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From 2011.igem.org

Chenkai iGem Notebook

Work Stack

CHECK-why does resourcemanager give the printout out of order? investigate

CHECK-tell user when new plate gets allocated

CHECK-record reaction history, also protocol history

CHECK-debugging purposes, log everything that happens

CHECK-add incubator

CHECK-add string name for wells and incubator slots, plates

CHECK-unique identifier for each well/sample

CHECK-fix duplicate restriction digests

CHECK-there are 50ul, 100ul, 200ul tip sizes, must specify

CHECK-if two wells have partial amounts, combine them

CHECK-swap column and row

CHECK-Talk to Jeno about Puppetshow GUI

-different buffer for each protocol

-be generic with plate dimensions, specifying locations (grid/site), this is only with the Tecan robots

-move transversing the tree out of assemblymanager, we want to a separate **program to annotated the tree and produce the protocol graph

-fix naming, 3 parts (UUIDS,User defined names,auto-generated linearized tree name)

-save resourcemanager state

Work Diary

• Wednesday 6/8

Just flew back from China, got to PHO209 at 4pm and caught up with other team members on what they are up to. Had a discussion with Viktor about the road ahead, what problems are on our to do list.

• Thursday, 6/9

Found a fix to the sample name duplication issue, instead of using sample names to identify sample, we are now adding a new UUID field to each liquid, this 8 digit randomly generated code will make sure no two samples of the same content will be confused with each other.

• Friday 6/10

Implemented tips of different sizes, 50ul, 100ul, 200ul

Removed duplicate entries from Puppeteer output

Implemented incubator functionality

• Monday 6/13

Planned and implemented history recording, reaction history and incubation history

Got the robot moving and tested in the wetlab

• Tuesday 6/14

Swapped rows with columns to optimize robot pippetting

Added feature to ResourceManager to combine liquids in multiple wells to minimize waste

• Wednesday 6/15

For debugging purposes, log everything that happens. More specifically, the content of what well should be pipetted to what well

Implemented Protocol History recording for samples

Talked to Janoo about what how the PuppetShow GUI show look like and what functionality it should have

• Thursday 6/16

Resource Manager now notifies the user when a new plate gets allocated

Helped Viktor debug Resource Manager, it was giving him a "java.lang.reflect.InvocationTargetException" exception. It turns out he was encountering a "WellOverFlowException" which simply shows up as a InvocationTargetException on the python side. I changed it so now it prints the error message instead of giving an unambiguous exception

Formulated a new way to name samples in Resource Manager, details are sketched out but awaiting for agreement from Viktor and Aaron

• Friday 6/17

Aaron came over today to discuss the issues of sample naming and sample history. He raised a good question during our discussion about how to implement sample history, he asked us what are we going to be doing with the history, and is it worth the time to look in sample history implementation or is it not critical at the moment. We agreed that it should be something to do in the longer term.

Took the protocol graph annotation out of AlgorithmManager and into a separate file called ProtocolGraphAnnotator.java. I emailed this file as well as SDSTree.java which I have modified to Janoo and he got the Puppeteer output generation working on his GUI.