Puppeteer Notebook

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

  • 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 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 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.