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jcline@ieee.org - Robotics - 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
(Contrary to popular belief, lab techs are not "free")
jcline@ieee.org - Robotics - Let's Do Something "Simple"
Let's Automate a bio-protocol and remove the busy-work!
- George Church Lab
- "MAGE": A Machine That Speeds Up Evolution
- "A genome-wide approach to genetic engineering greatly speeds the manufacture of bacteria for making drugs and biofuels."
Sounds great!
http://www.technologyreview.com/files/25028/evolution_machine_x220.jpg
- Problem: Little re-usability?
- "It's a great device for that experiment, and that experiment only"
- It's not a general purpose bio-protocol processor.
- Problem: Liquid Connectivity?
- "It's self contained and can't connect to a larger protocol."
- These are scalability and reuse problems.
- Also known as Integration issues (industry slang).
jcline@ieee.org - Robotics - Let's Do Something "Simple"
- Let's Automate a bio-protocol and remove the busy-work!
- This time let's build an arbitrary liquid-handler that can move drops anywhere!
- “AC Electrowetting Actuation of Droplets on a Digital Microfluidic Platform”
- “Rapid Prototyping in Copper Substrates for Digital Microfluidics”
- Problem: The droplets can only be moved by switching electricity by hand.
- U-Toronto: (A grad student's hand.)
- What??
- I'll use electronics & software.
Jonathan's version
http://biosx.com/88proof/synthetic_biology/blog/wp-content/uploads/2009/06/p6033652w.jpg
http://biosx.com/88proof/synthetic_biology/blog/wp-content/uploads/2009/07/p7023926swc-prototype.jpg
- Problem: Each movement of the droplet requires an electrical switch. There are many millimeters to move, so hundreds of switches.
- U-Toronto: "Even LabView makes it too complex."
- The software represents a significant portion of the total system... and doesn't exist yet.
- Problem: The chip only works about 1/3 of the time.
- Well, the physics guys can fix that eventually.
- These are scalability and reuse problems: control system issues and device interconnection issues.
- The fabrication problem will be solved by any one of 10,000 postdocs.
- Even when fabrication is solved, the control system problem still needs a solution.
jcline@ieee.org - Robotics - Let's Do Something "Simple"
- Let's Automate a bio-protocol and remove the busy-work!
- This time let's use a big robot! It can do anything!
- (at least, it costs enough, so it should be able to do anything.)
http://88proof.com/biotech/img/jcline-tecan-genesis-2000-1sw.jpg
- Problem: It can really only to certain things that the vendor allows.
- In fact, it can only move certain objects and perform a few operations.
- And, some of those operations fail, too.
- And, the vendor's software can't check for failure.
- Failure requires human intervention, or can ruin the experiment.
- What??
jcline@ieee.org - Robotics - Data Format
- Data 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
- 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 leveraging Long Tail
- Long Tail means a bunch of work is done today, and numerous incremental improvements occur by many people over decades..
- vs. single product lifetime of vendor's software and then the data is lost or the data format is unusable
jcline@ieee.org - Robotics - Data Format
One way (Wrong)
- W3C Recommendations for speech grammars and semantic interpretation
<rule id="order">
<tag>var index=0; out.pizza = new Array();</tag>
<item repeat="0-1"><ruleref uri="#start"/></item>
<item>
<ruleref uri="#pizza"/>
<tag>out.pizza[index]=$pizza; index+=1;</tag>
</item>
<item repeat="0-">
<item><token>and</token></item>
<item>
<ruleref uri="#pizza"/>
<tag>out.pizza[index]=$pizza; index+=1;</tag>
</item>
</item>
<item repeat="0-1"><ruleref uri="#stop"/></item>
</rule>
- Much too difficult to edit this
- Much too difficult to read this
- Much too difficult to learn this
jcline@ieee.org Robotics - Data Format
- W3C Recommendations for speech grammars and semantic interpretation
- Computer Scientist response: "Oh, but we can simplify that"
<emma:interpretation>
<pizza>
<number>1</number>
<size>medium</size>
<type>pepperoni</type>
</pizza>
<pizza>
<number>1</number>
<size>large</size>
<type>cheese</type>
<topping>sausage</topping>
<topping>onions</topping>
</pizza>
</emma:interpretation>
- Still Much too difficult to edit this
- Still Much too difficult to read this
- Still Much too difficult to learn this
- Now needs extra files to describe the custom format
jcline@ieee.org Robotics - Data Format - Device data
- Each device has data associated with operating it.
- 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 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 = Best current practice for readable data format
jcline@ieee.org Robotics - Data Format - Environmental data
- Each device has environment data associated with operating it.
- Points in space
- Containers
- Solids, liquids, gases
- 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 1.1
---
version: 2009-09-04
tecan:
genesis:
points:
roma0:
magnet-hover: '14056,1850,980,1800'
magnet-place: '14056,1850,687,1800'
sampletray-hover: '14057,2828,980,1800'
sampletray-place: '14057,2828,582,1800'
shaker-hover: '1780,3569,1535,1800'
shaker-put: '1780,3569,865,1800'
shaker-take: '1780,3569,865,1800'
shakerlock-1: '1762,1177,1535,900'
shakerlock-2: '1762,1177,815,900'
shakerlock-3: '1191,1177,808,900'
shakerlock-4: '1762,1177,815,900'
shakerlock-5: '1762,1177,1535,900'
shakerlock-6: '1780,3569,1535,1800'
shakerlock-hover: '1780,3569,1535,1800'
HOME1: '11165,2525,980,1800'
...
jcline@ieee.org Robotics - What's Running Now
- General purpose software to control FIAlab syringe pump and 10-way valve
- General purpose software to control part of the Tecan arm
- Network operation of the Tecan; run a bio-protocol from your desk
- Get the current operational status in real time
That's not much, yet
However: It's easy Perl.
- Perl = the #1 bioinformatics language.
sub Main {
$hw = Robotics::Tecan->new(
connection => 'network,Robotics::Tecan::Genesis,genesis0',
token => 'M1',
serveraddr => 'heavybio.dyndns.org:8088',
password => $ENV{'TECANPASSWORD'});
$hw->attach("o");
$_ = $hw->status();
exit -2 if !/IDLE/i;
# Load worktable
$hw->configure("client-traymove1test.yaml");
my @path = (
"shakerlock-hover",
"shakerlock-1",
"shakerlock-2",
"shakerlock-3",
"shakerlock-4",
"shakerlock-5",
"shakerlock-hover"
);
checkok $hw->move_path("roma0", @path);
checkok $hw->move("roma0", "shaker-take");
checkok $hw->grip("roma0");
checkok $hw->move("roma0", "shaker-hover");
checkok $hw->move("roma0", "sampletray-hover");
checkok $hw->move("roma0", "sampletray-place");
checkok $hw->grip("roma0", 'o', 120);
checkok $hw->move("roma0", "sampletray-hover");
checkok $hw->park("roma0");
checkok $hw->park("liha");
jcline@ieee.org Robotics - What's Running in a "Few Weeks"
- General purpose software to control FIAlab
- General purpose software to control Tecan arm & Tecan liquid handler & Tecan peripherals
- Network operation of all of the above; run a bio-protocol entire flow from your desk
- And get the data results back from MATLAB in real time
- Advanced error handling for Tecan bio-protocol problems: automatic re-trying
Medium Term Goal
- Get something simple working with the software framework.
- Swap out the existing devices for smarter ones.
- Far more versatile robotics devices are made every year by undergraduate mechatronics classes.
Long Term Goal
- Run a complete bio-protocol using the English language
- Meaning, bio-latin-english
jcline@ieee.org Robotics - Protolexer
Let's Do Something "Simple" : Revisited
- Feed the protocol directly to the computer.
- Computers are smart enough.
- The computer knows what devices are attached or available on the network.
- Integrate the devices together into a long chain.
- Bio-protocols have fairly standardized formats and standardized language.
- Or can be, with human editing of the English, and a human quickly verifying the "compiled" result before robotics operation.
http://biosx.com/88proof/synthetic_biology/blog/wp-content/uploads/2009/06/protolexer1.png
jcline@ieee.org Robotics - Data Format - Bio-protocols
%YAML 1.1
---
protocol: Mate-Paired Library Preparation for Sequencing
methods:
- &standard-purify purify with column:
- &cp1 Add 3 volumes of Buffer QG and 1 volume of isopropyl alcohol to the sheared
DNA. If the color of the mixture is orange or violet, add 10uL of 3M sodium
acetate, pH5.5 and mix. The color turns yellow. The pH required for efficient
adsorption of the DNA to the membrane is <= 7.5.
- &cp2 Apply 750uL of sheared DNA in Buffer QG to the column(s). The maximum
amount of DNA that can be applied to a QIAquick column is 10ug. Use more
columns if necessary.
- &cp3 Let the column(s) stand for 2 minutes at room temperature.
- &cp4 Centrifuge the column(s) at >= 10,000g (13,000 rpm) for 1 minute, then discard
the flow-through.
- &cp5 Repeat steps 2 and 4 until the entire sample has been loaded onto the column(s).
Place the QIAquick column(s) back into the same collection tube(s).
- &cp6 Add 750uL of Buffer PE to wash the column(s).
- &cp7 Centrifuge the column(s) at >= 10,000g (13,000 rpm) for 2 minutes, then discard
the flow-through. Repeat to remove residual wash buffer.
- &cp8 Air-dry the column(s) for 2 minutes to evaporate any residual alcohol. Transfer
the column(s) to clean 1.5-mL LoBind tube(s).
- &cp9 Add 30uL of Buffer EB to the column(s) to elute the DNA and let the column(s)
stand for 2minutes.
- &cp10 Centrifuge the column(s) at >= 10,000g (13,000 rpm) for 1 minute.
- &cp11 Repeat steps 9 and 10.
- &cp12 If necessary, pool the eluted DNA.
- &bead-purify purify with magbeads:
- &bp1 Add 100uL of DNA to 95uL of magbeads.
- &bp2 Vortex at 1,000RPM for 1 minute.
- &bp3 Incubate on magnets for 300 seconds at room temperature to allow DNA to
bind to beads and beads to settle.
- &bp4 Remove supernatant while beads are magnetized.
- &bp5 Elute while beads are magnetized using 100uL of EtOH.
Pause for 90 seconds during each wash to allow beads to settle.
Allow EtOH to evaporate until beads are dry and
cracks are visible in the bead surface.
- &bp6 Resuspend with 15 uL Buffer xx to resuspend beads.
- &bp7 Vortex at 1,000RPM for 20 seconds.
- &bp8 Incubate for 200 seconds on magnets at room temperature.
- &bp9 Save the eluted DNA.
- Easy to edit (it's text with indenting)
- Easy to read (no crazy formatting words)
- Very easy to share
- Standardized format
- Self-contained, no extra files needed
- Mostly easy to learn
- Easy for computers to read, process, write, share
- Defined in YAML
jcline@ieee.org Robotics - Competing Method: BioStream (MIT)
- "Towards a High-Level Programming Language for Standardizing and Automating Biology Protocols"
- "Abstraction Layers for Scalable Microfluidic Biocomputers", William Thies1 , John Paul Urbanski2 , Todd Thorsen2 , and Saman Amarasinghe, Computer Science and Artificial Intelligence Laboratory, Hatsopoulos Microfluids Laboratory, Massachusetts Institute of Technology, {thies, urbanski, thorsen, saman}@mit.edu
- Defines "high level" (like Java/C++) language for describing protocols
- Can take some standardized English protocols as input
- Can automatically generate the "high level language" for the computer
- Can output a human-readable clean English bio-protocol
- This is a "Validated-clean" version of original bio-protocol
http://88proof.com/biotech/img/Biostream-DNA%20extraction%20from%20tissue%20protocol-English-Output.png