User:Jonathan Cline/Notebook/Sensomatic/20130323
Previously this was a Slidey presentation but OpenWetWare no longer supports that rendering, but the content is still below.
Contents
- 1 Microbiology Sensor/Controller Board: The Sensomatic
- 2 Engineered Biology - Let's Do Something "Simple"
- 3 Engineered Biology - Let's Do Something "Simple"
- 4 Engineered Biology - Let's Do Something "Simple"
- 5 Engineered Biology - Let's Do Something "Simple"
- 6 Engineered Biology - Let's Do Something "Simple"
- 7 Engineered Biology - Let's Do Something "Simple"
- 8 Engineered Biology - Let's Do Something "Simple"
- 9 Engineered Biology - User/Software/Hardware Model
- 10 Engineered Biology - User/Software/Hardware Model
- 11 Engineered Biology - User/Software/Hardware Model
- 12 Engineered Biology - Data Format
- 13 Engineered Biology - Data Format
- 14 Engineered Biology - Data Format - Device data
- 15 Engineered Biology - Competing Method/Prior Art: BioBoard (Noisebridge)
Microbiology Sensor/Controller Board: The Sensomatic
© 2013
Engineered Biology - Let's Do Something "Simple"
- Make biology easier to engineer
- Make biology more reliable to engineer
by:
- Methods: Improving the means and methods for bio/synthetic design;
- Predictability: Improving repeatability and trust of experimental results and procedure;
- Reusability: Engineering biological components and biological tools to be reusable across designs or across experiments.
for:
- Increased productivity
- Less busywork, more Design time
- Less human interaction means less human error
- Decreased financial cost
- More experiments possible per day per person per lab
(Contrary to popular belief, lab techs & their time are not "free")
Engineered Biology - Let's Do Something "Simple"
Let's perform a cell culturing experiment and isolate some bacteria for bioengineering targets!
- Cory Tobin 2012-2013 (LA Biohackers ; Cal Tech)
- Nitrogenase Directed Evolution
- Plants need nitrogen in the form of ammonia, nitrates or nitrites (artificially via 'ammonium nitrate fertilizers')
- "The directed evolution of a thermophilic nitrogenase ... so that productivity of farmland crops would not be dependent on a non-renewable resource whose price can fluctuate drastically due to speculation, weather or global conflicts."
- Nitrogenase Directed Evolution
Sounds great!
http://wiki.biohackers.la/files/thumb/2/2b/N2-ase.png/500px-N2-ase.png Link
Engineered Biology - Let's Do Something "Simple"
Assuming we've got a potential soil sample which might contain the desired bacterial strain..
- Problem - Culture specific soil samples which might grow something.
- Problem - Identify if something grows.
- Problem - Isolate the bacteria which grows.
- Problem - Identify if the bacteria is the desired strain.
- Problem - Lather, rinse, repeat until the sequence matches.
Then finally begin the real experiment with the target bacteria!
These are lab automation and scalability problems.
- Also known as Bring-Up Issues (industry slang).
Engineered Biology - Let's Do Something "Simple"
Let's Automate this as a bio-protocol and remove the busy-work!
Cory's First Solution (Image Copyright 2012 Cory Tobin)
- Small scale bioreactor with valves
- Arduino breadboarded with various electronics and hand-wired connections.
"Found out the arduino has all these limitations and does not work here."
Spent months.. to bring up an environment to do the real experiment.
Engineered Biology - Let's Do Something "Simple"
Cory's Second Solution (Image Copyright 2012 Cory Tobin)
- Cheap Wal-mart insulated cooler.
- Give up on electronics and do everything by hand.
- Measure and adjust temperature multiple times per day.
- Refill reagents every other day.
"Finally successful, one time through. Same amount of effort to run through again."
- High maintenance.
- Human error.
Engineered Biology - Let's Do Something "Simple"
Jonathan Cline's version: The Sensomatic
- Use industrial-grade, low cost electronics; not Arduino
- Simple programmability, set up by any computer
Achieve simplicity, integration of function, and low cost
Solve a specific problem
Sense and Control:
- Heater element
- Temperature
- CO2
- OD
- Shaker
- Pump
- 120VAC outlet
Engineered Biology - Let's Do Something "Simple"
Jonathan Cline's version: The Sensomatic
http://88proof.com/synthetic_biology/blog/wp-content/uploads/2009/03/img_0012sm.jpg http://88proof.com/synthetic_biology/blog/wp-content/uploads/2013/03/mq5-sensor.jpg http://88proof.com/synthetic_biology/blog/wp-content/uploads/2013/03/LM35.jpg http://88proof.com/synthetic_biology/blog/wp-content/uploads/2013/03/ssr-10636-01_i_ma.jpg
- Low cost electronics
- Industry standard, available in volume
- Open source design
- Replaceable components
- Multiple functions on one device
Engineered Biology - User/Software/Hardware Model
Prior Art (non-integrated, single function devices)
http://88proof.com/biotech/img/Biolab-languages1.png
Industry-standard robotic automation systems (like Tecan or Beckman) use proprietary, high-level script commands (shown) and proprietary low level device operations unique to each device.
Engineered Biology - User/Software/Hardware Model
http://88proof.com/biotech/img/Biolab-interconnect-model.png
- Today's usage for devices is monolithic: each device is programmed separately
- Each device has it's own programming method
- Difficult to re-use software written for one device, on another device
- Biologist has to work harder; each experiment has unique elements
Engineered Biology - User/Software/Hardware Model
http://88proof.com/biotech/img/Biolab-interconnect-model2.png
- Bio-protocol application can be re-used
- Robotics software framework abstracts "hardware operations" from real devices or network devices
Device data is stored in the database
- Each device has operational data and environmental data
- One-time setup that is YAML and sharable
- Standardization of environment is one of the most important aspects of automation
Engineered Biology - Data Format
Data storage formats are very important:
- Make the data usable today
- Make the data editable today
- Make the data survive into the future; no obtuse or ridiculously hard to learn format
- Make the data sharable
Watch out -
- Computer scientists love inventing data formats
- Leading to the problem of... too much complexity
- Vendors love inventing data formats
- Leading to the problem of... patent / proprietary lockup
- Open formats are important for innovation and scalability over long term
Engineered Biology - Data Format
- Need to represent robotic environment and bio-protocol actions
- Computer Scientist response: "Oh, but we can simplify that with XML"
<?xml version="1.0"?> <Experiment Name="JCSG Erbeta+Org1+Org2"> <ID>351</ID> <User>Valerie</User> <Container>Corning pZero 3550</Container> <DatePrepared>2007-10-04T11:05:38.5170000+02:00</DatePrepared> <SetupTemperature>20</SetupTemperature> <IncubationTemperature>20</IncubationTemperature> <ExperimentPlates> <ExperimentPlate PlateNumber="1"> <ID>406</ID> <DateDispensed>10/4/2007 12:45:40 PM</DateDispensed> <Wells> <Well WellNumber="15"> <WellVolume>75</WellVolume> <WaterVolume>37.5</WaterVolume> <Drops> <Drop DropNumber="3" ProteinFormulation="Erbeta+Org2" ProteinVolume= "0.25" WellVolume="0.25" /> <Drop DropNumber="2" ProteinFormulation="BufferC" ProteinVolume="0.2 5" WellVolume="0.25" /> <Drop DropNumber="1" ProteinFormulation="Erbeta+Org1" ProteinVolume= "0.25" WellVolume="0.25" />
Just say No to XML
- Much too difficult to edit this
- Much too difficult to read this
- Much too difficult to learn this
- Now needs extra files to describe the custom format
- XML, HTML, anything that ugly, is a Bad Idea
Engineered Biology - Data Format - Device data
- Each device has control commands (a dozen or several hundred).
- Storing that data in an easily readable and editable format is very important for software re-use.
- YAML Format is Human readable, Human editable and Computer Readable
- YAML allows references to prior definitions and either simple or complex assignments
%YAML 1.1 --- # Fialab-Microsia address: syringe: A valve: C peristaltic: D external: B valve: send: # delay after cmds 100ms - 1 sec NP_SET: desc: set number of physical ports opcode: NP args: - 1 - numport:4-12 redundancy: 2 # send cmd twice delay: 100 # ms recv: ok: ~ err: ~ NP_GET: desc: get number of physical ports opcode: NP args: - 0 redundancy: 2 # send cmd twice delay: 100 # ms recv: ok: ~ err: ~ peristaltic: send: # delay after cmds 100ms - 1 sec SET_SPEED: desc: set pump speed opcode: G args: - 1 - speed:0-100 delay: 100 recv: ok: ~ err: ~ SET_DIRECTION: desc: set pump direction, direction:1=counterclockwise or 2=clockwise opcode: W args: - 1 - direction:1-2:default=1 delay: 5000 recv: ok: ~ err: ~ syringe: send: # delay after cmds 100ms - 1 sec INIT_ALL: desc: init all (both) pumps opcode: _Z0R args: - 0 delay: 100 recv: ok: ~ err: ~ SET_INPUT: desc: position valve in for given pump opcode: /$1IR args: - 1 - pumpnum:1-2:default=1 delay: 100 recv: ok: ~ err: ~
- Made to be readable and editable
- Made to be scalable
- Contains all definitions of a device's operation
- YAML is Best current practice for readable data format
Engineered Biology - Competing Method/Prior Art: BioBoard (Noisebridge)
"an Arduino-controlled sensor package that allow users to monitor a range of physiochemical factors related to microbiological processes"
http://88proof.com/synthetic_biology/blog/wp-content/uploads/2013/03/noisebridge-bioboard-450px-NIRprobe6.jpg http://88proof.com/synthetic_biology/blog/wp-content/uploads/2013/03/BioBoardAppNewProject.png