Awesome Therapeutics Liquid Handling LIMS Integration
Be sure to share on LinkedIn that you are attempting this problem! The more discussion there is for part one the easier part two is!
It’s been a while! I’m back with an ambitious ask for the tinkerers and programmers! I want to say first… look this took me months to make in my off time, so it is supposed to be a long term thing to chip away at.
Or I’m just way waaay dumber than I already think I am…
Setup
Your company, Awesome Therapeutics, is skyrocketing in its growth phase! 
Congratulations You’ve amassed a fantastic collection of samples in tubes and find yourself deep in combinatorial hell. Your scientists, Alice and Bob, are sifting through this remarkable biobank, searching for the perfect combination of samples that will send Awesome Therapeutics soaring to new heights.
Alice and Bob have refined their search in the biobank and devised a combinatorial strategy. The first step is to find the optimal combination of CEL and DNA samples that yield the highest signal reading of midi-chlorians. That’s right, it’s a secret, but Awesome Therapeutics is on the verge of making the force a reality! They just need your automation engineering expertise to help bring it to life.
Some Observations
During their extensive combinatorial efforts, Alice and Bob have made several scientific observations that have shaped their lab new massive automation investment.
(a) Too Many Combinations = Bad
Alice has found that if combinations include an excessive number of CEL or DNA samples, they inhibit the midi-chlorians. The specifics are unclear, but the result seems consistent: the signal diminishes to zero if there are too many of the same type, whether CEL or DNA, and it’s especially pronounced when both are present in high amounts.
(b) Volume Independence
Bob has noticed that the amount of volume to add of each sample to increase the signal is independent of sample composition. That is the optimal volume to add is unique to each sample. It doesn’t change when other samples are introduced in a composition.
ALL (Awesome Lab LIMS)
Deploy a local version to your machine using:
git clone https://github.com/smohler/labio-all.git
Consult the README.md for instructions on starting the example web-api to test and explore. This repository is an evolving example, so not everything may be pertinent to this task. It should be pretty simple though as I’ve provided some build scripts that should set everything up and even launch a web-browser for you to interact with the API via a Swagger UI.
Mac Users
$ chmod +x run.sh
$ ./run.sh
Windows Users
\> labio-all\run.bat
After you run either of these scripts you should see either an error (sorry…) or a web browser should open allowing you to interact with the API. Close the browser, enter Ctrl + C in the terminal, to properly quit the app. If you close the terminal you started the local server on then it will die. I have not set up a legit web-server to run this so you will have to run it locally.
SUGGESTION I highly recommend you have docker installed on your computer. This seems to be the most stable build I can ensure works. Download the daemon here.
Measuring Samples
Awesome Therapeutics engineering department has developed a custom plate reader to measure the midi-chlorian activity in the wells of a 384 well plate.
It is highly sensitive to samples containing CEL or DNA. However, it is a descrutive measurement and consumes sample.
If any BAC or PRO material get into the machine new parts will need to be ordered!
Included in this repo is an executable file (for Windows or Mac) called measure.exe. This command line app simulate the measurement of one well.
In essence, it mimics a real-world function where, given a list of sampleIDs and volumes, it returns the measurement value with some noise.
Some example usage of a windows user of this program would be as such.
\> labio-all\measure\windows\measure.exe --help
# get some help...
\> labio-all\measure\windows\measure.exe --test
# measure a randomly generated sample
# Warning: There is a small chance this will break your plate reader, so don't brut force it to generate a data distribution.
\> labio-all\measure\windows\measure.exe --ids CJU49IKLE DHF00043J --volumes 199.2 1233.89
# simulate measuring a sample by providing the sampleIDS and volumes.
# Note: the lists of --ids and --volumes but be the same length
\> labio-all\measure\windows\measure.exe --ids PJU49IKLE BHF00043J --volumes 199.2 1233.89
# This will break your plate reader and lock you out for 30 minutes!
WARNING - You can break your plate reader if you ever pass it a sample ID where the first character is “B” or “P”.
If you break the plate reader you will have to wait 30 minutes to use it again!
Sample ID
In the future I plan for seq value to point to much larger sequence data stored in s3 buckets for now we will just play with the characters sampleID.
Awesome Tx decided go for meaningful IDs for samples. The ID is 9 characters long.
- The first char is the material type.
B,C,D,P - The next eight characters are in Base36 and represent 8 features about the sequence.
- Number of tandem repeats greater than 4 and less than or equal to 16 = 4^2.
- Number of tandem repeats greater than than 16 and less than 64 = 4^3.
- Number of tandem repeats greater than 64.
- Longest repeating sequence of ‘G’
- Longest repeating sequence of ‘T’
- Longest repeating sequence of ‘C’
- Longest repeating sequence of ‘A’
- Number of occurrences of a sub-sequence Alice & Bob believe to be unique to midi-chlorians.
Liquid Handler
Iggy = {8-Channel, 16 x 24 1.5mL tube rack adapters, plate gripper, barcode scanner, 20 deck positions}
The choice of liquid handler is arbitrary. You may need to have a stack (or multiple stacks) of 384 well plates on the deck. The tube adapters are designed to hold 1.5mL tubes, and their configuration will vary based on the chosen liquid handler.
Labware
Plates = {384 Well Microtiter Plates, 1.5 mL cylindrical tubes}
Regarding the 1.5mL tubes, we won’t fuss over the specific vendor or capping/decapping processes. Assume Bob will meticulously prepare all the tubes to be open, with barcode labels properly positioned for scanning.
What Bob cannot do is put the tubes in order given a worklist. The barcodes on the tubes matches the sampleID in ALL the tube labels were printed based on ALL. The point is, if your liquid handler can scan barcodes it can know where where the tubes are.
Plate Reader
The plate reader in this challenge requires the use of measure.exe found in the repo. The main challenge is ensuring the liquid handler updates the registry accurately after loading plates, reading them, and receiving the data.
This program only measures the content of a single well and it takes a non-negligible time to compute actually, so brut-forcing will be tough.
Additionally, be cautious: the plate reader must not have any samples of material type BAC or PRO placed in it. If this occurs, the entire device will need parts replaced which takes time.
There is no interface to provide measure with a list of 384 wells and their contents. This is something you can build on your own or just run a 384 loop from within your liquid handling program. Plates take awhile to read and so will this program!
You have to feel the wetlab time scale programmers. Not everything can go the speed of light racing thru patterns on stones.
Task 1 (Bench Work)
This is primarily a commentary-based challenge. No programming is required, only strategic planning to develop an experimental plan.
Devise an experimental plan ensuring that, post-experiment, you have garnered significant insights and can refine the combinatorial set to a much smaller search space. This is an excellent opportunity to delve into DOE or Multi-Objective optimization.
Pay close attention to Alice and Bob’s observations and the inherent combinatorial challenges, consider your strategy carefully, keeping in mind the practical constraints of actual lab work which is simulated by the long run time ofmeasure
Task 2 (Automation)
With Task 1 complete, you should have a much smaller search space. The next step is implementing another larger scale experiment.
Ensure you update the LIMS in real-time (or post-experiment) as you extract samples from the tubes.
Post your maximum midi-chlorian activity reading and let’s see how high the community can get!
Remarks / Hints
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Use of ML
Feel free to employ machine learning. But remember, ML typically demands vast amounts of data. If you’re inclined to let your computer spend hours developing a dataset for an ML algorithm to discern patterns, that’s feasible, and why not. Let’s all use any tools available to us, however this entire toy problem is just a translation from an old 1970’s DOE book I have. I just tweaked it to have a set of local maxima instead of a single maxima to simulate the messy landscape of biology. -
A mathematician once said “Variation of sets (or the topology of your problem) far out weigh variation of the elements, if you begin by varying elements at best you can hope for O(2^n) so good luck, vary sets and you can at least hope for nothing or a great break thru. I’ll take my chances.”
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I am not perfect. If there are any clunky bugs in
measureplease start a github issue on the labio-all repo and I will fix is as soon as I can. Issues · smohler/labio-all · GitHub