DNA Now Stands For Data And Knowledge Accumulation

February 18, 2020 by Bob Baddeley 33 Comments

Technology frequently looks at nature to make improvements in efficiency, and we may be nearing a new breakthrough in copying how nature stores data. Maybe some day your thumb drive will be your actual thumb. The entire works of Shakespeare could be stored in an infinite number of monkeys. DNA could become a data storage mechanism! With all the sensationalism surrounding this frontier, it seems like a dose of reality is in order.

The Potential for Greatness

The human genome, with 3 billion base pairs can store up to 750MB of data. In reality every cell has two sets of chromosomes, so nearly every human cell has 1.5GB of data shoved inside. You could pack 165 billion cells into the volume of a microSD card, which equates to 165 exobytes, and that’s if you keep all the overhead of the rest of the cell and not just the DNA. That’s without any kind of optimizing for data storage, too.

This kind of data density is far beyond our current digital storage capabilities. Storing nearly infinite data onto extremely small cells could change everything. Beyond the volume, there’s also the promise of longevity and replication, maintaining a permanent record that can’t get lost and is easily transferred (like medical records), and even an element of subterfuge or data transportation, as well as the ability to design self-replicating machines whose purpose is to disseminate information broadly.

So, where is the state of the art in DNA data storage? There’s plenty of promise, but does it actually work?

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Deep Discounts Yield Deep Reverse Engineering Of Biotech Hardware

January 15, 2019 by Kerry Scharfglass 21 Comments

Hitting the electronic surplus shop is probably old hat to most of our readership. Somewhere, everyone’s got that little festering pile of hardware they’re definitely going to use some day. An old fax is one thing, but how would your partner feel if you took home an entire pallet-sized gene sequencing rig? Our friend [kaspar] sent along an interesting note that the folks at Swiss hackerspace Hackteria got their hands on an Illumina HiSeq 2000 last year (see funny “look what we got!” photo at top) and have generated a huge amount of open documentation about whats inside and how to use it.

Okay first off, what the heck is this machine anyway? The HiSeq is designed to automatically perform the sequencing step of Illumina’s proprietary multi step gene sequencing process (see manufacturer’s glossy for more), and to do so with minimal human intervention. That means that the unit contains a microfluidics system to manipulate samples, an extremely high performance optical scan system complete with controllable stage, imager, fluorescence modes, etc, and lots of other things this author isn’t sufficiently trained to guess at.

The folks at Hackteria have done a pretty thorough teardown of the system and produced block diagrams of most of its modules. They’ve also run some of the tools and recorded logs of what they were up to, including the serial commands sent to and from the machine to control certain subsystems. Of course a tool like this was meant to be driven by Illumina’s specific software, but unusually those are available and surprisingly usable which is how the aforementioned logs were captured. Right now it looks like Hackteria has put together tools to use the system as a fluorescent microscope.

Oddly the most interesting thing here might be how available these systems are. It appears that they’re being replaced en masse and have become easily available in the range of thousands of dollars on the secondary market. At that price point they’re almost worth snapping up for the enclosure and parts! But we prefer Hackteria’s goal of enabling the Citizen Scientist to make use of these incredible machines for their intended purpose. Who knows what exciting projects we’ll find when hackers start sequencing their cats!

Thanks for the tip [kaspar]!

Reverse Engineering A DNA Sequencer

August 9, 2018 by Tom Nardi 19 Comments

Improvements in methodology have dramatically dropped the cost of DNA sequencing in the last decade. In 2007, it cost around $10 million dollars to sequence a single genome. Today, there are services which will do it for as little as $1,000. That’s not to bad if you just want to examine your own DNA, but prohibitively expensive if you’re looking to experiment with DNA in the home lab. You can buy your own desktop sequencer and cut out the middleman, but they cost in the neighborhood of $50,000. A bit outside of the experimenter’s budget unless you’re Tony Stark.

But thanks to the incredible work of [Alexander Sokolov], the intrepid hacker may one day be able to put a DNA sequencer in their lab for the cost of a decent oscilloscope. The breakthrough came as the result of those two classic hacker pastimes: reverse engineering and dumpster diving. He realized that the heavy lifting in a desktop genome sequencer was being done in a sensor matrix that the manufacturer considers disposable. After finding a source of trashed sensors to experiment with, he was able to figure out not only how to read them, but revitalize them so he could introduce a new sample.

To start with, [Alexander] had to figure out how these “disposable” sensors worked. He knew they were similar in principle to a digital camera’s CCD sensor; but rather than having cells which respond to light, they read changes in pH level. The chip contains 10 million of these pH cells, and each one needs to be read individually hundreds of times to capture the entire DNA sequence.

Enlisting the help of some friends who had experience reverse engineering silicon, and armed with an X-Ray machine and suitable optical microscope, he eventually figured out how the sensor matrix worked electrically. He then designed a board that reads the sensor and dumps the “picture” of the DNA sample to his computer over serial.

Once he could reliably read the sensor, the next phase of the project was finding a way to wash the old sample out so it could be reloaded. [Alexander] tried different methods, and after several wash and read cycles, he nailed down the process of rejuvenating the sensor so its performance essentially matches that of a new one. He’s currently working on the next generation of his reader hardware, and we’re very interested to see where the project goes.

This isn’t the first piece of DIY DNA hardware we’ve seen here at Hackaday, and it certainly won’t be the last. Like it or not, hackers are officially fiddling with genomes.