duckbot

Custom Worfklow Automation with Jubilee

Machine Agency, University of Washington
Jan 28, 2023

Scientific research is results-driven

Sometimes by any means necessary

Duckweed is a small aquatic plant with a very simple structure; just a frond which floats on the water, and some species have roots, and they're quite small with different species ranging from fractions of a millimeter wide to a couple millimeters. Here we're looking at some duckweed in a well plate, and a thermal image of a 96-well plate. As I've learned from working with duckweed scientists, it's these sorts of images that might provide information to answer particular research questions; maybe we're interested in tracking how that duckweed grows over time, under various environmental conditions. Less relevant to answering those sorts of questions is the story of how that duckweed got into that well. Probably, a research assistant was responsible for moving individual fronds into each well by hand. Not only is this sort of manual work time-consuming and tedious, but there's also high stakes; in order to trust the final data, we need to be confident that the right duckweed went into the right wells, which were filled with the right media, which are adequately randomized around the well plates, and so on. This sort of work is currently a necessary bottleneck in getting to some desired result.

Previously: “dull, dirty, and dangerous”

Robots have historically been for mass-production.

They are expensive, tedious to program, and difficult to customize & run.

Automation as a Tool for Creative Exploration

In negotiating these two positions, of fully manual and fully automated approaches, our lab is interested in automation as a tool for creative exploration. For science, that might look something like this: defining an experiment up front in a way that accommodates niche experimental design; being able to compile that experiment to instructions which can be run on a machine-- and maybe this requires physically configuring the machine for your custom application, and finally collecting data, where the operator--the scientist in this case-- can have some role to play at runtime. In addition to, say, scaling up an individual experiment, our research interest here is in how we can provide flexible infrastructure which allows scientists to build, customize, and run machines across a range of applications. It takes significant time, skill, & effort to build a system for a specific task. We want to lower the threshold to automation in a way that allows scientists design and reuse systems without compromising the level of control over the experiment.

Automation as a Tool for Creative Exploration

requires...

Modular, Low-cost, Extensible Hardware

Human-centered Systems for Programming/Running Experiments

This picture of automation requires some infrastructure distinct from that of the mass-automation machines we were looking at. First, niche applications require niche tools, we can't take advantage of high volume sales & production to offset costs. Instead, we need modular, low-cost, and extensible hardware to customize one-off applications. And after we build a machine, we need good ways of actually running it. Control is commonly enacted from an interface built for a specific task. We are interested alternative controls, including writing code which compiles to machine instructions to allow reusability and flexibility in defining experiments, as well as live sensor readings to interactively control the flow of the experiment at runtime. These are two areas of research that our lab has been been actively engaged in.

Modular, Low-cost, Extensible Hardware

Open-source design for distributed manufacturing

design for precise repeatable positioning

To the first point, this is Jubilee; a multi-tool changing platform previously developed in our lab. Jubilee looks like a conventional 3D printer- it has a carriage that can move around in the x-y plane, and the bed can move up and down. It's interior volume is 300x300x300mm. It also has the ability to automatically pick up and change tools. That's shown on the right, where we see the carriage features this twist lock shaft. Each tool has a matching wedge plate, and the shaft can engage the tool and twist to lock it. By virtue of some clever mechanical design, these pickups are repeatable, so every time we grab a tool we can be sure its in the same place. Jubilee is fully open-source, and designed to be fabricatable. This means it is made with parts that are available in low volume, or made with readily available tools & equipment, and distributed with documentation which inludes all the information needed to build one. The parts to build a Jubilee cost just over 1500 dollars. There are at least 170 Jubilees in the world which have been independentely built, and this success in the communinity resulted in it being made available as a kit with all the parts needed to build one.

Modular, Low-cost, Extensible Hardware

Digital fabrication of modular and customizable hardware

Jubilee's tool-changing ability allows us to build up multi-tool processes. We can park multiple tools on Jubilee, and change between them as the machine runs. This allows us to build custom tools. Take this microscope tool shown here for example-- it's almost entirely 3D printed, with a few standard screws and the like thrown in. In terms of electronics, Jubilee features both control boards for motion planning and controlling things like motors, as well as a Raspberry Pi for some computing power. This means we can plug this USB microscope in to the Raspberry Pi to take & analyze images while moving it around. Along with the documentation, Jubilee has an active user community, particularly on Discord. This has proved to be a significant resource for community members to share designs files and ideas for replication by others. Part of our research here is trying to understand how we can bootstrap communities to integrate these sorts of automation into their own work. One difficult thing about custom tools, though, is the need to control them. For example, the software which controls the machine doesn't know anything about how to take and save pictures. This requires domain-specific software.

Duckbot

A Jubilee outfitted with tools and associated control software for handling duckweed