Reverse Engineering a DNA Sequencer

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.

Is It On Yet? Sensing the World Around Us, Starting with Light

Arduino 101 is getting an LED to flash. From there you have a world of options for control, from MOSFETs to relays, solenoids and motors, all kinds of outputs. Here, we’re going to take a quick look at some inputs. While working on a recent project, I realized the variety of options in sensing something as simple as whether a light is on or off. This is a fundamental task for any system that reacts to the world; maybe a sensor that detects when the washer has finished and sends a text message, or an automated chicken coop that opens and closes with the sun, or a beam break that notifies when a sister has entered your sacred space. These are some of the tools you might use to sense light around you.

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DIY Multi-Touch All the Surfaces

Ever wanted to build a touch table or other touch-input project, but got stuck figuring out the ‘touch’ part? [Jean Perardel] has your back with his multi-touch frame over on IO that makes any surface touch-reactive. In [Jean]’s case, that surface is ultimately a TV inside of a table.

Of course, it’s a bit of a misnomer to say the surface itself becomes touch-reactive. What’s really happening here is that [Jean] is using light triangulation to detect shadows and determine the coordinates of the shadow-casting object. Many barcode scanners and consumer-level document scanners use a contact image sensor (CIS) to detect objects in the path of IR LEDs. These are a low-power, lower-resolution alternative to the CCDs found in high-grade scanners.

As [Jean] explains in the video below, an object placed in the path of a single IR LED facing a sensor array of either type will block the light from reaching the sensors. Keep adding LEDs and their emission angles will begin to overlap, increasing the detection precision. [Jean] reverse engineered a couple of different types of scanners until he found a suitable one. He ended up with CIS that has 2700 light sensors lined up in the space of 20cm (7.87″).

[Jean] designed a 3D-printable frame to hold 96 IR LEDs in stacks of three. A Teensy turns on the LEDs, detects the touch event, calculates the position, and sends those coordinates to a Pi to be displayed on the screen. He eventually went wireless and then built a nice looking touch table to house a 32″ TV.

This is not the only way to build a multi-touch table, nor is it the simplest. Here’s one that uses finger presses to scatter light and an industrial strength projection-based table that was open-sourced a few years ago.

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Giving a 4k Webcam Special Eyes

It’s a problem as old as photography: your camera is only as good as your lens. As cameras shrink, so do lenses, and so do the options for upgrading to a better lens. And forget about switching to a different focal length or aperture — it’s often just not an option. Unless you make it an option by adding a CS lens mount to a high-end webcam.

We’ll stipulate that at 4k resolution and packed with all sorts of goodies, the Logitech Brio Pro is a heck of a nice camera. And the lens isn’t bad either, as you’d hope for a camera with almost 9 megapixels at its disposal. But with an optical field of view optimized for video conferencing, it’s hard to use this premium camera for much else. [Saulius] fixed that by taking the camera apart and adding a new case with a built-in C- and CS-mount, resulting in literally thousands of lens choices. [Saulius]’ post has valuable teardown information, which includes exposing the CCD sensor completely. The new case is sold as a kit, but it looks like a 3D-printed case would be pretty easy to whip up.

[Salius] sure seems to love those optical hacks, whether they be a budget microscope camera, high-resolution LIDAR, or capturing license plates at great distances.

Eclipse 2017: Was Einstein Right?

While most people who make the trek to the path of totality for the Great American Eclipse next week will fix their gazes skyward as the heavenly spectacle unfolds, we suspect many will attempt to post a duck-face selfie with the eclipsed sun in the background. But at least one man will be feverishly tending to an experiment.

On a lonely hilltop in Wyoming, Dr. Don Bruns will be attempting to replicate a famous experiment. If he succeeds, not only will he have pulled off something that’s only been done twice before, he’ll provide yet more evidence that Einstein was right.

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Being a Friend to Man’s Best Friend

When [Jason Dorie] tipped us off on this, he said, “This barely qualifies as a hack.” We disagree, as would any other dog lover who sees how it improved the life of his dog with a simple mood-altering doggie-bed carousel.

[Jason]’s hack lies not so much in the rotating dog bed – it’s just a plywood platform on a bearing powered by a couple of Arlo robot wheels. The hack is more in figuring out what the dog needs. You see, [Thurber] is an old dog, and like many best friends who live a long life, he started showing behavioral changes, including endlessly pacing out the same circular path to the point of exhaustion. Circling in old dogs is often a symptom of canine cognitive dysfunction, which is basically the dog version of Alzheimer’s. Reasoning that the spinning itself was soothing, [Jason] manually turned [Thurber]’s dog bed on the floor. [Thurber] calmed down immediately, so the bittersweetly named “Dementia-Go-Round” was built.

Sadly, [Thurber] was actually suffering from a brain tumor, but he still really enjoyed the spinning and it gave him some peace during his last few days. Looking for hacks to help with human dementia? We’ve had plenty of those before too.

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Own the Night with this Open Source Night Vision Monocular

If you’ve always wanted to see in the dark but haven’t been able to score those perfect Soviet-era military surplus night vision goggles, you may be in luck. Now there’s an open-source night vision monocular that you can build to keep tabs on the nighttime goings-on in your yard.

Where this project stands out is not so much the electronics — it’s really just a simple CCD camera module with the IR pass filter removed, an LCD screen to display the image, and a big fat IR LED to throw some light around. [MattGyver92] seemed to put most of his effort into designing a great case for the monocular, at the price of 25 hours of 3D printer time. The main body of the case is nicely contoured, the eyepiece has a comfortable eyecup printed in NinjaFlex, and the camera is mounted on a ball-and-socket gimbal to allow fine off-axis angle adjustments. That comes in handy to eliminate parallax errors while using the monocular for nighttime walks with both eyes open. One quibble: the faux mil-surp look is achieved with a green filter over the TFT LCD panel. We wonder if somehow eliminating the red and blue channels from the camera might not have been slightly more elegant.

Overall, though, we like the way this project came out, and we also like the way [MattGyver92] bucked the Fusion 360 trend and used SketchUp to design the case. But if walking around at night with a monocular at your face isn’t appealing, you can always try biohacking yourself to achieve night vision.