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title: "IWBDA2020 Lab Automation 1.2: \U0001F352 CERISE \U0001F352"

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# IWBDA2020 Lab Automation 1.2: 🍒 CERISE 🍒

## **C**herrypick-**E**fficient  **R**educed **I**nstruction **S**et **E**ngine

<p style="font-size: 0.9rem;font-style: italic;"><img style="display: block;" src="https://upload.wikimedia.org/wikipedia/commons/3/3a/Cherry02.svg" alt="File:Cherry02.svg" width=200><a href="https://commons.wikimedia.org/w/index.php?curid=35231380">"File:Cherry02.svg"</a><span> by <a href="https://commons.wikimedia.org/wiki/User:JohannPoufPouf">JohannPoufPouf</a></span> is licensed under <a href="http://creativecommons.org/publicdomain/zero/1.0/deed.en?ref=ccsearch&atype=html" style="margin-right: 5px;">CC0 1.0</a><a href="http://creativecommons.org/publicdomain/zero/1.0/deed.en?ref=ccsearch&atype=html" target="_blank" rel="noopener noreferrer" style="display: inline-block;white-space: none;margin-top: 2px;margin-left: 3px;height: 22px !important;"><img style="height: inherit;margin-right: 3px;display: inline-block;" src="https://search.creativecommons.org/static/img/cc_icon.svg" /><img style="height: inherit;margin-right: 3px;display: inline-block;" src="https://search.creativecommons.org/static/img/cc-cc0_icon.svg" /></a></p>

**Alexis Casas and Jeremy Cahill**

## Introducing 🍒CERISE

- 🍒**CERISE** is a project to optimize biolab robot instruction sets.
- Given a cherry-pick list, we will output a reduced instruction set executable by a robot.
- Cherry-picking lists are "universal" and can be interpreted by most platforms.
- They can be generated both manually and algorithmically.

## Scope

- Today, researchers write most cherry-picking lists by hand in spreadsheet software.
- Actions in a protocol are usually grouped and executed sequentially.
   - ex. distribute the water and the master mix before the DNA.
- We want to optimize these essential protocol steps in a reduced instruction set.
- The engine will group these actions as instructions, optimizing along objective functions.
   - ex: distribute the same reagent in one go, save time, save tips.

## Proof of Concept

- For our proof of concept, we will target the Opentrons OT-2 platform.
- We have selected this platform because it is affordable, open-source, and widely-adopted.
- Therefore it is accessible to the greatest number of labs possible.

## Deliverables

 - Reduced instruction set
    - See: Linked proposal for 'Testify' system
 - Definition of the cherry-picking list schema
 - Software to transform the cherry-picking list into instructions
 - Instruction set implemented on one open platform: the Opentrons OT-2

## Links

- [IWBDA2020 Lab Automation Pitch Notes](https://hackmd.io/43yXR751QCylQfsZ6Kk7lw)
- [Autoprotocol](https://autoprotocol.org)
- [Opentrons](https://opentrons.com)