning and quick group edits.  If it picked up some of the file/course organization components of GoBinder, and perhaps the voice recording/what-you-we-writing-at-that-moment feature from OneNote, I’d be a super happy note-taker.  Otherwise I’m merely happy.

Work (web/multimedia)
Handbrake - Converts video (VOB files) painlessly into various divx formats, including for ipods
VirtualDub - Make simple video edits/effects for AVI files
Audacity - Record or edit sound. I believe you have to obtain a mp3 codec separately to make it export to mp3 though - their website explains how.
WAMP - An all-in-one package that runs a local Apache web server with the latest versions of PHP and MySQL. Can also be set up to run multiple versions of PHP and MySQL or set up as a “live” webserver. Includes SQLite I believe, but I don’t use it.
FileZilla - FTP tool. The latest version lets you edit files based on OS-associated file extensions.
Firebug - Firefox extension for checking code in browsers and examining CSS.
TortoiseCVS, TortoiseSVN - Used on Windows machines for CVS/SVN code management - integrates nicely into your shell context commands.
PuTTY - Blame sourceforge. Used for SSH and telnet-kinds of things. Mostly command-line.
GIMP for Windows - Weaning myself off of Adobe, painful as it is. I still don’t like the windowless setup of GIMP, and I don’t recognize all the editing icons, but it works. Grab the English-language manual too - it’s a separate download.
Inkscape - This is really cool.  It pretty much does everything I need to do without the price tag of Illustrator.
Scribus - I’ve deleted this for now, as I found it to be too unstable on my computer.  Maybe in 6 months or so it’ll be less wonky.  Supposed to be an InDesign-type program.
Notepad++ - I’ve resolved my coding in general issues with Notepad++ and a large number of plugins/settings. I tried this first without any plugins and it irritated the hell out of me with not being able to do what I wanted to do.  The deal-maker was really the ftp plugin and the PHP syntax highlighting/function autocomplete feature.  I almost don’t use FileZilla due to it.  Other nice plugins were  compare (side-by-side textfile comparison), search in files, tabbed setup for multiple windows, reopening last files on startup, and support for regex search and replace.  There are about a zillion other features too that will appeal to you (and me) at least partly.  It also highlights syntax for virtually any language structure you can think of - from xml to old school batch files to assembly to C#.  Crazy.
MixMeister BPM analyzer - a little program that lets you drop in your mp3 directory and it’ll recursively go through it, detech BPM, and update the ID3 tags.  A little slow if you have lots of files, but almost always works.
RegexBuddy - I tend to install then uninstall this program, but it’s sticking a bit more now that I remember more bits of Regex.  Has a great regex building component and a large library of common regex tasks’ expressions that you can use as-is or modify.

Work (research/academic)
Zotero (with OpenOffice/Word extensions for in-document citing) - This is an amazing firefox addon that lets you download RDF/DOI data (think autofilling of citation fields) from most places, including PubMed, and store the pdf/article in the database, AND you can tag and it’ll do fulltext searches within both citation info and the pdfs on the fly. The extensions let you cite from it and formats automatically into a lot of typical citation styles with either endnotes or footnotes. Also has some cool timeline features if you want to see a birds-eye view of your citation history.
OpenEpi - Offline or online (but browser-based) interface to a lot of common biostatistical/epi/public health calculations, such as sample size or chi stuffs. Also explains decently what these calculations are for. I think for me it’s the replacement to EpiInfo’s utilities components.
WeftQDA - Haven’t used it for real, but it’s a qualitative data analysis tool similar to ATLAS.ti
FreeMind - Used for mind-mapping - multi-branched tree-like structures that are great for group work and discussions or medium-sized planning sessions where you want to focus on gathering all ideas then refining/organizing them
UW proxy tool - Used with Firefox or IE to toggle on or off UW netid authentication when looking for articles and what-not. Helps for finding full-text versions.
PSPP - A open-source equivalent to SPSS. It doesn’t have all the bells and whistles, but it does have the basics - descriptives, common T tests, and linear regression. I don’t do more than this anyway - and its interface is almost identical to SPSS and has file compatibility. Definitely replaces EpiInfo for me from a data analysis standpoint. The site linked to is where you can download Windows-compatible installers rather than the source code, which is the way it’s typically distributed.

Fun
VideoLan - Great media player - plays virtually anything and will try to fix corrupted files
Songbird - I’m not yet all onboard with it, as it’s missing some major features I like in iTunes (namely, smart playlists and a relatively sane podcast management piece), but maybe the next version will work out…
QuickPlay with ZSNES, Kega Fusion, Nestopia, Project64 - Old video games! And Quickplay serves as a management frontend for the various systems and stuff. However, just about all of these products have terrible documentation. If playing on a computer, though, try looking for video filters that say HQ3X, HQ4X, or SaI2X. In theory you can do netplay too - nothing like playing Dr. Mario over the internet a continent away…
StepMania - DDR clone for computers. Many many many songs are available online, and with a laptop with tv-out and a usb-based “dance” pad, you have DDR for real. Also has cool announcer packs and extreme (nonstop) modes.
Last.fm - Loosely defined as software, it in theory will help with the dry spell I have here in new music. Essentially notes what you like and don’t like, and it’ll provide suggestions for you, plus biographical/discography info for your current stuff. Interfaces with iTunes to automagically do this.
KOTOR II Restoration Project - very soon, I’ll be replaying this game bwahaha. It’s a fan-based project for a massive patch to KOTOR II to enable cut/lost game material, which is significant. For now I’m playing Phantasy Star on the Sega Master System and Star Ocean on SNES.
Goodreads, Project Gutenberg, GutenMark, proTeXt, TOR website - Reading resources for me - free ebooks, chapter excerpts, and generally helping me keep track of books I’d like to read someday.  I use GutenMark to post-process the plain-text ebooks into LaTeX (text-based brilliant and more-predictable-once-you-get-the-hang-of-it inDesign-style document layout language); seems like Wikitext borrowed some from it), then use MikTeX to finetune the conversion and export PDF versions which are, if I say so myself, orders of magnitude easier to read than the originals.  And with pictures sometimes.

Utilities
AVG - I don’t use it as I’m still covered by UW’s McAfee site license, but I’ve used it on others’ computers here and it seems to work fine.
InfraRecorder - Burns CDs, DVD, or makes ISOs painlessly.
WinDirStat - Cool utility for looking at your hard drive’s space usage graphically to identify where you have random large amounts of crap. Also has cool pacman hourglass-equivalent icon while analyzing your drive.
USBVirusScan - Needs some setup (futzing witha batch file or VBS file), but in the end will execute a program (e.g., a virus scanner) upon insertion of any removable disk.
Spybot - Malware/web-based exploit protection software. May be becoming obsolete with more virus scanners including this kind of module…
7Zip - Open-source that has the features I like in WinRAR (namely, explorer-style browsing of archives). Doesn’t have RAR compression support, but it’ll open/extract just about anything.