Team:BostonU/PUP

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<title>BostonU iGEM Team: Welcome</title>  
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<h2>Puppeteer Notebook</h2>
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<strong><h7>Goal:</h7></strong> Work with Computational team to develop Puppeteer app that will produce protocols for both humans and liquid-handling robot</p>
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<strong>Subgoals:</strong>
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    <li>Adapt protocols for liquid-handling robot</li>
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    <li>Constitutive Promoter Characterization Project:</li>
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    <li>Develop RIG (Resource Instance Map) that will map out entire lab</li>
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    <li>Have robot build 10 level 1 devices </li>
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            <li>Have human do same protocol side-by-side and compare efficiency of results </li>
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<h2>June</h2>
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<h10>June 5, 2013</h10>
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<p>Today was our first Puppeteer meeting so we were able to meet the computational (comp) part of the CIDAR lab that we'll be working with for the project. The people working on this project include Traci, Shawn, Pooja, Devina, Swapnil, Janoo, Alejandro, Denise, and Eda. We also got a better idea of what Puppeteer can do and the capabilities of the liquid handling robot (TECAN). The team discussed goals for the summer as well as the differences between a human running an experiment and a robot running the same one.</p>
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<h10>June 11, 2013</h10>
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<p>This meeting we talked about what exactly we wanted to accomplished this summer in greater detail. We reached an agreement that the robot will perform 10 level 1 MoClo reactions that will all have J23100_EB, E0030_CD, B0015_DF, and DVL1_EF. Only the RBS will change in each construct. We will be using B0032_BC, B0034_BC, B0034m1_BC, B00343m2_BC, BCD1_BC, BCD2_BC, BCD8_BC, BCD12_BC, BCD13_BC, and BCD16_BC.</p>
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<p>The wet lab team then showed the comp team the various protocols that would be required to make these 10 devices.</p>
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<center><img src="https://static.igem.org/mediawiki/2013/a/a1/PUP_061113.jpg" width="700px"></center>
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<p>The comp team then discussed designing a protocol map and showed us an example of one.</p>
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<p>Since there will be many experiments using the above parts, the wet lab team decided to prepare extra plasmid stocks.</p>
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<h10>June 18, 2013</h10>
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<p>At today’s meeting the comp team showed us the protocol map they had developed for the level 1 devices. We were able to go through each of the steps in their design to ensure it was correct. The comp team also illustrated how<a href="http://cidar.bu.edu/ravencad/" style="color:#B22222; display:inline;background-color:white">Raven</a>and Puppeteer would interact together. Additionally, we discussed how the robot would required more detailed protocols than the ones we use in the lab. For example the robot needs instructions on how many tubes would be required and where each reagent is located. Lastly, we brainstormed a possible system to label all experimental samples.</p>
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<h10>June 25, 2013</h10>
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<p>The comp team showed us their refined protocol map and the wet lab side helped answer any questions they had about the procedures. We then discussed how the robot would be able to handle possible variations in the procedures. For example, if the gel showed that sample looked incorrect, how would the robot know to go back and re-pick colonies? For next week we decided to go over the human protocols and make ones for the robot that would include greater detail.</p>
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<h2>July</h2>
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<h10>July 2, 2013 </h10>
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<p>In today’s meeting the computational team showed us their updated protocol graphs which included a feature that allow the technician to indicate whether a particular step in a protocol was successful. If the step failed, the program would adjust the protocol to retry the failed step. Denise then showed us a preliminary robot protocol which was really cool!</p>
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<h10>July 9, 2013</h10>
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<p>At this week’s meeting the comp team showed us an example of a RIG (resource instance graph) that they had developed. They needed to know the very detailed locations of the supplies that would be used for each protocol, starting with the CAB building, the second floor, room 219, etc. We used the whiteboard to help design a RIG of the wet lab starting with the CAB building to describing what was located on each bench. For next week we will take what was written on the whiteboard and convert it to code.</p>
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<h10>July 16, 2013</h10>
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<p>We met with the Development team and discussed our RIG code.  We discovered that our code would need even more detail and discussed how to proceed updating the code.</p>
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<p>We also answered some of their questions about our protocols and resource allocation.</p>
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<h10>July 18, 2013</h10>
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<p>We met with the Development team again to go over some of their questions about our protocols.</p>
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<h10>July 23, 2013</h10>
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<p>We met with the Development team again to go over some of their questions about our protocols.</p>
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<li><a href="https://2013.igem.org/Team:BostonU/Protocols">Protocols</a></li>
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                        <li><a href="https://2013.igem.org/Team:BostonU/NotebookML">Characterization Notebook</a></li>
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        <li><a href="https://2013.igem.org/Team:BostonU/PUP">Puppeteer Notebook</a></li>
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                        <li><a href="https://2013.igem.org/Team:BostonU/TroubleShooting">Troubleshooting</a></li>
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<li><a href="#">Acknowledgements</a>
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<b>June 5, 2013</b><br>
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Design to Direction<br>
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compare contrast doing things via puppeteer vs. human (~100-200 parts in two weeks?)
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<br> hope to reduce error and
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<br> could use tecan to switch out backbone.
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<br>maybe create basic moclo XFP transcription units
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<br>Robot does:
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<br>Moclo rxn
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<br>Transformation
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<br>Ligation
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<br>Restriction Digest
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<br>resource tracking, when to replace
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Come up with hypothesis of human vs. machine
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<br> Efficiency of Robot? Puppeteer speed up planning for robot? Error of human and reaction failure?
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<br>For human error - have a partner checking for errors
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Human errors
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<br>- setting plates up wrong(have partners)
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<br>- make sure dilutions are right (excel errors? have partners do excel together)
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<br>- just always have partners.
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<br>- don’t rush
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Protocols must be adapted to go with puppeteer/robot. Testing to optimize.
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<br>Aiming to test by making ten devices in duplicate
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<i>Target for Tuesday June 11</i>
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<br>figure out steps of protocol for robot in excel sheet with exact buffer/enz/etc.
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<br>10 devices
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ADD WHITEBOARD PICTURE FROM DROPBOX FOLDER
 
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<b>June 11, 2013</b>
 
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<br>See picture for parts that need to be made * 4
 
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<br>dilute to 25 fmol
 
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<br>Janoo sent working csv files for Raven
 
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<br><br>
 
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ADD WHITEBOARD PICTURE FROM DROPBOX FOLDER
 
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<br><br><br>
 
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<b>June 18, 2013</b>
 
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<br>download arcs  file from Raven.
 
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<br>Arcs = raven to puppeteer
 
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<br>upload arc file into puppeteer
 
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<br>In puppeteer, select arc file, and personnel involved.
 
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<br>→ then assembly graph and protocol graph generated
 
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<br>*went over process in the assembly graph.
 
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<br>
 
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<br><i>next step: know details of the protocols themselves</i>
 
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<br>require the specific instruction of the protocol. more detailed than excel sheets and how to allocate resources. <br>how much and what resources are needed to go from 1 rxn to 10 rxn etc
 
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<br><br>
 
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Want higher level details--> pick up this tube, etc
 
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<br><br>
 
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labels are 8 letter labels. generated in raven/puppeteer that needs to be written on the container. (randomly generated), doesn’t tell us about the contents of the sample
 
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<br><br>
 
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Showed current naming protocol for L1
 
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<br>*brain storming about labeling*
 
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<br>maybe send out a survey to wetlab about labeling
 
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Latest revision as of 21:53, 26 August 2013



Puppeteer Notebook

Goal: Work with Computational team to develop Puppeteer app that will produce protocols for both humans and liquid-handling robot

Subgoals:
  • Adapt protocols for liquid-handling robot
    • Constitutive Promoter Characterization Project:
    • Develop RIG (Resource Instance Map) that will map out entire lab
    • Have robot build 10 level 1 devices
      • Have human do same protocol side-by-side and compare efficiency of results

June

June 5, 2013

Today was our first Puppeteer meeting so we were able to meet the computational (comp) part of the CIDAR lab that we'll be working with for the project. The people working on this project include Traci, Shawn, Pooja, Devina, Swapnil, Janoo, Alejandro, Denise, and Eda. We also got a better idea of what Puppeteer can do and the capabilities of the liquid handling robot (TECAN). The team discussed goals for the summer as well as the differences between a human running an experiment and a robot running the same one.


June 11, 2013

This meeting we talked about what exactly we wanted to accomplished this summer in greater detail. We reached an agreement that the robot will perform 10 level 1 MoClo reactions that will all have J23100_EB, E0030_CD, B0015_DF, and DVL1_EF. Only the RBS will change in each construct. We will be using B0032_BC, B0034_BC, B0034m1_BC, B00343m2_BC, BCD1_BC, BCD2_BC, BCD8_BC, BCD12_BC, BCD13_BC, and BCD16_BC.

The wet lab team then showed the comp team the various protocols that would be required to make these 10 devices.

The comp team then discussed designing a protocol map and showed us an example of one.

Since there will be many experiments using the above parts, the wet lab team decided to prepare extra plasmid stocks.


June 18, 2013

At today’s meeting the comp team showed us the protocol map they had developed for the level 1 devices. We were able to go through each of the steps in their design to ensure it was correct. The comp team also illustrated howRavenand Puppeteer would interact together. Additionally, we discussed how the robot would required more detailed protocols than the ones we use in the lab. For example the robot needs instructions on how many tubes would be required and where each reagent is located. Lastly, we brainstormed a possible system to label all experimental samples.


June 25, 2013

The comp team showed us their refined protocol map and the wet lab side helped answer any questions they had about the procedures. We then discussed how the robot would be able to handle possible variations in the procedures. For example, if the gel showed that sample looked incorrect, how would the robot know to go back and re-pick colonies? For next week we decided to go over the human protocols and make ones for the robot that would include greater detail.



July

July 2, 2013

In today’s meeting the computational team showed us their updated protocol graphs which included a feature that allow the technician to indicate whether a particular step in a protocol was successful. If the step failed, the program would adjust the protocol to retry the failed step. Denise then showed us a preliminary robot protocol which was really cool!


July 9, 2013

At this week’s meeting the comp team showed us an example of a RIG (resource instance graph) that they had developed. They needed to know the very detailed locations of the supplies that would be used for each protocol, starting with the CAB building, the second floor, room 219, etc. We used the whiteboard to help design a RIG of the wet lab starting with the CAB building to describing what was located on each bench. For next week we will take what was written on the whiteboard and convert it to code.


July 16, 2013

We met with the Development team and discussed our RIG code. We discovered that our code would need even more detail and discussed how to proceed updating the code.

We also answered some of their questions about our protocols and resource allocation.


July 18, 2013

We met with the Development team again to go over some of their questions about our protocols.


July 23, 2013

We met with the Development team again to go over some of their questions about our protocols.


Retrieved from "http://2013.igem.org/Team:BostonU/PUP"