Your protocols will be assimilated
Friday, June 01, 2018
Aquarium is undergoing rapid development, with several new minor releases appearing since Aquarium 2.0 came out. The latest
version will include much better documentation, a docker installer, and improvements to the plan designer / editor. We also
are introducing Trident, a python library for interacting with Aquarium that allows you to define your samples and experiments
in code, and extract your data from Aquarium to send to whatever analysis software you might like to use in Python.
We have made the Aquarium github repo public. It is free for academic and non-profit research use. Industry folks should contact firstname.lastname@example.org. A new web page for Aquarium is here, where you can learn about the details.
Saturday, November 11, 2017
The UW BIOFAB has been awarded a new contract by DARPA to be on of three cloud labs running synthetic biology experiments for the Synergystic Discovery and Design program. This program supports dozens of researchers in synthetic biology, machine learning, and high performance computing. The goal is to create a complete software/hardware pipeline going from experimental design, to experimental execution, to data storage, to data analysis for synthetic biology. The other cloud labs are Ginkgo Bioworks and Transcriptic, and our computing partners include the Texas Advanced Computing Center. The Aquarium software will play a central role in our work, allowing us to manage experiments, but also connect to upstream design software and downstream analysis software developed by other research groups.
Tuesday, April 18, 2017
At the heart of any good organization you will find creative, passionate, and dedicated people. At the BIOFAB we are incredibly lucky to have two excellent lab managers: Michelle Parks, and Cameron Coudrey. They are in charge of day to day operations such as running protocols, maintaining the inventory, keeping the lab safe, and managing and training technicians. They also invent new processes, provide strategy and tactics, organize new systems, help customers, and track down bugs. Most importantly, Michelle and Cami implement the vision of the BIOFAB as an end-to-end cloud-based lab that runs our customer’s experiments inexpensively, quickly, and reproducibly. Connecting that vision to the reality in the lab is no easy task, but they do it with grace and skill. We are incredily fortunate to have them running the show.
Monday, April 10, 2017
Aquarium version 2.0 is in beta testing now with a select group of UW users. The new version features completely modular, strongly typed operations that are composable into many different workflows. It has an integrated design environment for building new operation types and their associated protocols. Protocols can be tested with the click of a button with randomly generated i/o. The Aquarium Workflow Language (AWL) is incredibly concise, and has allowed us to refactor our protocols to have about 50% as much code. Finally, Aquarium 2.0 has a planner that automatically backchains from a desired goal to produce a task-specific plan meeting the researcher’s needs. Join the BIOFAB staff on April 14, 2017 in EE 403 for the Aquarium 2.0 launch party! You’ll get a BIOFAB t-shirt!!
Wednesday, February 22, 2017
The Klavins lab has received a $100,000 award from Amazon via its Catalyst program. The funding will go toward building out a mammalian cell workflow that will allow researchers to order cell lines made to their specifications. Graduate Student Justin Vrana has built out a unique tissue culture room for this workflow, complete with a projector inside the hood with foot-pedal operated version of Aquarium running in it. Look for mammalian cells offered through the BIOFAB by the end of the summer 2017.
Monday, June 20, 2016
We are happy to annouce the UW BIOFAB, a new UW cost center. Researchers at the University of Washington may use the Aquarium software to remotely submit molecular biology and microbiology jobs. Technicians in the BIOFAB execute the protocols following Aquarium workflows and upload the results into the Aquarium database. Cloning projects can be executed from start to finish, without the client ever having to touch a pipette! Records of all jobs and samples are permanently stored in the Aquarium inventory database, eliminating the need for messy lab notebooks and complex inventory systems. Thanks to Michelle Parks, Yaoyu Yang, and Tina Montgomery for all of their hard work making this happen.
Tuesday, March 15, 2016
We just finished teaching EE/CSE/BIOEN 425: Laboratory Methods in Synthetic Biology. This year we tried something very different. We had students design their DNA and strains in Coral, and use the Aquarium Python API to upload their jobs into Aquarium. Then they sit back and watch as their experiments are done by our technicians. How’s that for a laboratory method? It was great to see how easily computer science and electrical engineering students were able to understand synthetic biology when you abstract all of the details of the lab.
Tuesday, November 03, 2015
Aquarium is being developed into a commercial product that you will be able to use in your lab! See the aquarium.bio web page for more information.
Sunday, March 15, 2015
We just finished teaching EE/CSE/BIOEN 425: Laboratory Methods in Synthetic Biology. We were even more successful than last year, with students building and testing all sorts of CRISPR/dCas9 circuits based on Miles Gander’s technology (http://biorxiv.org/content/early/2016/03/02/041871). As part of the ISTC smart wetlab project, we also installed three cameras on each lab bench workstation and collected a total of 18 TB of video data showing each step in each protocol that was done by the students. They all agreed to be recorded, by the way. Our machine learning collaborators will be crunching these data for quite a while!
Monday, February 02, 2015
Aquarium has been up and running in the Klavins lab for a little over a year. Since that time, we’ve seen big changes. Initially, not everyone in the lab wanted to use the system. They had to put all of their samples into the inventory management system, they had to give up control over their own Gibson assemblies, they had to learn a new system. Plus, Aquarium was initially pretty buggy and limited in what it could do. Since then, we’ve gone through three different protocol representation languages, produced over 11,000 items in the inventory, and run thousands of jobs. We are currently running more than 350 jobs per week between research and teaching. These jobs are associated with a growing library of more than 200 protocols ranging from preparing media to Gibson assembly to flow cytometry. New protocols are added and tested every month.
And we continue to grow. By May of 2015, we will have added two new technicians and we are looking for a lab manager to run the system on weekends. Interested? See here for positions available.
Saturday, November 01, 2014
We now have five wonderful Aquarium technicians each working half time in the lab. Toghether with our amazing lab manager Michelle Parks, the technicians now do 99% of the cloning (Gibson Assembly) and media prepration in the Klavins lab, and they do cloning for our some of our collaborators in the Seelig, Nemhauser, and Carothers labs. They also do about 60% of the yeast work, including integration, verification, flow cytometry, and similar protocols. Each technician is an undergraduate student with little or no prior background in molecular biology lab work. To train them, we use the same set of protocols we use to teach our Laboratory Methods in Synthetic Biology course. They also get careful supervision by Michelle to learn everything that is not in Aquarium. It takes a new technician about a month to get up to speed, and then they are cloning away.
Wednesday, August 27, 2014
Our collaborators at the Intel ISTC on Pervasive Computing have been outfitting our lab with a variety of cameras and other sensors to capture what the Aquarium technicians are doing. They take the video and apply amazing activity recognition methods to parse the activity into useful information that could help debug protocols, train new technicians, and improve workflow. Below is a montage of some of the various methods and angles they have tried. Thanks to Anthony LeMarca (Intel) for putting this video together!
Tuesday, July 01, 2014
Prof. Eric Klavins recently spoke at a independently organized TEDx event on programming biology and described the motivation for Aquarium. Until approximately 2008, Klavins lab research was primarily in computer science and robotics. At about that time, Eric learned the basics of genetic engineering completely switched fields to synthetic biology and now runs an interdisciplinary group of engineers, biologists, experimentalists, and theorists – all focused on engineering life. In particular, Eric’s research concerns developing programming languages and abstractions that can be used to design, fabricate, test, and refine new organisms. Example applications include synthetic multicellular consortia that digest plant matter and produce biofuels, diagnose disease, or assemble into complex patterns and shapes. This talk describes an outsiders view on the biology lab, how biology labs are different from engineering, and the thought process that went into the Aquarium project.
Thursday, May 08, 2014
The UW Center for Innovation annouces funding for Aqaurium in the classroom. Here’s the description: A group of faculty from the Intel Science and Technology Center for Pervasive Computing will collaborate with faculty in the synthetic biology program tobuild a semi-automated, human-in-the-loop laboratory. For this framework protocols and methods will be encoded in a new programming language. Software will guide students through every step of every protocol with touchscreen interfaces, simple text, images, movies and otherfeatures. Sensors such as cameras, Google Glasses and radio-frequency identifications tags will monitor supplies, reagents and equipment as the protocols are being performed. Detailed logs will be used to refine protocols and methods and to catch mistakes. The goal for teaching will be to develop a sequence of life sciences research protocols students work through independently and then refine. Subsequently we will teach the students how to author their own protocols and methods. Through this process students will learn basic protocols, how to author new protocols and methods, and how to design and test a new organism from first principles. The course melds engineering, computer science and life sciences into a hands-on experience in synthetic biology.
Thursday, January 09, 2014
The first big test of Aquarium is to use it to teach UW’s Laboratory Methods for Synthetic Biology course in the Winter 2014 quarter. In the first five weeks students learn basic laboratory skills, molecular cloning, Gibson assembly, and how to knock out genes using the Keio method. We write the protocols and methods in Plankton and Oyster, and Aquarium does the rest while we sit back and watch the data accumulate. In the second five weeks, the students will learn to write their own protocols and run them on Aquarium. So far, after the first week and a few bugfixes, the system is running like a charm! Two hundred sixteen jobs, of which about 75% were successful and most of the rest just cancelled because they were scheduled accidentally.
Update (Feb. 10): We’re done with the first five weeks. Almost all protocols were completed successfully, except some knockouts did not work in the last week. The students are now breaking into groups to write their own protocols and methods (everything from qPCR to measure gene expression to gene assembly) to run in Aquarium. Each method will be run once a week for four weeks (starting next week) by four different groups. In between runs, students have a chance to improve their protocols based on feedback from their peers.
Monday, July 01, 2013
The UW Intel Center for Pervasive Computing (ISTC) has named the “Smart Wetlab” as one of its two capstone projects. This means Aquarium workstations will be augmented with sensors and Aquarium will be used as a testbed by ISTC researchers working on everything from activity recognition to natural lagnuage processing. Why is Intel interested in synthetic biology? First of all, The Intel ISTC is interested in making new technology pervasive in everyday life, including in the workplace. And it turns out that biofabrication and microfabrication have a lot in common. Manufactuing processes need to be reproducible. Technician training needs to be reliable. The synthetic biology lab is, thus, perfect for trying out new ways to help people do their work by tracking their samples, providing a video-enriched lab notebook, outfitting everything with sensors, and using activity recognition and machine learning to provide real time suggestions.