---
# System prepended metadata

title: Slides - IWBDA2020 Lab Automation - Problem Area 1.2 - DRAFT FOR EDITING

---

# Slides - IWBDA2020 Lab Automation - Problem Area 1.2 - DRAFT FOR EDITING

[Slides - IWBDA2020 Lab Automation - Problem Area 1.2](https://hackmd.io/OBGAYRJtQkKkMJsqtl3JXQ)

# 🍒 CERISE 🍒

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

CERISE is a project to optimize biolab robot instruction sets.

Starting from a cherry-pick list, we want to output a reduced instruction set that can be executed by a robot.

Cherry-picking lists are "universal" and can be interpreted by most platforms.

They can be generated both manually and algorithmically.

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 the cherry-picking actions as instructions that minimize/maximize certain objective functions.
- ex: distribute the same reagent in one go, save time, save tips.

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.

We will implement the instructions on an open platform that is accessible by most labs: the Opentrons OT-2 platform.

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)

### Heilmeier Catechism

- What are you trying to do? Articulate your objectives using absolutely no jargon.
- How is it done today, and what are the limits of current practice?
- What is new in your approach and why do you think it will be successful?
- Who cares? If you are successful, what difference will it make?
- What are the risks?
- How much will it cost?
- How long will it take?
- What are the mid-term and final “exams” to check for success?

### Notes

- Jeremy
   - I imagine that at minimum we can do this as something like a "TOC generator" type cli, where we run a `command --platform-flag target-document-to-rewrite`


::: info

meta cruft in case (a) naming the thing and (b) explaining the context of cherry pick lists are important

==X is a project to optimize the biolab robot instruction sets.==
==Liquid-handling robots used in research labs all read cherry-picking lists which are ==
==These lists allow the robots to complete much more mundane work than human researchers could, but they are very inefficient.==

:::