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| {{Slides}}
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| {{:OpenWetWare:Presentations/default.css}}
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| <div class="slide">
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| =jcline@ieee.org - Robotics - Data Format=
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|
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| Data formats are very important:
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| * Make the data usable today
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| * Make the data editable today
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| * Make the data survive into the future; no obtuse or ridiculously hard to learn format
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| * Make the data ''sharable''
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| * Computer scientists love inventing data formats
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| ** Leading to the problem of... too much complexity
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| * Vendors love inventing data formats
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| ** Leading to the problem of... patent / proprietary lockup
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| * Open formats are important for innovation and scalability leveraging Long Tail
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| </div>
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|
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|
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|
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| <div class="slide">
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| =jcline@ieee.org - Robotics - Data Format=
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|
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| ===One way (Wrong)===
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| * W3C Recommendations for speech grammars and semantic interpretation
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| <pre class="incremental">
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| <rule id="order">
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| <tag>var index=0; out.pizza = new Array();</tag>
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| <item repeat="0-1"><ruleref uri="#start"/></item>
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| <item>
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| <ruleref uri="#pizza"/>
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| <tag>out.pizza[index]=$pizza; index+=1;</tag>
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| </item>
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| <item repeat="0-">
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| <item><token>and</token></item>
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| <item>
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| <ruleref uri="#pizza"/>
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| <tag>out.pizza[index]=$pizza; index+=1;</tag>
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| </item>
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| </item>
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| <item repeat="0-1"><ruleref uri="#stop"/></item>
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| </rule>
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| </pre>
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| ** Much too difficult to edit this
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| ** Much too difficult to read this
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| ** Much too difficult to learn this
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| *** XML, HTML, anything that ugly, is a Bad Idea
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| </div>
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|
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Data Format=
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| * W3C Recommendations for speech grammars and semantic interpretation
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| ** Computer Scientist response: ''"Oh, but we can simplify that"''
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|
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|
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| <pre class="incremental">
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| <emma:interpretation>
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| <pizza>
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| <number>1</number>
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| <size>medium</size>
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| <type>pepperoni</type>
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| </pizza>
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| <pizza>
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| <number>1</number>
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| <size>large</size>
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| <type>cheese</type>
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| <topping>sausage</topping>
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| <topping>onions</topping>
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| </pizza>
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| </emma:interpretation>
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|
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| </pre>
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|
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| ** Still Much too difficult to edit this
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| ** Still Much too difficult to read this
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| ** Still Much too difficult to learn this
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| ** Now needs extra files to describe the custom format
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| *** '''Still a Bad Idea'''
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| </div>
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|
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|
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Data Format - Device data=
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|
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|
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| *Each device has data associated with operating it.
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| *Storing that data in an easily readable and editable format is very important for software re-use.
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| * YAML Format is Human readable, Human editable and Computer Readable
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| * YAML allows references to prior definitions and either simple or complex assignments
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|
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|
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| <pre class="incremental">
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| %YAML 1.1
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| --- # Fialab-Microsia
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| address:
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| syringe: A
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| valve: C
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| peristaltic: D
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| external: B
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| valve:
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| send: # delay after cmds 100ms - 1 sec
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| NP_SET:
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| desc: set number of physical ports
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| opcode: NP
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| args:
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| - 1
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| - numport:4-12
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| redundancy: 2 # send cmd twice
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| delay: 100 # ms
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| recv:
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| ok: ~
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| err: ~
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| NP_GET:
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| desc: get number of physical ports
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| opcode: NP
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| args:
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| - 0
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| redundancy: 2 # send cmd twice
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| delay: 100 # ms
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| recv:
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| ok: ~
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| err: ~
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| peristaltic:
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| send: # delay after cmds 100ms - 1 sec
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| SET_SPEED:
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| desc: set pump speed
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| opcode: G
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| args:
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| - 1
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| - speed:0-100
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| delay: 100
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| recv:
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| ok: ~
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| err: ~
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| SET_DIRECTION:
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| desc: set pump direction, direction:1=counterclockwise or 2=clockwise
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| opcode: W
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| args:
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| - 1
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| - direction:1-2:default=1
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| delay: 5000
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| recv:
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| ok: ~
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| err: ~
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| syringe:
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| send: # delay after cmds 100ms - 1 sec
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| INIT_ALL:
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| desc: init all (both) pumps
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| opcode: _Z0R
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| args:
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| - 0
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| delay: 100
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| recv:
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| ok: ~
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| err: ~
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| SET_INPUT:
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| desc: position valve in for given pump
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| opcode: /$1IR
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| args:
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| - 1
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| - pumpnum:1-2:default=1
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| delay: 100
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| recv:
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| ok: ~
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| err: ~
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|
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|
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| </pre>
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|
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| * Made to be readable and editable
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| * Made to be scalable
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| * Contains all definitions of a device's operation
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| * [http://yaml.org YAML] is Best current practice for readable data format
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| </div>
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|
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Data Format - Environmental data=
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|
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|
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| *Each device has environment data associated with operating it.
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| ** Points in space
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| ** Containers
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| ** Solids, liquids, gases
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| *Storing that data in an easily readable and editable format is very important for software re-use.
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| * YAML Format is Human readable, Human editable and Computer Readable
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|
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| <pre class="incremental">
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| %YAML 1.1
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| ---
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| version: 2009-09-04
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| tecan:
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| genesis:
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| points:
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| roma0:
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| magnet-hover: '14056,1850,980,1800'
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| magnet-place: '14056,1850,687,1800'
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| sampletray-hover: '14057,2828,980,1800'
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| sampletray-place: '14057,2828,582,1800'
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| shaker-hover: '1780,3569,1535,1800'
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| shaker-put: '1780,3569,865,1800'
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| shaker-take: '1780,3569,865,1800'
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| shakerlock-1: '1762,1177,1535,900'
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| shakerlock-2: '1762,1177,815,900'
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| shakerlock-3: '1191,1177,808,900'
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| shakerlock-4: '1762,1177,815,900'
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| shakerlock-5: '1762,1177,1535,900'
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| shakerlock-6: '1780,3569,1535,1800'
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| shakerlock-hover: '1780,3569,1535,1800'
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| HOME1: '11165,2525,980,1800'
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|
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| ...
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|
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| </pre>
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|
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|
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|
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| </div>
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - What's Running Now=
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|
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| * General purpose software to control FIAlab syringe pump and 10-way valve
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| * General purpose software to control part of the Tecan arm
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| * Network operation of the Tecan; run a bio-protocol from your desk
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| ** Get the current operational status in real time
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| *'''That's not much, yet'''
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| * 2 releases already made to the public internet software archive for Perl (CPAN)
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|
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| The end user writes a simple Perl application to control all devices and robotics.
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| * Perl is '''the #1 bioinformatics language.'''
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|
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| <pre class="incremental">
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|
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| sub Main {
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| $hw = Robotics::Tecan->new(
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| connection => 'network,Robotics::Tecan::Genesis,genesis0',
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| token => 'M1',
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| serveraddr => 'heavybio.dyndns.org:8088',
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| password => $ENV{'TECANPASSWORD'});
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|
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| $hw->attach("o");
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| $_ = $hw->status();
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| exit -2 if !/IDLE/i;
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|
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| # Load worktable
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| $hw->configure("client-traymove1test.yaml");
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|
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| my @path = (
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| "shakerlock-hover",
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| "shakerlock-1",
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| "shakerlock-2",
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| "shakerlock-3",
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| "shakerlock-4",
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| "shakerlock-5",
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| "shakerlock-hover"
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| );
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| checkok $hw->move_path("roma0", @path);
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|
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| checkok $hw->move("roma0", "shaker-take");
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| checkok $hw->grip("roma0");
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| checkok $hw->move("roma0", "shaker-hover");
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|
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| checkok $hw->move("roma0", "sampletray-hover");
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| checkok $hw->move("roma0", "sampletray-place");
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| checkok $hw->grip("roma0", 'o', 120);
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| checkok $hw->move("roma0", "sampletray-hover");
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| checkok $hw->park("roma0");
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|
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| checkok $hw->park("liha");
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|
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|
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| </pre>
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|
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|
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| </div>
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - What's Running in "Upcoming Weeks"=
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|
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| * General purpose software to control FIAlab
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| * General purpose software to control Tecan arm & Tecan liquid handler & Tecan peripherals
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| * Network operation of all of the above; run a bio-protocol ''entire flow'' from your desk
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| ** And get the data results back from MATLAB in '''real time'''
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| * Advanced error handling for Tecan bio-protocol problems: automatic re-trying
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|
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| Medium Term Goal
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|
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| * Get something simple working with the software framework.
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| ** Swap out the existing devices for smarter ones.
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| *** Far more versatile robotics devices are made every year by undergraduate '''mechatronics''' classes.
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|
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| Long Term Goal
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|
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| * Run a complete bio-protocol ''using the English language''
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| ** '''Meaning, bio-latin-english'''
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| </div>
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|
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Long List of Benefits=
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|
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| *Allows many devices to be controlled from the same user program
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| *Allows device operations not supported by the vendor
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| ** This includes much better error handling & re-trying
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| *Allows abstraction of the devices: swap out one device for another
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| **Removes vendor lock-in, creating more competitive forces to drive innovation among various devices
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| *Plug in new custom devices, can quickly operate with same user program
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| *Network operation
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| **The controller PC will miss fewer commands since vendor application does not take CPU time
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| **The user PC doesn't have to be Windows to run a device (many benefits there)
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| **The user can access device status and device output from anywhere (lab or home)
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| *The user can program complex algorithms using multiple devices, creating a control system with feedback to optimize a protocol or make arbitrary decisions
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| **The "Robot Scientist" was claimed to have identified new targets "on it's own" - using data feedback and prediction
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| </div>
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Protolexer=
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|
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| Let's Do Something "Simple" : Revisited
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|
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| * Feed the protocol directly to the computer.
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| * Computers are smart enough.
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| * The computer knows what devices are attached or available on the network.
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| * '''Integrate''' the devices together into a long chain.
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| * Bio-protocols have fairly standardized formats and standardized language.
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| ** Or can be, with human editing of the English, and a human quickly verifying the "compiled" result before robotics operation.
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|
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| http://biosx.com/88proof/synthetic_biology/blog/wp-content/uploads/2009/06/protolexer1.png
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|
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| </div>
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|
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Data Format - Bio-protocols=
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|
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| <pre class="incremental">
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|
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| %YAML 1.1
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| ---
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| protocol: Mate-Paired Library Preparation for Sequencing
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| methods:
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| - &standard-purify purify with column:
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| - &cp1 Add 3 volumes of Buffer QG and 1 volume of isopropyl alcohol to the sheared
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| DNA. If the color of the mixture is orange or violet, add 10uL of 3M sodium
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| acetate, pH5.5 and mix. The color turns yellow. The pH required for efficient
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| adsorption of the DNA to the membrane is <= 7.5.
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|
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| - &cp2 Apply 750uL of sheared DNA in Buffer QG to the column(s). The maximum
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| amount of DNA that can be applied to a QIAquick column is 10ug. Use more
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| columns if necessary.
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|
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| - &cp3 Let the column(s) stand for 2 minutes at room temperature.
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|
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| - &cp4 Centrifuge the column(s) at >= 10,000g (13,000 rpm) for 1 minute, then discard
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| the flow-through.
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|
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| - &cp5 Repeat steps 2 and 4 until the entire sample has been loaded onto the column(s).
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| Place the QIAquick column(s) back into the same collection tube(s).
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|
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| - &cp6 Add 750uL of Buffer PE to wash the column(s).
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|
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| - &cp7 Centrifuge the column(s) at >= 10,000g (13,000 rpm) for 2 minutes, then discard
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| the flow-through. Repeat to remove residual wash buffer.
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|
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| - &cp8 Air-dry the column(s) for 2 minutes to evaporate any residual alcohol. Transfer
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| the column(s) to clean 1.5-mL LoBind tube(s).
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|
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| - &cp9 Add 30uL of Buffer EB to the column(s) to elute the DNA and let the column(s)
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| stand for 2minutes.
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|
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| - &cp10 Centrifuge the column(s) at >= 10,000g (13,000 rpm) for 1 minute.
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|
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| - &cp11 Repeat steps 9 and 10.
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|
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| - &cp12 If necessary, pool the eluted DNA.
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|
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| - &bead-purify purify with magbeads:
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| - &bp1 Add 100uL of DNA to 95uL of magbeads.
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|
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| - &bp2 Vortex at 1,000RPM for 1 minute.
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|
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| - &bp3 Incubate on magnets for 300 seconds at room temperature to allow DNA to
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| bind to beads and beads to settle.
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|
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| - &bp4 Remove supernatant while beads are magnetized.
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|
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| - &bp5 Elute while beads are magnetized using 100uL of EtOH.
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| Pause for 90 seconds during each wash to allow beads to settle.
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| Allow EtOH to evaporate until beads are dry and
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| cracks are visible in the bead surface.
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|
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| - &bp6 Resuspend with 15 uL Buffer xx to resuspend beads.
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|
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| - &bp7 Vortex at 1,000RPM for 20 seconds.
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|
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| - &bp8 Incubate for 200 seconds on magnets at room temperature.
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|
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| - &bp9 Save the eluted DNA.
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|
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|
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| </pre>
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|
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| * Easy to edit (it's text with indenting)
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| * Easy to read (no crazy formatting words)
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| * Very easy to share
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| ** Standardized format
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| ** Self-contained, no extra files needed
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| * Mostly easy to learn
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| * Easy for computers to read, process, write, share
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| * Defined in YAML
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| </div>
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|
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|
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Competing Method: BioStream (MIT)=
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|
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| * "Towards a High-Level Programming Language for Standardizing and Automating Biology Protocols"
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| **"Abstraction Layers for Scalable Microfluidic Biocomputers", William Thies , John Paul Urbanski , Todd Thorsen , and Saman Amarasinghe, Computer Science and Artificial Intelligence Laboratory, Hatsopoulos Microfluids Laboratory, Massachusetts Institute of Technology
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|
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| ** Defines "high level" (like Java/C++) language for describing protocols
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| ** Can take some standardized English protocols as input
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| ** Can automatically generate the "high level language" for the computer
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| ** Can output a human-readable clean English bio-protocol
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| *** This is a "Validated-clean" version of original bio-protocol
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| </div>
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|
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Competing Method: BioStream (MIT)=
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|
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| BioStream "clean English output" for '''[http://openwetware.org/wiki/DNA_extraction_from_tissue '''DNA extraction from tissue protocol]'''
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|
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| http://88proof.com/biotech/img/Biostream-DNA%20extraction%20from%20tissue%20protocol-English-Output.png
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|
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| </div>
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|
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| <div class="slide">
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| =jcline@ieee.org Robotics - Competing Method: BioStream (MIT)=
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|
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| "Towards a High-Level Programming Language for Standardizing and Automating Biology Protocols"
| |
|
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| BioStream "high level language" for '''[http://openwetware.org/wiki/DNA_extraction_from_tissue '''DNA extraction from tissue protocol]'''
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|
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| http://88proof.com/biotech/img/Biostream-DNA%20extraction%20from%20tissue%20protocol-Source-Output.png
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|
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|
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| </div>
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