TGen News Dashboard Widget For Mac OS X


Download now!

The Translational Genomics Research Institute (TGen) is a non-profit 501(c)(3) organization focused on developing clinically relevant medical diagnostics and smarter treatments related to genomic profiling. I’ve had the pleasure of working with the institute for over a year on a project related to breast cancer, and thought I’d share a widget I wrote keep you up to date on TGen’s latest news items.

The TGen News: Dashboard Widget for Mac OS X v1.1 gives you an always up-to-date set of headlines, pulled straight from the TGen news feed.

If you enjoy this widget, please donate a few dollars to the TGen Foundation and do your part to support the many causes that TGen pursues. Enjoy!

From the TGen website:

At TGen, investigators are pushing the limits of cutting-edge research and technology to discover the genetic cause of disease. Experiments that were impossible and impractical only a few years ago are now conducted every day.

Discovery fuels TGen’s translational research and lies at the heart of our scientific investigations. TGen’s research divisions are designed to foster a wide range of genetic discoveries. These divisions draw heavily upon TGen’s scientific platforms to expedite findings. TGen’s labs are staffed by teams of researchers focused on making genomic discoveries in common diseases and disorders in the areas of oncology, neurogenomics and metabolic disease.

Note: This free product is provided by Preston Lee, and is neither officially endorsed nor supported by TGen.

LaTeX Broken On MacPort “texlive” Update

I spent about 4 hours today troubleshooting a stupid, stupid issue with the “texlive +full” package as provided by MacPorts, which is required to run certain GUI LaTeX editors such as TeXShop. Several days ago I ran an innocuous-looking…

preston$ sudo port sync
preston$ sudo port upgrade outdated

…and amongst many things that updated, texlive was one of them. Unfortunately, running tools such as the command-line “latex” command or GUIs such as TeXShop started giving me the following error:

This is pdfTeX, Version 3.1415926-1.40.11 (TeX Live 2010/MacPorts 2010_0)
restricted \write18 enabled.
—! /opt/local/var/db/texmf/web2c/pdftex/pdflatex.fmt doesn’t match pdftex.pool
(Fatal format file error; I’m stymied)

After much fruitless searching and hair pulling, I stumbled upon this ticket that notes the solution as:

preston$ sudo fmtutil-sys –all

After running this, LaTeX seems to work properly again. Sheesh.

(Note to product developers: I would personally pay at least $50 for a simple, clean, stand-alone OS X app that does LaTeX really well. TeXShop and TextMate both do a good job, but I’d really like a 5-star “just works” editor that doesn’t install a bunch of system-level stuff like MacTeX. Just sayin’. 🙂 )

Upgrading From Ruby 1.9.1 to Ruby 1.9.2

I’ve spent half the day so far inbeded in the furious stressful upgrade process of a handful of Ubuntu Linux 10.04 and Mac OS X Snow Leopard systems from Ruby 1.9.1 to Ruby 1.9.2. I haven’t even gotten to the Rails 3.0.0 stuff yet: just the baseline Ruby installation. I’ve gone through the upgrade process on both types of systems so far and the base issues have been the same. Here’s a common issue that many people are running into:

preston$ gem1.9

/opt/local/lib/ruby1.9/site_ruby/1.9.1/rubygems/source_index.rb:68:in `installed_spec_directories’: undefined method `path’ for Gem:Module (NoMethodError)
from /opt/local/lib/ruby1.9/site_ruby/1.9.1/rubygems/source_index.rb:58:in `from_installed_gems’
from /opt/local/lib/ruby1.9/site_ruby/1.9.1/rubygems.rb:883:in `source_index’
from /opt/local/lib/ruby1.9/site_ruby/1.9.1/rubygems/gem_path_searcher.rb:81:in `init_gemspecs’
from /opt/local/lib/ruby1.9/site_ruby/1.9.1/rubygems/gem_path_searcher.rb:13:in `initialize’
from /opt/local/lib/ruby1.9/site_ruby/1.9.1/rubygems.rb:841:in `new’
from /opt/local/lib/ruby1.9/site_ruby/1.9.1/rubygems.rb:841:in `block in searcher’
from <internal:prelude>:10:in `synchronize’
<…and so on…>

Assuming you’re upgrading from a previous Ruby installation, note that the “site_ruby” directories are no longer used, and will eff up your 1.9.2 installation if you fail to delete them after the install. On OS X, run:

sudo rm -rf /opt/local/lib/ruby1.9/site_ruby/

On Ubuntu Linux 10.04, run:

rm -rf /usr/local/lib/ruby/site_ruby/

…to correct this issue. All note that you may see errors such as this:

root@li92-132:~# rake –version

/usr/local/lib/ruby/1.9.1/rubygems.rb:340:in `bin_path’: can’t find executable rake for rake-0.8.7 (Gem::Exception)

from /usr/local/bin/rake:19:in `<main>’

…despite have a rake gem installed. Apparently 1.9.2 comes with a version of rake internally, but is unable to find it for some reason relating to the rake.gemspec file. Remove the file to fix this issue. On Ubuntu Linux 10.04, run:
rm /usr/local/lib/ruby/gems/1.9.1/specifications/rake.gemspec
Notice the “1.9.1” path of the PATH. Yeah.. it’s weird. But for compatibility reasons your 1.9.2 installation will continue to use a path with 1.9.1. To quote the Ruby 1.9.2 FAQ page:
The standard library is installed in /usr/local/lib/ruby/1.9.1
This version number is “library compatibility version”. Ruby 1.9.2 is mostly compatible with the 1.9.1, so its library is installed in the directory.
I’m sure there’s a wonderful technical reason for this, but it’s still misleading and confusing as hell. I ended up manually deleting a bunch of stuff I shouldn’t have because I thought I was innocently “cleaning up” after the old version. Whatever. Additional suggestions:
  • Just to keep things clean, you may also want to remove your old Ruby 1.8.x builds. (I recommend doing so unless you have older apps that haven’t moved to 1.9.x yet.)
  • Phusion Passenger seems to work fine on Ubuntu 10.04 with the latest version of Apache 2 as of this writing, though don’t forget to recompile, reinstall, reconfigure and restart apache2 when you do so.
  • Check if you still need rack v1.0.1 installed (for older Rails app) before nuking everything. 🙁
I need a beer!

3D Desktop Ruby Applications On Linux

Over the past year I’ve put out a few working demos of how to develop full 3D, OpenGL-based OSX applications using Ruby. Most of the comments I’ve received have been positive, but I think the high learning overhead has been the prime limiting factor in addoption. I also decided to focus exclusively on Mac OS X, further limiting the potential audience.

I’m pleasing to learn that Martin “monkstone” Prout has successfully run the code contained within my–basically a folder of code on a OS X system that looks and behaves like an .exe does Windows–on a Kubuntu Linux system. I haven’t personally tried to replicate this myself due to a lack of time, but you can read how monkstone did it on his blog.

3D OSX Applications With Ruby-Processing Screencast

A two-part screencast series demonstating two different 3D ruby-processing applications. A slide presentation from 2009 created for the Phoenix Ruby Group is also attached as bonus material. Enjoy!

Part 1: Starfield

Demo of a 3D starfield simulation written in pure Ruby, running on the JRuby runtime as a nicely packaged .app program for Mac OS X. (Runs on Snow Leopard and Leopard.)

Part 2: Twiverse

3D Twitter client written in pure Ruby, running on the JRuby runtime as a nicely packaged .app program for Mac OS X. (Runs on Snow Leopard and Leopard.)

Slide Show

Free Copy Of Portal With New Mac Steam Client

Got a Mac? Like games? Great news! Value’s “Steam” software finally launched for Mac, allowing you to purchase some great gaming titles on your OS X machine. When a game is available on multiple platforms, a purchased license appear to be portable as well. And as a launch promotion, Value is giving away free copies of “Portal” (an awesome title in its own right) through May 24th, 2010. Grab it!

MacPort MySQL “Can’t find file: ‘./mysql/host.frm'” Error

I recently set up a new Mac OS X Snow Leopard laptop for software development purposes. After going through my usual MacPorts installation and installed MySQL using the following steps

  1. sudo install mysql5-server
  2. sudo cp /opt/local/var/macports/software/mysql5/5.1.44_0/opt/local/share/mysql5/mysql/my-medium.cnf /opt/local/etc/mysql5/my.cnf
  3. sudo -u mysql mysql_install_db5
  4. sudo launchctl load -w /Library/LaunchDaemons/org.macports.mysql5.plist

A few days past, and one day I notice that launchctl was loading the script, but `nmap localhost` did not show the the process listening on port 3306 as expected. I looked at the log file:

sudo tail -f /opt/local/var/db/mysql5/preston.local.err

..and noticed it was terminating with the following errors:

100331 12:05:30 [ERROR] /opt/local/libexec/mysqld: Can’t find file: ‘./mysql/host.frm’ (errno: 13)
100331 12:05:30 [ERROR] Fatal error: Can’t open and lock privilege tables: Can’t find file: ‘./mysql/host.frm’ (errno: 13)

100331 12:05:30 [ERROR] /opt/local/libexec/mysqld: Can’t find file: ‘./mysql/host.frm’ (errno: 13)100331 12:05:30 [ERROR] Fatal error: Can’t open and lock privilege tables: Can’t find file: ‘./mysql/host.frm’ (errno: 13)

After a considerable amount of grief I evertually discovered that the contents of /opt/local/var/db/mysql5/ need to be owned by the appropriate mysql user (in my case “_mysql”), but some files were being owned by the “root” user. After correcting all file ownership and restarting the service…

  1. sudo chown -R _mysql /opt/local/var/db/mysql5/
  2. sudo launchctl unload -w /Library/LaunchDaemons/org.macports.mysql5.plist
  3. sudo launchctl load -w /Library/LaunchDaemons/org.macports.mysql5.plist

Everything now seems to work fine again. Hope this helps!

Getting iTunes To Convert/Export/Bounce To Other File Formats

You’d think iTunes 9 would have a menu option to convert selected, non-DRM’d files to .MP3, .AAC and such. It doesn’t, but there’s a quick–if not silly–workaround to get iTunes to covert your tracks to a supported format.

Mac instruction for iTunes v9

  1. Open Preferences -> General -> Import Settings. Change the “Import Using option to the format to which you want to convert.
  2. Within iTunes, select the file you want converted.
  3. Under the “Advanced” menu, you should now see a “Create XYX Version”. Click it and your selected file(s) will be converted in the background while retainer your originals.
  4. Remember to change your import preference settings back to normal!

Done. 🙂

Virtual OS X Server Screenshots

Apple now allow you to virtualize OS X Server instances. While your virtualization options are limited, it’s very easy to set up on your existing OS X Server.

This is an virtualized OS X Leopard Server guest running in Parallels Server on a host OS X Leopard Server. You can see that the guest system is treated similarly to other Windows and Linux VMs in the Parallels Management Console.

Note that a distinct serial number/license seems to be required. The serial number for the host machine will not validate (I thought Apple was going to allow one VM instance???), so to use the sweet service configuration tools available in Server Admin, it appears you’ll need a separate license for now.


Bargain Of The Month: Apple + Adobe + HP + Crucial

If you qualify for an educator/student discounts from the Apple store and want a new machine, check out this crazy deal which I just did at OpenRain


  1. MacBook 2.4GHz White: $1300 – $100 .edu discount = $1200.
  2. iPod Touch 8GB: $300 – $300 MIR == $0.
  3. HP Photosmart C4480 All-In-One Scanner/Printer/Copier: $100 – $100 MIR = $0.
  4. Adobe Creative Suite 3 Web Premium: $1600 – $1300 IR = $300. (OMGWTFBYOB!!!)
  5. Crucial 2 x 2GB SODIMM RAM: $100


Total: $1600 + taxes and express shipping ~= $1800. That’s one helluva bargain for a great midrange laptop (w/4GB RAM mind you) and the powerhouse of Adobe CS3 alone. The iPod and scanner just add to the sweetness! Rock on!