Monthly Archives: May 2015

CRISPR-Cas9 is so hot in synthetic biology right now (just like how React is so hot in front-end development).

It’s a biological mechanism found in bacteria, newly appropriated to cut specific DNA for genome engineering.

Development and Applications of CRISPR-Cas9 for Genome Engineering (recommended to me by an awesome postdoc) is an excellent paper that summarizes a lot of the developments.

Interestingly, the PDB (Protein Data Bank) also summarizes the basics of CRISPR-Cas9 in a very short and very pretty post. It’s far more digestible than the Wikipedia entry.

loading cas9 gif...

Above is a Cas9 visualization I made from its structural data (PDB ID: 4un3). The pink is the Cas9 protein. The orange is the sgRNA. The blue is the target DNA. The barely visible green is the non-target DNA.

Feels good to be looking at synbio again. 😀

Having been in Boston a couple of weeks now, I’m back on the Meetup scene.

I met up with PyLadies Boston Tuesday and Boston Python yesterday.

At PyLadies Boston, I got to met a cool software engineer with 20+ years of experience. It gives me hope I might still be in this field years from now.

At Boston Python, I heard this really neat talk from Karen Rudin, a product manager for Quantopian. She presented on her tale of writing a trading algorithm that focused on the presence of women CEOs.


Very cool.

PyLadies Boston and Boston Python are some of my all-time favorite Meetups. While NYC does have its Meetup gems, I really missed these two while I was gone. Definitely check ’em out if you’re in the area!

Today I decided to roll up my sleeves and figure out how to run Blender headless. I’ve been telling people that it’s possible (based on documentation), but haven’t tried it out myself.

Until now!

It’s actually pretty simple. Here are some steps. I’m on a Mac, so the paths might be slightly different if you’re on another operating system (check out these instructions for for Windows).

1. Figure out the path of the Blender executable. If you’ve ran the Blender console window before, it’s the same executable.

To find it via GUI, open up where the downloaded Blender zip was extracted.

Blender package

On a Mac, show package contents and navigate to the blender executable.

Blender executable

Actual path:


(I currently have the extracted Blender 2.74 package on the Desktop for simplicity so my path reflects that.)

2. Run the executable with the -b argument to run Blender without the GUI. You can add the path to your PATH or run ./blender.

With path added:

blender -b

Run locally:

./blender -b

3. You can pass scripts into Blender while running Blender headless.

blender -b -P /Users/Jenny/Desktop/

4. Passing arguments into your script is a little bizarre. The documentation specifies the -- (double dash) syntax to signal to Blender to stop reading those arguments and have them processed by your script. However, inside your script, if you’re trying to parse out the arguments, you get all the arguments, not just the ones after the --. You must parse them out yourself. Here’s an example below. I’m using argparse instead of sys.args because argparse is very powerful and handles a lot of edge cases (plus it’s just darn good practice).

blender -b -P /Users/Jenny/Desktop/ -- --number 5 --save '/Users/Jenny/Desktop/cube.obj'

The example script creates a number of cubes and exports them.

import argparse
import bpy

def get_args():
  parser = argparse.ArgumentParser()

  # get all script args
  _, all_arguments = parser.parse_known_args()
  double_dash_index = all_arguments.index('--')
  script_args = all_arguments[double_dash_index + 1: ]

  # add parser rules
  parser.add_argument('-n', '--number', help="number of cubes")
  parser.add_argument('-m', '--save', help="output file")
  parsed_script_args, _ = parser.parse_known_args(script_args)
  return parsed_script_args

args = get_args()
number_of_cubes = int(args.number)

# create cubes
if number_of_cubes > 1:
  for x in range(0, number_of_cubes):
    bpy.ops.mesh.primitive_cube_add(location=(x, 0, 0))

# export scene

Running the script will give you an exported OBJ with the cubes.

There you have it: how to run headless Blender. Most people use headless Blender to farm out rendering jobs and increase render speeds, but you can do all sorts of neat stuffs by providing a script. Have fun!

Yesterday, I went to Jeff Benzaon’s thesis defense. It was my first time spectating a defense live (I watched Sir Rice’s defense virtually), so I was super excited!

Jeff was presenting on Julia, a programming language.

Jeff Bezanson

It was a great presentation and I learned neat stuffs. I’m sure I could’ve gotten a lot more out of it I wasn’t such a complete novice at programming language theory.

Best quote:

I don’t think people will adopt some new syntax for a language they already know, but will fully embrace an entirely new language. ~ Jeff

Hope I get to sneak into more of these defenses. They’re super sweet. 😀