Geekygrad's Blog

Geekygrad’s Mac software mix

geekygrad — Fri, 08 May 2009 20:20:29 +0000

I thought I’d do a quick tour of some interesting programs I’ve found useful on the Mac. Some are geeky, some not so geeky:

Bibdesk - Excellent reference manager that natively uses the BibTeX format. Files PDF’s and lets you search databases such as PubMed and ISI Web of Science. Very extensive applescript support. BibDesk is free software, and has a great user community and plenty of contributed scripts.

OmniFocus - GTD task management application that has excellent integration with AppleScript, Mail.app and iCal. Also has a companion application for the iPhone that can be sync’ed via Bonjour/WiFi or over the air to a WebDAV share. OmniFocus is available from the OmniGroup, and is well worth the price. Student discounts are available and the support is excellent.

Audacity – finally we’ve got a professional-grade audio recording program that’s usable by an amateur yet has all tools a professional needs. I use it for everything, from recording narration to digitizing old records and cassette tapes. It exports the final product to all major audio formats and appears to have support for VST plugins as well as having its own plugin architecture. Audacity is free software and has an extensive Wiki on its web page.

Quicksilver - the swiss army knife of launch applications and documents. I’ve barely scraped 10% of the functionality of this application yet, but in the right hands it’s a great time saver. Quicksilver is available from Blacktree software free of charge.

Aquamacs - If you’re an emacs user you’ll love Aquamacs. It keeps all the functionality of emacs, including plugins, but has a beautiful cocoa-based interface that uses the native Mac OS X system services as much as possible. The interface is well thought out and the program appears to be under active development. Aquamacs is free software, available online.

Boxee - media center based on XBMC with some social networking features built in. Very nice interface and plays most file formats. Boxee is available on its website, and sign-up is required.

Calaboration – easily set up your Google Calendar using the CalDAV access protocol. Simple program that does the job well. Calaboration is free software, available from Google Code.

Delicious2safari - puts your delicious bookmarks into a bookmarks folder on Safari. Works from a GUI, and doesn’t seem to have a command-line interface but it does the job very well indeed. Delicious2safari is free software, available online.

Audio Hijack – lets you directly capture audio from any application you have running. Great for saving realplayer streams and radio streams from the web without getting annoying system sounds into the mix. Audio Hijack Pro is on sale from Rogue Amoeba software and well worth the money.

Subverting LaTeX Part One

geekygrad — Thu, 30 Apr 2009 20:19:25 +0000

Anyone new to LaTeX quickly learns how a missing brace or bracket can suddenly break your document – and always at the wrong time. Even worse is when users of more conventional word processors sneer that you “can’t even track changes” – well, with a little help, you can! There’s quite a few ways to do this, but I’ll just fill you in on what’s worked for me. Best of all, it’ll very quickly fix those sudden compilation errors. LaTeX-using collaborators can even join in on the fun because it’s easy to incorporate network access to your document too.

Since LaTeX separates content from presentation to a large degree, the approach we’re going to take will do this too. I’m assuming that you’re Linux or Mac – some of the instructions will need some tweaking to work on Microsoft Windows. (On Mac, use /Users/geekygrad/Documents instead of /home/geekygrad.) We’re going to start in this installment by getting our document into revision control and looking at some layout issues.

Let’s get started – the first thing we need is a means to recall different versions of the source files. The computer programming community luckily have a lot of experience in this area to keep source code under control, and have invented what are called Revision Control Systems. The one I’m going to recommend using first is Subversion. It’s a powerful but simple revision control system and there are plenty of front-ends for it; there’s also a number brilliant tutorials for it online. It’s network-aware too, so you can start collaborating with others in no time.

Let’s assume we’ve got mydoc.tex, and a bibliography file called mydoc.bib. The first thing we need to do is create arepository for it, which will act as a datastore:

mkdir /home/geekygrad/svn-repository
svnadmin create /home/geekygrad/svn-repository/mydoc

Then we need to check out a “working copy”, so from in our home directory we type:

svn co file:///home/geekygrad/svn-repository/mydoc mydoc

Copy the TeX file and the bibliography into it:

cp /home/geekygrad/mydoc.tex /home/geekygrad/mydoc/mydoc.tex
cp /home/geekygrad/mydoc.bib /home/geekygrad/mydoc/mydoc.bib

Then we add them to the subversion revision control

cd mydoc
svn add mydoc.tex mydoc.bib

And type

svn ci

If all goes well, you’ll get the command-line editor (nano) at the prompt. Type a brief message and press enter. Now you can make changes, safe in the knowledge that if you do something that breaks the document, you can safely revert it by typing:

svn revert mydoc.tex

When you’ve made a few changes and are happy with how it compiles and looks, commit your changes as before

svn ci

and press enter. Then enter a brief description. You can view all your change messages by typing

svn log

That should be enough to get you started – don’t forget not to delete or try playing with the subversion repository folder we created at the start. That’s where all your revision history lives. In Part Two we’ll look at how to get back to a specific revision and I’ll show you how you can track changes. Then we’ll move on and look at some more advanced repository layouts that open some new possibilities.

As always, I’d love to see questions or comments!

UCD Robo Rugby 2009 Final

geekygrad — Thu, 23 Apr 2009 21:32:37 +0000

Twitter

geekygrad — Mon, 30 Mar 2009 22:48:44 +0000

Yes I’m on Twitter, so try following geekygrad for some sporadic updates!

BibTeX meets Word 2008

geekygrad — Thu, 26 Feb 2009 22:07:13 +0000

I’m a LaTeX guy, which means I’m a regular user of BibTeX too. In fact, I keep my master bibliography under the control of the very good BibDesk application. There’s a few occasions, however, where I need to write a technical document in Microsoft Word. Often, a smaller regional conference may require it for assembling the program material. Of course, these documents usually need citations. For the regular LaTeX user exiled to Word, there are a few possibilities:

Manually inserting citations
This method works fine for documents with fewer than five or six separate references. I submitted two one-page conference abstracts by now using this methods, and it does work fine. It does require some cross-checking to ensure that the reference list matches the citations and that each citation is consistently formatted.

Applescripts and other helper applications
Bibfuse is a set of Applescripts that will interface Word to your BibTeX library, using the BibDesk application.

Microsoft Word 2007/2008′s Citation Manager
Microsoft Word 2008 (and the corresponding Word 2007 version for Windows) introduced a built-in citation manager. Each reference, called a ‘source’, is stored as part of the User preferences. Although the facility is quite welcome, one issue I was not going to deal with was keeping to separate bibliography libraries. So I was on the lookout for a facility to automatically push the BibTeX file to Word. One great application I’ve seen so far is Bibim.

I’ve left out the obvious one here, Endnote. Given that I don’t use Word that often, Endnote requires more manual intervention to export to BibTeX format, and does not offer the same functionality as BibDesk. For now, I’m sticking with Bibim. One thing I’ve got on my todo list is to figure out how to do this using Applescript – which would allow the push to Word to happen automatically when BibDesk saves the master file.

Moved to WordPress

geekygrad — Wed, 25 Feb 2009 20:34:36 +0000

For a few reasons I’ve moved my blog over to WordPress – thanks for reading!

Bazaar iDisk

geekygrad — Sun, 22 Feb 2009 21:24:00 +0000

For a while now I’ve been using the Bazaar distributed revision control system to let me manage a few LaTeX documents and a lot of analysis code written in MATLAB. I use it to sync changes among my home and office computers plus my Macbook Pro. While one of the brilliant features of Bazaar is the idea that every computer has full history and can work disconnected, I was thinking it would be great idea if a Bazaar branch could also be on my iDisk.

Turns out you can’t do this – although Bazaar will see it as a normal directory it doesn’t support some file locking functionality that Bazaar needs. I suspect this is more to do with translating filesystem operations to WebDAV requests, rather than any particular problem with iDisk. Unfortunate however, when you consider WebDAV would be ideally suited to this task.

iPhone Wish List

geekygrad — Fri, 23 Jan 2009 14:44:00 +0000

Allow unsigned apps – Apple doesn’t necessarily have to let anything and everything into the App Store, they just need to let people build applications, distribute them themselves and have the user import them using iTunes.
Allow Sync over WiFi - iTunes already has the functionality needed for network syncing – because the AppleTV uses it. Most people don’t shift that much content when syncing, so speed would not be an issue.
Turn by Turn Directions - Either Apple should do it themselves or else stop restricting it being done.
Complete Bluetooth Stack - The Nokia 6680 that my iPhone replaced could transfer files to and from the desktop, why can’t my iPhone? Perhaps allow syncing through bluetooth as well?
Tethering - I paid for my data plan, now can I use my full allocation please?
Podcast download over 3G/EDGE - see comment on #5, this can be infuriating if you’re stuck on a bus and want to download the next episode in a series. File size shouldn’t matter – perhaps pop a warning to tell people it’ll take a while.
Video Recording - no reason this shouldn’t be in the base product. My old phone did it too.
iTunes syncing conduits - this is an interesting one. Some desktop apps, like OmniFocus for example, have an iPhone companion app. Often, these will in fact sync with the desktop app using WiFi and Bonjour, because Apple does not support syncing third party data through iTunes syncing… Kind of ironic considering #2.
Call recording - this can be legally a touchy subject. However it could be useful when trying to deal with delinquent cable cos.
Flash - take the head out of the sand there Apple.

Bye bye MobileMe

geekygrad — Wed, 24 Dec 2008 12:31:00 +0000

Hi everyone, it’s the Geeky Grad here and I’m an addict. I have a Macbook Pro, a Time Capsule, two iPods, an iPhone and an AppleTV. Yes, before you ask I’ve got serious fanboy issues. However I’m less than impressed with MobileMe, so much so that I’m moving away from it.

MobileMe, Apple’s cloud computing service was supposed to be like ‘Exchange for the rest of us’. It wasn’t. The real reason I liked it was the promise of push email and over-the-air update of bookmark, contact and calendar information. I own my own domain name and had toyed with the free edition of Google Apps, but I decided to go with MobileMe for the integration it claimed to offer with other Apple products. Here’s what I found:

The IMAP server is slow, as is the webmail interface.
The system does not integrate well with personal domain names. You can redirect a domain name to your web space on it, but there’s no facility for e-mail handling. It’s basically not designed for that kind of usage.
The web interface will not function on IE6. I’m no lover of that browser, but it is often the only one installed on public computers. When I was in a hotel New York a while back, I had no access to my e-mail because MobileMe wouldn’t let me use IE6. There should at least be a graceful downgrade to non-javascript HTML.
Whilst I was in an airport, MobileMe decided to delete all my contacts off my iPhone. That’s just not on in a paid-for product.
MobileMe on Windows was a disaster – I ended up with duplicated contacts and some calendar items didn’t sync at all. (I will admit my Workstation uses XP x64 which isn’t well supported by iTunes, I just wanted Windows so I could also sync to our Sun ONE calendar in college).

By contrast

Google Apps is free – other than buying your domain in the first place. For zero cost you get hosted GMail, Google Calendar, Google Docs and Google Sites.
The web interface is tried and tested, it works on pretty much any browser you throw at it. The calendar interface in particular is just fantastic. It’s insanely fast and downgrades well on older browsers.
GMail’s integration with Apple Mail can be a bit quirky, but once you set up the folders correctly it works very well.
Google Apps can share calendars and documents with people on GMail.
The Google Sites tool is just awesome.
You can make up unlimited aliases, like on GMail. So if an e-mail address does get spammed, it’s easy to find the culprit.

The only downside to the move is that syncing needs to be manually set up, and I can’t sync to my iPhone over-the-air. I tend to plug it in each evening, however so it’s not exactly a problem. (Another day’s discussion is why Apple won’t implement WiFi-sync – that would solve this problem too!)

On the sync front I had tried Spanning Sync to put my calendar on Google’s normal calendar service, and happily that’ll work with Google Apps calendars too! It’ll also sync your contacts as well and seems to do it reliably. It’s well worth the $65 in my opinion and it’s got an active development team behind it. (Google also have a new sync tool themselves which may be worth checking out.)

The whole setup seems to be working very well after a couple of days – I’ve already got most of my personal e-mail moved over and my calendars are live too. Only thing left to do now is cancel that MobileMe subscription.