I’ve been playing kickball every Wednesday.
We’re in a kickball league competing with other companies.
Despite being completely not into sports as a kid, I actually really like adult kickball.
I get to hang out with coworkers that I don’t usually get to hang out with, and everyone’s really friendly.
The first time I went into lab after my PyCon hiatus, I found a broken centrifuge on Marcelle’s bench.
Died of a broken heart. Marcelle you are missed.
Marcelle had just left the lab group for medical school a few weeks prior.
3D printed with plastic and conductive silver on the Voxel8 Development Kit
Designed with Blender
For a while now, Harry has been trying to get me to 3D print a light up Ralph, the mascot of Thoughtbot. While folks have 3D printed Ralph before, they didn’t have access to printers that can print conductive traces. Luckily, I work for Voxel8, a company the makes 3D printers that specializes in printing electronic devices.
I used the Voxel8 Development Kit to print Ralph.
For modeling, I turned an SVG of Ralph into a 3D model via Blender. Then I used Curves to create the traces. That’s it! It’s really awesome that Voxel8’s slicer, Euclid, is smart enough at path planning that I didn’t have to manually create tracks for the silver to sit in.
Design and printing took about an hour each. Once Ralph came off the printer, all I needed was an LED and a battery, and viola!
This Ralph was printed in a single try. If I spent a little more time, I could’ve improved the design and print quality, but I’m kinda lazy.
Anyhoo, there you have it, a light up Ralph!
Much like how you should use a csv library to generate csv files, you should use a library to generate GenBank files.
In Python, you can use Biopython!
Here’s a small recipe you get to started. It creates a GenBank from a sequence, and even includes an annotation.
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
from Bio.SeqFeature import SeqFeature, FeatureLocation
# Create a sequence
sequence_string = "ggggaaaattttaaaaccccaaaa"
sequence_object = Seq(sequence_string, IUPAC.unambiguous_dna)
# Create a record
record = SeqRecord(sequence_object,
id='123456789', # random accession number
description='An example GenBank file generated by BioPython')
# Add annotation
feature = SeqFeature(FeatureLocation(start=3, end=12), type='misc_feature')
# Save as GenBank file
output_file = open('example.gb', 'w')
SeqIO.write(record, output_file, 'genbank')
LOCUS Example 24 bp DNA UNK 01-JAN-1980
DEFINITION An example GenBank file generated by BioPython
1 ggggaaaatt ttaaaacccc aaaa
Check out the really good Biopython documentation for more details!
Extra! Extra! Read all about it!
Next stop for the CRISPR revolution: RNA guided epigenetic regulators.
Since we all love stats, I have:
Special thanks to Su, Marcelle, and Alex, for being awesome peeps.
PyCon 2016 just ended! I had a far more relaxing time this year, since I didn’t have to give a talk.
Ned gave an amazing machete-mode debugging talk this year.
I’ve seen a couple of his talks over the past years, and this one is my favorite.
I bought a super cute PyLadies Seattle tshirt, featuring plaid hair!
Lars gave an incredible keynote! It was also great to see him again. 😀
I’m not sure if it was the talks or the general atmosphere, but I felt excited/inspired about software development in a way that I hadn’t been for a while.
I also got to see a lot of friends I don’t usually get to see, which was great.
Until next year, PyCon!