DIYBIOFTW

structured protocols

Biological protocols are terse, telegraphic recipes that document common wetlab tasks, for instance, sorting DNA molecules by length via gel electrophoresis, growing a liquid culture of E coli, or extracting plasmid DNA from E coli.

Protocols are generally written and shared in plain text with no machine-friendly structure, which is a shame, because all protocols have some elements in common: they specify functionally important inputs, outputs, and a series of biological operations that will transform the inputs into the outputs. Protocols are wetlab functions composed of a series of biological operations with well-defined inputs and outputs.

I’ve been discussing this in the context of wetlab workflow planning at the diybio google group. Here are some of my thoughts:

A simple way to play with structured protocols would be to establish a small controlled vocabulary for describing the inputs and outputs to various protocols. Meta-protocols could be created by searching for a path from a desired input to a desired output. For example, here is an input and output that would require stitching together several protocols:

Input: 10 ug 1uM plasmid DNA (BBa_I20259)
Output: 400 Relative Fluorescence Units, 500nm.

The input / output controlled vocabulary is potentially very complex. I’m not sure how to deal with units.

Looking forward, if the vocabulary of available biological operations (verbs) and inputs/outputs (nouns) was structured in a machine-readable way, it could form the basis of a biological “test-driven development” system. First, desired biological outcomes would be expressed using the vocabulary. Then the biologist would execute an automatically-generated protocol until the tests passed.

To start with, it would be interesting to try expressing several protocols in the oManual XML standard, which is supported by Dozuki, the web app that runs ifixit.com.

Teardown of e-gel “go” portable gel electrophoresis power supply and transilluminator. Hi resolution photos available on flickr.

Amplicons from three peeps in my fungal barcoding workshop visualized on a gel*. We amplified the 5.8s rRNA subunit using the standard fungal ITS primers.

Patrick used a mildew sample from his shower head in his bathroom, Sara used a Shitake mushroom a local supermarket, and Jesse isn’t telling where his fungal sample came from :)

Amplicons are expected to be around 650bp (see this hackpad for more info). Patrick’s sample worked best. Patrick & Sara’s lanes have smaller bands with a series of smaller amplicons. Perhaps this is because they took surface samples from their mushrooms that were contaminated with other ambient fungi. Perhaps sequencing will be a mess or perhaps it will work… stay tuned.

*2% Gel Electrophoresis on Life tech E-Gel Go unit w/ SybrSafe & E-Gel 1 Kb Plus Ladder.

Use a custom machined aluminum bracket to repurpose just about any off the shelf machine - such as this CoolerMaster CPU heatpipe, now adapted for the core of an OpenPCR machine (Taken with instagram)

Startup Weekend: Hadware Edition. Our project: DIY GEL DOC

edit: we won a prize! “Most Likely to Change the World! Wooooo! Thanks team! Thanks Startup Weekend! You can write the $1,000,000 seed funding prize check to diybioftw.com!

It works!

Magic ingredients for a gel doc: light source, pre-filter, & post-filter. This set works with gelgreen and sybrsafe. Suppliers:

• LED matrix: LC2088TB1A from LC-LED.com
• pre-filter (blue): Acrylic 2424 Blue from Ridout Plastics
• post-filter (orange): Acrylic 2422 Orange/Amber from ridout plastics

Jenzie Hallifax and Maike Rentel hard at work glueing together the first gel doc prototype - getting the illumination shelf set at just the right height.

Wiring the LED matrix I came with was more challenging than I expected. Here’s data sheet.

Test cuts. Trying to make a press-fit laser-cut joint from 1/4” plywood.

I’m pitching a DIY gel doc project at Startup Weekend: Hardware edition this weekend.

Interesting graffiti carved into campsite picnic table (Taken with instagram)

Sam & co at Field Test Film Corps have been working on a Synthetic Biology documentary film. I love their aesthetic. It’s hilarious - “guy in a tie” retro science edutainment, ironically deployed to explain the cutting edge of biotechnology.

And it’s beautiful. They are taking inspiration from one of my all-time favorite illustrators, David Goodsell and introducing me to a classic artist, too: Charlie Harper.

Their documentary is going to be a visual and intellectual treat. Can’t wait. For more animations and artwork, check out their Project Updates at Kickstarter.

Collected some fish samples from a dubious sushi joint on Casto downtown Mtn View. I asked for a take-out box to put my “snacks” in. (Taken with Instagram at Downtown Mountain View)

We got an office in Mountain View, Dana x Castro. Yay! Setting up the lab this week.