Molecular Information Systems Lab – UW News /news Thu, 18 Apr 2019 22:40:08 +0000 en-US hourly 1 https://wordpress.org/?v=6.9.4 Lunar library to include photos, books stored in DNA /news/2018/09/27/memoriesindna_in_space/ Thu, 27 Sep 2018 16:11:18 +0000 /news/?p=58989
A selection of images submitted to the #MemoriesInDNA project. Photo: 天美影视传媒

People who have submitted photos to the have selected images of family members, favorite places and tasty food that will be preserved for years in the form of synthetic DNA. Now this collection 鈥 which currently contains more than 3,000 images and is still growing 鈥 will be headed to the final frontier: space.

analog microfiche on thin sheets of nickel with a dime for scale
The Lunar Library will also contain pages stored as (dime for scale). The team is still working on how the DNA contents of this library will be stored. Photo: Arch Mission Foundation

The , which creates archives that can survive for a long time in space, that it will be partnering with researchers at the 天美影视传媒, Microsoft and Twist Bioscience to include media stored in DNA in its newest shipment, which is destined to go to the moon in less than two years.

Researchers at the at the 天美影视传媒 and Microsoft plan to provide both the #MemoriesInDNA project and a DNA archive of e-books for this mission. The Arch Mission Foundation’s will also include instructions for how to sequence DNA and how to access the contents of the archive.

To prepare the DNA for its life in space, the researchers have been developing new methods to package and protect the information it stores.

“Sending DNA into space is a great opportunity for us to make our storage system more robust,” said , a professor in the UW鈥檚 Paul G. Allen School of Computer Science & Engineering. “How can we protect the DNA so that it will still be readable thousands of years into the future?”

Group shot of the Molecular Information Systems Lab
Researchers at the Molecular Information Systems Lab plan to provide both the #MemoriesInDNA project and a DNA archive of e-books for this mission. Photo: Dennis Wise/天美影视传媒

Storing electronic data in DNA molecules saves a lot of storage space. Data centers require acres of land and account for in the United States, but DNA molecules can store information millions of times more compactly using less energy.

“DNA is so dense that we can store a lot of information in a single gram,” said Ceze. “This is huge because room is so limited in space missions.”

The basic process converts digital data’s strings of ones and zeroes into the four basic building blocks of DNA sequences: adenine, guanine, cytosine and thymine. The team is working with to create synthetic DNA molecules in a lab. This DNA doesn’t come from living organisms. Instead, it is synthesized from scratch base by base (letter by letter).

In space, stray cosmic rays could break DNA strands, making them unreadable. So Ceze and his team have been working on methods to ensure that they can still decode all the information, even if some of the DNA degrades.

The first method, called physical redundancy, involves adding multiple copies of each strand of DNA to the archive. So if one copy is destroyed, there are still many other copies with the same information. The team is considering adding billions of copies of each strand to account for degradation over time, Ceze said.

The second method, called , attaches information about the data within the DNA itself, like adding information about how two puzzle pieces go together. That way if all copies of a DNA strand go missing, the researchers can piece together what was lost and still get all of the data.

For example, to store two numbers 鈥 two and three 鈥 researchers would also store the information that two plus three equals five. So if something happened to the number two, the numbers five and three would still exist. That logic could be reversed to conclude that the missing information is five minus three 鈥 or two.

Now that the team is working with the Arch Mission Foundation, it has a strict deadline to finalize all packaging and storage plans: The Lunar Library is expected to be .

“We鈥檙e proud that this partnership with Arch continues to push the boundaries of what鈥檚 possible in increasingly exciting ways and remarkable directions,鈥 said collaborator , a senior researcher at Microsoft and a UW affiliate associate professor of computer science and engineering. “This is an incredibly exciting project and we have a great multidisciplinary team working on it: coding theorists, computer architects, engineers and molecular biologists, all coming together to make this new technology a reality.”

The moon as seen from space
An image of the moon (top right) that is included in the #MemoriesInDNA project. Photo: 天美影视传媒 #MemoriesInDNA

For more details about how to include your own images in the #MemoriesInDNA project, visit the or email lunarlibrary@memoriesindna.com. Note: To be included in the DNA image collection, photographs cannot be copyrighted by any other party and must be free of violent or inappropriate content. The image dataset will be preserved in DNA indefinitely and shared with researchers worldwide.

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For more information, contact misl-info@cs.washington.edu or visit the #MemoriesInDNA Project website: .

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#MemoriesInDNA Project wants to store your photos in DNA for the benefit of science 鈥 and future generations /news/2018/01/24/memoriesindna-project/ Wed, 24 Jan 2018 16:56:41 +0000 /news/?p=56276
A selection of images submitted to the #MemoriesInDNA Project. Photo: 天美影视传媒

If you could pick an image to be preserved for thousands of years, what would it be? A picture of your family, an endangered landscape, a page of poetry, or a snapshot that sends a message to the future?

Researchers from the at the 天美影视传媒 and Microsoft are looking to collect 10,000 original images from around the world to preserve them indefinitely in synthetic DNA manufactured by . DNA holds promise as a revolutionary storage medium that lasts much longer and is many orders of magnitude denser than current technologies.

The team has already encoded important compositions in DNA molecules, including The Universal Declaration of Human Rights, the top 100 books of Project Gutenberg, songs from the and an .

The invites the public to submit original photographs that they鈥檇 like to see preserved in DNA for millennia. The images 鈥 which can be uploaded at the 鈥 will be encoded in synthetic DNA and made available to researchers worldwide. The researchers also are encouraging people to share their images on social media with the hashtag #MemoriesInDNA and include a story about why the photograph or video is important to them.

Lead researchers on the UW/Microsoft DNA data storage project include (left to right) Georg Seelig, UW associate professor of electrical engineering and of computer science and engineering; Luis Ceze, the Torode Family Career Development Professor of Computer Science & Engineering; and Karin Strauss, a Microsoft researcher and UW affiliate associate professor of computer science and engineering. Photo: Tara Brown Photography

鈥淚t鈥檚 your turn to show us what should be preserved in DNA forever,鈥 said , professor in the UW鈥檚 Paul G. Allen School of Computer Science & Engineering. 鈥淲e want people to go out and take a picture of something that they want the world to remember 鈥 it鈥檚 a fun opportunity to send a message to future generations and help our research in the process.鈥

DNA data storage has emerged as a potential solution to bridge the growing gap between the amount of digital data generated today 鈥 by everything from commercial video to space imagery to medical records 鈥 and our ability to affordably and efficiently store that data.

Unlike data centers, which require acres of land and account for in the United States, DNA molecules can store information millions of times more compactly. The basic process converts the strings of ones and zeroes in digital data into the four basic building blocks of DNA sequences 鈥 adenine, guanine, cytosine and thymine. It employs synthetic DNA molecules created in a lab, not living DNA.

The team of UW computer scientists and electrical engineers, in collaboration with Microsoft researchers and working with Twist Bioscience, holds the for the amount of data stored in DNA.聽 So far they have been able to encode photographic images and video in DNA and retrieve and convert those individual molecular 鈥渇iles鈥 back into digital data.

Their next challenge involves exploring how to perform meaningful data processing directly in DNA 鈥 without having to convert the images back into their electronic form.

鈥淟et鈥檚 suppose you have a trillion images encoded in DNA and want to find all the photographs that have a red car in them, or to find out whether a person鈥檚 face exists in those images,鈥 said Ceze. 鈥淲e want to be able to do that information processing in DNA directly 鈥 to search in a smart way and make the molecules themselves carry out that computer vision work.鈥

A digital microfluidics prototype in the UW’s Molecular Information Systems Lab. Photo: Dennis Wise/天美影视传媒

The team will encode approximately 10,000 of the crowdsourced images in manufactured snippets of DNA. The researchers鈥 approach to searching images directly in DNA relies on the fact that certain nucleotides stick to others 鈥 A binds to T and C binds to G.

They can introduce strips of DNA into the solution that contains a coded 鈥渜uery鈥 鈥 essentially, a string of complementary DNA that causes all photographs with a red car or certain facial features or whatever meets the criteria of the query to bind to it. By attaching magnetic nanoparticles to the query DNA, they can use a magnet to pull out all the similar images that have stuck to it.

鈥淚t is thrilling to bring computer science and molecular biology together in this project,鈥 said Microsoft senior researcher and collaborator Karin Strauss. 鈥淭here has been amazing progress recently in both areas and, when combined, they can be very powerful in tackling problems created by the massive amounts of data we鈥檝e been generating.鈥

鈥淗aving a set of diverse images from around the world will help us invent new ways to make molecules work with each other to carry out these computations directly,鈥 said Microsoft partner architect and collaborator .

An Illumina NextSeq flow cell, which is used by researchers in the UW’s Molecular Information Systems Lab to sequence DNA samples that contain digital data. Photo: Dennis Wise/天美影视传媒

The team will employ machine learning to devise methods to map and encode all the visual features contained in a photograph 鈥 such as colors, curves, lines and objects 鈥 in DNA. The main challenge is doing that in a way that allows scientists to extract similar things and perform meaningful data processing.

鈥淲e will use neural networks to explore ways to classify visual patterns in the images and video that we encode in DNA,鈥 said , UW associate professor of electrical engineering and in the Allen School. 鈥淔or example, are there more red cars than blue cars in a photograph? Or are there people riding bicycles?鈥

鈥淲ith proof-of-concept achieved for DNA as a digital data storage media, we are working to drive down the cost of synthesizing DNA to enable its potential as a widely-available commercial solution for the growing body of precious data in digital format, such as archival data, financial and health record backups, and all long-term data retention where current media is not practical,鈥 said Emily M. Leproust, CEO of Twist Bioscience. 鈥淢emoriesInDNA is a fabulous project to showcase the technological, scientific and cultural importance of DNA worldwide and we look forward to our role in this historic event.鈥

#MemoriesInDNA will provide an important library of images to be encoded in a separately funded project supported by the Defense Advanced Research Projects Agency (DARPA) . UW was recently awarded $6.3M to accelerate the pace at which data can be encoded in DNA, and to develop new capabilities to process this data through image search and classification. The work will build the foundation on which UW can advance its next-generation work in molecular information processing.

Note: To be included in the DNA image collection, photographs cannot be copyrighted by any other party and must be free of violent or inappropriate content. The image dataset will be preserved in DNA indefinitely and shared with researchers worldwide. For more details about how to upload and share images, visit the .

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For more information, contact misl-info@cs.washington.edu or visit the #MemoriesInDNA Project website: .

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