An Open Letter to the US Copyright Office

The Copyright Office’s 2010 exemption to the DMCA for jailbreaking of cellphones will soon expire. EFF and the Software Freedom Law Center are encouraging people to submit comments to the copyright office in support of renewing the exemption, and also extending it to all other general purpose computing devices such as tablets and gaming consoles.

Read the letter I submitted below the cut.

Compiling py26-pyqt4 in Mac OS X 10.6 (Snow Leopard) with MacPorts

(…when it just doesn’t fucking work)

So, I was trying to install ETE to do some phylogenetic tree visualizations. The recommended method, MacPorts (sudo port install py26-ete2), kept failing while attempting to install the py26-pyqt4 pre-req package. Noted in the log was the following unhelpful error message*:

configure couldn't open "/System/Library/Frameworks/Tcl.framework/Versions/8.5/Resources/tclIndex": no such file or directory

*HINT: This isn’t the actual problem.

The problem is that sip (a prereq to py26-pyqt4) is not being properly referenced.

To fix it, run the following:

sudo ln -s /opt/local/bin/sip-2.6 /opt/local/bin/sip

which will create a soft-link between the installed sip binary (sip-2.6) and what is being called by py26-pyqt4 configure script (just sip).

Then, when you run the macports install command again, it will succeed in installing py26-pyqt4, and the rest of the prereqs.

(keywords: MacPorts ETE ete2 Mac OS X Leopard Python py26-pyqt4 QT4 sip)

Light Interactions

So, because of various (not really at liberty to discuss) stuffs happening, plus epic cat health drama, bright points are a little hard to come by. But today, this thing happened, and it made me happy.

In The Service of Euphemism

You have a beautiful smile means
You have spent thousands of dollars
On a thing
No other creature in the universe
Could look upon
And think beautiful

A Couple Things

Boy, I’ve been remiss in my blogging duties.

Item the first, The Architecture of Open Source Applications, in which Titus Brown and I have a chapter, is out! Woohoo!

Second, we just wrapped up our second year of Analyzing Next Generation Sequencing Data. This year’s tutorials are up on the ANGUS site, along-side last years’.

(keywords: bio-informatics, next-generation sequencing, tutorials, Python, continuous integration, Unix, Amazon EC2)

Pesto Quiche

I keep making things, and then not posting the recipes. This makes two quiches.

2 9-inch frozen pie crusts

8 cloves garlic (crushed, pressed, or minced is fine)
2 large onions (chopped)
1/2 cup pesto (storebought is fine)

6 eggs
1 cup butter (the good kind)
1 cup half & half or heavy cream
1 cup milk
1 cup Ricotta cheese
3 cups grated Romano cheese

Preheat oven to 350. Pre-bake the pie crusts @ 350 for 5 minutes.

Melt the butter in the pan, then sautee the onions and garlic until translucent. Allow to cool (I do this by popping the whole pan in the freezer for a few minutes).

Combine Ricotta, milk/cream, eggs, Romano, pesto. Add cooled butter/onions/garlic. Mix well.

Pour into pie dishes. If you have extra, pour into ramekins sans crust. It’s still pretty good.

Bake for, I dunno, 40 minutes? Poke a fork in it after 40 minutes and if it’s done, pull it out.

This next bit is very important. ALLOW IT TO COOL BEFORE SERVING. This lets the quiche set, so you don’t end up with a gooey (but delicious) mess on your plate.

Compiling Matplotlib 1.0.1 on 64-bit Mac OS X Leopard for Python 2.7

(…when you don’t already have freetype installed in a sane location as might happen with a different version of X, or sometimes if you’ve got a fancy version of LaTeX)

What a huge pain in the ass to figure this out.

Anyway:

1. Download and install the Python 2.7 DMG.
2. Download and install  Numpy 1.6.0b1. *Yes, it’s the 2.6 one. :/ It works, though.
3. Download and expand Matplotlib 1.0.1 source package.
4. In the root source directory

   cp setup.cfg.template setup.cfg

5. Edit setup.cfg, uncomment line 10, and make it read:

   basedirlist = /usr/X11

6. In the root source directory, run:

   python2.7 setup.py build **You want to do install, not build. Thx Ivan.
   python2.7 setup.py install

7. Have a beer in celebration.

(keywords: Matplotlib 64-bit Mac OS X Leopard Python 2.7 freetype2)

Epic Lasagna

So, this recipe is half made up, but turned out pretty well. It is based very loosely on this recipe.

Spicy-ish Tomato Sauce

• 3 tablespoons olive oil
• 1 medium onion, finely chopped
• 6 garlic cloves, minced or pressed
• 1 teaspoon dried oregano
• 1 teaspoon dried basil
• 1 teaspoon dried marjoram
• generous sprinkling of chili powder (to taste)
• 2 28-ounce cans Italian-style diced tomatoes
• 1 cup canned crushed tomatoes with added purée
• 1/2 cup dry red wine
• generous splash of balsamic vinegar
• 1/2 teaspoon of salt (or to taste)

Set the tomatoes, wine, balsamic vinegar, and salt stewing in a large sauce pan, at a gentle simmer.

Sautee the onions, garlic and spices in the olive oil until the onions start to become transparent. Add to the sauce, and allow to simmer for at least an hour to an hour and 15 minutes. Stir periodically.

Lasagna

• 1 1/2 pounds ground beef
• 1 15-ounce container Ricotta cheese
• 3 cups grated Romano cheese
• 1 cup grated Parmesan cheese
• 3 large eggs
• 12 ounces heavy whipping cream
• 1 teaspoon dried basil
• 1 teaspoon dried oregano
• 1/2 teaspoon ground black pepper
• 1/4 teaspoon salt (or to taste)
• 9 (or whatever) uncooked lasagna noodles
• 6 oz sliced fresh mozarella.

Brown the ground beef and set aside.

Reserve 1 cup of the grated Romano.

Combine Ricotta, the other 2 cups of Romano, eggs, heavy cream, basil, oregano, black pepper, and salt. Mix well, until Ricotta is smooth.

Combine ground beef and sauce.

Preheat the oven to 375.

In a 13″ x 9″ x 2″ lasagna pan, layer as follows:

1. meat sauce
2. lasagna noodles
3. meat sauce
4. cheese sauce
5. sprinkle of romano and parmesan
6. lasagna noodles
7. meat sauce
8. cheese sauce
9. sprinkle of romano and parmesan
10. lasagna noodles
11. meat sauce — VERY IMPORTANT TO RESERVE ENOUGH MEAT SAUCE FOR THIS LAYER
12. cheese sauce
13. the last of the romano and parmesan
14. mozarella medallions.
15. generous sprinkle of ground black pepper.

Cover the lasagna tighly with foil, and bake for 50 minutes. Then remove foil, and bake for an additional 20 minutes, or until top layer is bubbly and noodles are tender. Remove from oven, and rest for 15 minutes.

Serve with garlic bread. :D

Pesto Mac & Cheese

For those that asked. This is Jack’s recipe, with some minor modifications. I take no credit except for a passable implementation.

The recipe doubles easily.

Ingredients

• 16oz of Pasta (Rigatoni is recommended)
• 2 C grated Romano cheese
• 3 eggs
• Fresh mozzarella cheese
• 12oz Pesto of your choice. Storebought works fine.
• 12oz Heavy Cream
• 4 largeish cloves garlic, finely minced, or garlic-pressed.
• 3-4T butter
• Black Pepper to taste

Directions

Boil 16oz Pasta to Al-dente, with salt, but no oil. Drain well.

Gently sautee garlic in butter. Allow to cool briefly.

In a large bowl, combine grated cheese, eggs, and heavy cream. Add garlic/butter to sauce and mix thoroughly.

Add pasta to sauce bowl, and mix thoroughly.

In a medium casserole dish with reasonably high sides, spread one layer of pasta.

Spread all the pesto over that layer. Add second layer of pasta.

Place mozzarella medallions over the top layer. If the medallions are thick, full coverage is not required. Don’t over-do it. This isn’t a pizza.

Apply a generous sprinkle of black pepper, to taste.

Bake at 350 for 30-45 minutes, or until it’s done. If the mozzarella is starting to brown, it’s ready.

Serve!

Bacon-Fried Garlic Bread

This latest installment in our series “Cooking With Ingredients!” brings us to possibly the least healthful thing I have ever made. It beats out bacon & bacon-fried potatoes (because potatoes are a vegetable), and candied bacon (because, candy!). This food has no redeeming nutritional or social value whatsoever.

Ingredients:

1lb’s worth of leftover bacon grease
2 slices of white bread (the whiter the better. No ground black people in this one.)
garlic and olive oil paste, to taste.

Tear the white bread into pieces, and fry in the grease with a dollop of garlic and olive oil paste. Fry until the bread has browned, and your gall-bladder has shriveled in sympathy. Remove from pan and drain on paper towels. Wait, who am I kidding? Forget the draining.

Smear fried bread with more olive oil paste until you cover the greasy flavor and the tang of broken dreams with the delightful taste of garlic and decadence.

Serve with a side of the candied bacon you made earlier.