Thesis toolbox

I’m almost done. About a month to oral defence. But, here are the tools I used to gather data, process it, whip up visualizations, and write the thesis:

  • Papers (for storing the 598 papers I worked through during the process).12
  • Dropbox (for having the files available on any computer I’m using, storing revisions, and making me not freak out about backups)3
  • Noteshelf – best notebook iPad app I’ve used. Did CoI coding data in it. Tracked progress in it. Sketched visualization ideas in it. Etc…
  • SurveyMonkey (for the online survey. wish I hadn’t used it, though, because I didn’t spring for a paid license and my data was trapped)
  • a custom HTML page and CGI processor hosted by UCalgary for gathering ethics consent from participants
  • Chrome (save web page… provided the online discussion archives)
  • BBEdit (for processing the discussion archives)
  • Excel (for storing the metadata and coding data, processing the data, and generating some visualizations)4
  • Gephi (for playing with visualizing online communities – wound up dropping most of those from the thesis, though)
  • OmniGraphSketcher (for creating many of the visualizations. FANTASTIC app for playing with data visualization)
  • OmniGraffle Pro (for the concept map visualization and some supporting media)5
  • Acorn (for processing all graphics)6
  • iPhone Voice Recorder app (for recording instructor interview)
  • VLC (for playing the instructor interview slowly without going mental)
  • Word (for writing the thing)7
  • WordPress (category on my blog for running notes on journal articles)
  • likely a handful of other handy apps thrown in for good measure

The irony… my thesis basically boils down to “it’s not the tool, it’s how you use it.” And I write a “these are the tools I used” post…

  1. Used the Mac, iOS and Windows versions, synced via Dropbox (and then gave up on syncing because my library was too fracking big) []
  2. the search tool in Papers is awesome. I found stuff in it that was difficult or impossible to find elsewhere, and the library proxy support was a HUGE timesaver. []
  3. raw online discussion data didn’t go here because of ethics implications – I’d said that would only be secured on my home computer []
  4. pivot tables are magic, or science fiction. I was amazed at how easy it was to play with the data once it was all normalized into a spreadsheet. yeah, not a hardcore True Database. Whatever. Did the job. []
  5. I dabbled with Visio on Windows, but compared to OmniGraffle, it just. sucks. so. badly. []
  6. absolutely LOVE Acorn. So good. []
  7. found myself not hating spending this much time in Word. Sure, it’s not perfect, and it has its quirks, but it worked well enough… []

back to Fever˚

I tried switching to Pulp as my RSS reader a couple of weeks ago. The interface was interesting, and it syncs across multiple devices (Mac and iOS) using iCloud, so there’s no Google-tracking. Sounded interesting. Worth a shot.

Yeah. Well. That didn’t work out so well. The iCloud syncing never worked well for me. Not sure if I subscribe to more feeds than it can handle, but there you go. Constant issues with getting feeds and state synced across a couple of computers. But, that’s not the end of the world. It was the interface just doesn’t work for extensive use. It’s like the Pepsi Challenge thing. It seemed great on the screenshots, and with initial usage, but it just didn’t work with lots of feeds, over a couple of weeks.

Pulp tries really hard to be a shiny newspaper. But it tries really hard to be just that. Little quirks like showing all items in a page, but just fading already-read items out to barely legible grey. And not showing the new stuff without making you wade through multiple pages and scrolling through a bunch of columns. A reader should help me blast through feeds without hunting for unread items and squinting to read stuff.

So, back to Fever˚. And, with the latest version of the Reeder app for iOS (adding support for using Fever˚ for the sync – hopefully the iPad and Mac apps get feature parity with the iPhone version soon…), I can have the full interface on any computer with a browser, and an optimized mobile app for the road. Best of both worlds.

more Papers love

I’ve been slowly working on my MSc research proposal. Still **far** to early to post any of it online, but it’s starting to take shape. I’m using [Papers](http://mekentosj.com/papers/) to gather journal articles for reference as I’m working. Today, I added 33 articles to the stack, on top of the 63 I’ve already gathered. That’s not manageable. But Papers has some great tools to help cut through stuff quickly. I can sort the articles by the number of citations they have, which pushes “important” articles up to the top of the list. Then I can work through them all more effectively, without worrying about missing anything important.

Of course, Papers is also to blame for the tall stack of papers to read. It makes it almost **too easy** to find articles.

A giant list of 96 papers with 33 new additions becomes a filtered list of 31 papers to read first, sorted by “importance”. Now, if I had an iPad to read the papers without being tethered to a computer (or killing a forest of trees, and draining several unicorns of their blood for inkjet printer cartridges…)

Papers_sorted.png

on censorship in the Apple app store

I’ve been trying to be a voice of reason when it comes to how Apple operates. I’d rather see them as generally trying to do the right thing, but struggling sometimes with some of the nitty gritty things. Like letting individuals interpret blanket policies for what is and is not acceptable in the app store.

I’m fine with Apple deciding that an app is unacceptable if it crashes the iPhone. If it hijacks the cellular network. If it leaks memory, data, or something.

I’m not fine with Apple censoring apps. They hold the exclusive entry for software to get installed on an iPhone or iPod Touch. There is no other authorized way to install apps, without going through the Apple app store. And that means Apple has a very serious responsibility to act honourably, and in the best interests of its customers.

The latest app store controversy is swirling around Ninjawords. An application that provides a slick UI on top of the online Wiktionary dictionary database.

Someone at Apple decided to test the app by explicitly and manually searching for “fuck” “shit” and a few other stopwords. The software was designed to disable text autocompletion for questionable terms, so the only way to find them is to type them in yourself. But the developers missed “cunt” in their autocomplete filter in the last version. So Apple responds by slapping the app with a restricted 17+ rating – meaning kids don’t have access to a good dictionary on their Apple mobile devices.

Apple, this is not cool. You don’t get to censor content, especially content in a FUCKING DICTIONARY. Jesus fucking h. christ.

fucking-dictionary

ps. this screenshot was taken of the Dictionary.app that came pre-installed on my Mac – the same Dictionary.app that my 6 year old son has unrestricted access to.

Update: Phil Schiller responded to John Gruber as a result of his post on DaringFireball.net – the response is a good one, but John’s take is pretty much the same as mine – even if Apple doesn’t censor the app themselves, there is pressure put on developers to censor themselves to avoid age-restrictive ratings. The inconsistent application of these ratings means writing an app can be a bit of  crap shoot. But, Schiller’s email is a very good sign.

cruz

Cruz is a new webkit-based browser that supports Greasemonkey scripts, plugins, and stuff like integrated tinyurl creation and a full screen mode. It can generate thumbnails for search results on Google, and has a CoverFlow view of search results. Very cool stuff. I think I’ll be switching…

Hey! You got Firefox in my Safari! You got Safari in my Firefox! 2 great tastes…

My iDVD is borked

I’ve got a fully updated copy of iDVD on my MacBook Pro that refuses to cooperate. I can create a project, save it, and burn it to DVD. But, if I decide I want to quit iDVD, it borks the next time I launch it. It gets past “loading themes” and then just hangs. I can nuke my prefs, and get the “new project” dialog, but if I create a project, I get the same thing if I quit. Which makes editing an iDVD project a bit, well, problematic. I currently have to recreate the project from scratch every time I want to make a modification. Which makes the process a bit more tedious than it needs to be.

I’ve done searching on the Apple Support site. I’ve tried Googling. I’ve poked through manuals and documentation. No joy. Here’s all I get when I launch my incredibly awesome, soon-to-be-Oscar™-winning iDVD project:

iDVD borkage

The strange thing, if I click “Close”, it pauses for a few seconds, the “Unexpected Quit” dialog disappears, and the shell of the iDVD app remains. I can select menu items, and click on interface buttons (but they don’t do anything). I have to then Quit (or Force-Quit) the app to make it really go away.

Nothing in the crash log jumps out at me. I’ve uninstalled all of my InputManagers, all of the extra QuickTime codecs, anything I can think of that’s non-stock-MacOSX. No luck yet. Very frustrating.

Crossover for MacOSX

Alan posted about the grief he’s been having with running Windows on his MacBook Pro. He rarely fires up Windows, but when he does, it’s a painful and ugly process. The last recommended updates just hosed his Windows install. Again.

But, there’s a better way. Crossover for Mac – it’s a polished commercial version of the open source Wine tool/library which provides a way to run Windows applications in MacOSX without having to install Windows. Basically, it provides a self-contained environment where applications are tricked into thinking they’re running on Windows, but they’re actually running on a bridge between the Windows API and MacOSX (and X-11 for display). You set up a “container” or a “bottle” to hold an application or two, and Crossover takes care of system-level stuff. You get an application icon that’s right at home in your dock, too.

Here’s what a cross-platform browser test might look like. Safari, Firefox and IE6/Win all on one screen:

crossover cross-platform browser testing

Text rendering goes from great to craptastic, from left to right. Also, apparently there are a few *cough*issues*ahem* rendering my blog in IE6/Win. Sorry. Shows how often I’ve used IE over the last year…

For something simple like browser testing, Crossover can’t be beat. It also runs with a bunch of other apps (including HalfLife). I tried to install NASA WorldWind, but didn’t get past the .Net install. I’ll try again after doing a bit of research first.

Alan posted about the grief he’s been having with running Windows on his MacBook Pro. He rarely fires up Windows, but when he does, it’s a painful and ugly process. The last recommended updates just hosed his Windows install. Again.

But, there’s a better way. Crossover for Mac – it’s a polished commercial version of the open source Wine tool/library which provides a way to run Windows applications in MacOSX without having to install Windows. Basically, it provides a self-contained environment where applications are tricked into thinking they’re running on Windows, but they’re actually running on a bridge between the Windows API and MacOSX (and X-11 for display). You set up a “container” or a “bottle” to hold an application or two, and Crossover takes care of system-level stuff. You get an application icon that’s right at home in your dock, too.

Here’s what a cross-platform browser test might look like. Safari, Firefox and IE6/Win all on one screen:

crossover cross-platform browser testing

Text rendering goes from great to craptastic, from left to right. Also, apparently there are a few *cough*issues*ahem* rendering my blog in IE6/Win. Sorry. Shows how often I’ve used IE over the last year…

For something simple like browser testing, Crossover can’t be beat. It also runs with a bunch of other apps (including HalfLife). I tried to install NASA WorldWind, but didn’t get past the .Net install. I’ll try again after doing a bit of research first.

Playing with Aperture

I got a copy of Aperture this week, just in time to get to play with the new 1.5 update. I'm really impressed with the application. It blows iPhoto out of the water.

I was trying out some of the new features, and thought I'd see if I could tweak one of my favourite photos of Evan to make it "pop" a bit more. On the left, the original, "in camera" image. On the right, a version with white balance correction, and an application of the new "Spot & Patch" tool to remove some blemishes.

Evan - tweaked (before and after)Evan – tweaked (before and after)

The tweaked image definitely "pops" more. Might be a bit too warm, but I was just messing around with Aperture. I'm realizing a couple of things:

  1. shooting in RAW is awesome (I went for a walk around campus today, shooting RAW for 90% of it. what a difference…)
  2. I have huge gaps in knowledge/understanding of photography. I'm having fun slowly learning, but man, do I have a long way to go.

King jokingly suggested I should quit my job to be a photographer. If that would pay the mortgage, I'd do it in a heartbeat.

I got a copy of Aperture this week, just in time to get to play with the new 1.5 update. I'm really impressed with the application. It blows iPhoto out of the water.

I was trying out some of the new features, and thought I'd see if I could tweak one of my favourite photos of Evan to make it "pop" a bit more. On the left, the original, "in camera" image. On the right, a version with white balance correction, and an application of the new "Spot & Patch" tool to remove some blemishes.

Evan - tweaked (before and after)Evan – tweaked (before and after)

The tweaked image definitely "pops" more. Might be a bit too warm, but I was just messing around with Aperture. I'm realizing a couple of things:

  1. shooting in RAW is awesome (I went for a walk around campus today, shooting RAW for 90% of it. what a difference…)
  2. I have huge gaps in knowledge/understanding of photography. I'm having fun slowly learning, but man, do I have a long way to go.

King jokingly suggested I should quit my job to be a photographer. If that would pay the mortgage, I'd do it in a heartbeat.

Ideas for improving TextMate

I’ve been using TextMate for about a week now, and while it’s almost universally an incredible piece of magical software, I have been keeping a list of things that could use tweaking (you know, to make it even magicaller).

  • Arrange Windows. BBEdit’s got a great way to tile open windows. It’s very handy to compare multiple open documents. Would be very handy in TextMate. Something like “tile all open windows in evenly spaced columns” or “tile them all in equal-sized windows arranged nicely across that 20 inch cinema display”
  • Split window view. Terminal has it. XCode has it. BBEdit has it. Makes it really easy to work on 2 different parts of the same document.
  • Reindent code. Like Tidy does for HTML. But for other code. JEdit has a pretty good one. XCode’s got a really good one. It makes it very easy to keep source code looking clean and tidy. Bonus points for optionally adding documentation stubs for languages that use that sort of thing (javadoc tags, etc…) It looks like I could mess around with the Bundle Editor for various languages, but having this as stock behaviour would be a better way to share with the rest of the class.
  • HTML and CSS reformatting – flat, compact, hierarchical. It’s surprising how handy that is. Sometimes having the Official Tidy Cleanup Version isn’t what you need.
  • Tear-off bundle palettes. The “Select Bundle Item” menu/palette is close, but not task-specific. It’s not as handy having to constantly search for a function. I’d like to just tear off the HTML, or CSS, or maybe both.
  • Search all open files – if I’ve got a bunch of files open, from various locations (and perhaps on different servers) – they won’t be in the same Project, so I can’t use Find in Project.

I’ve been using TextMate for about a week now, and while it’s almost universally an incredible piece of magical software, I have been keeping a list of things that could use tweaking (you know, to make it even magicaller).

  • Arrange Windows. BBEdit’s got a great way to tile open windows. It’s very handy to compare multiple open documents. Would be very handy in TextMate. Something like “tile all open windows in evenly spaced columns” or “tile them all in equal-sized windows arranged nicely across that 20 inch cinema display”
  • Split window view. Terminal has it. XCode has it. BBEdit has it. Makes it really easy to work on 2 different parts of the same document.
  • Reindent code. Like Tidy does for HTML. But for other code. JEdit has a pretty good one. XCode’s got a really good one. It makes it very easy to keep source code looking clean and tidy. Bonus points for optionally adding documentation stubs for languages that use that sort of thing (javadoc tags, etc…) It looks like I could mess around with the Bundle Editor for various languages, but having this as stock behaviour would be a better way to share with the rest of the class.
  • HTML and CSS reformatting – flat, compact, hierarchical. It’s surprising how handy that is. Sometimes having the Official Tidy Cleanup Version isn’t what you need.
  • Tear-off bundle palettes. The “Select Bundle Item” menu/palette is close, but not task-specific. It’s not as handy having to constantly search for a function. I’d like to just tear off the HTML, or CSS, or maybe both.
  • Search all open files – if I’ve got a bunch of files open, from various locations (and perhaps on different servers) – they won’t be in the same Project, so I can’t use Find in Project.