Self-Driving Experiments with the EcoBOT

An all-in-one station called “EcoBOT” studies plants as they grow. See how the platform built by the Environmental Genomics & Systems Biology division at Berkeley Lab  takes human error out of the sampling process.

Transcript

00:00:04 the ecobot is an all-in-one station where we can study plants in their microbiomes as they're growing one of the challenges of microbiome science is that it's very hard to compare data across different laboratories because everybody's doing things a little bit differently having the ecobot do the sampling takes human error out of the equation making

00:00:24 the data much more reproducible and so we've been working on this for a long time this vision of being able to build laboratory ecosystems where we can get at how genes and interactions between organisms ultimately affect ecosystem level processes the ecobot fits in our larger fabricated ecosystem effort which is really focused on reproducibility and

00:00:49 that means that we want to make sure our experiments are robust and reliable and that we get the same results every time we do them and not only that but someone else could do the same experiment and get the same result and that might seem obvious but sometimes subtle variations can cause differences in results so first the ecobot selects an eco fab from the growth chamber eco-fab stands

00:01:13 for fabricated ecosystem and these are essentially hand-held environments where we can study plants in their microbiomes using different methods once it selects an eco-fab it delivers it to the liquid handling unit and it removes the caps to access the root zones then the ecobot directly samples from the ecofab root zone to see which

00:01:34 chemicals the plants and microbes are making we then refill the eco-fab with nutrients or microbial communities depending on the experiment once the sample has been removed and liquid has been added we then recap the eco-fab to keep it sterile the ecobot can then take the eco fab from the liquid handling unit and move it to our different imaging stations

00:01:57 where we can collect data on the roots and the plant growth there are two imaging stations underneath the ecobot one is an inverted microscope that can automatically scan all the root zones we can do things from low magnification like getting root phenotypic data or higher power magnification if we want really detailed information on the plant roots or look

00:02:19 for microbes that are colonizing the roots the second imaging station is a hyperspectral camera that takes hyperspectral images of the plant from three different angles and that allows us to get size estimations on the plant without taking it out and measuring it what i'm most excited about with the ecobot is the potential for self-driving

00:02:40 experiments meaning ones that aren't just carried out according to a particular timeline but that actually change and evolve with the results that come out the ecobot is located at berkeley lab but it's part of a collaborative project that involves a number of other labs in particular the pacific northwest national laboratory and so collaborators

00:02:58 at other institutions are already participating in planning and executing these experiments as well as analyzing the data that comes out and in the long run we hope that the work we're doing on building and developing the ecobot will make it easier for others to implement that same sort of work and build their own ecobots in their own labs and so this fills a really large scale vision

00:03:19 of disseminating microbiome scientific tools to the larger scientific community and standardizing it so that it doesn't matter whether you do an experiment or i do an experiment we can compare the data [Music]