Gelfoo - smart gel imaging for everyone

by Mac Cowell

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$0.00 pledged of $45,000 goal
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By Mac Cowell
$0.00 pledged of $45,000 goal
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About

DNA!

It’s everywhere!

And for less than the price of a laptop, you can put together a personal molecular biology lab to explore the secrets hidden DNA all around us. Search your genome for mutations, examine your ancestry, check for specific microbes, or other organisms, or watch for GMOs marker genes, or look for any other DNA sequence you can dream up!

You only need three basic pieces of lab equipment, a few inexpensive reagents, and a couple free afternoons to teach yourself the techniques.

There’s just one problem:

Four basic pieces of molecular biology equipment are all you need to analyze DNA: Pipettes, PCR, Gel Electrophoresis system, & a Gel Imaging system. Surprisingly, imaging systems are an order of magnitude more expensive than the other equipment.
Four basic pieces of molecular biology equipment are all you need to analyze DNA: Pipettes, PCR, Gel Electrophoresis system, & a Gel Imaging system. Surprisingly, imaging systems are an order of magnitude more expensive than the other equipment.

Here's your shopping list:

  • a set of pipettes,
  • a gel box and power supply,
  • a PCR machine, 
  • $100 of basic reagents and plasticware, and
  • a gel transilluminator and imager,

Excluding the gel imaging system, everything else can be acquired for less than about $1500 new or about $500 used (but expect old equipment if you go with the latter). 

But gel imagers are still ridiculously expensive. As in, $800 used, $5000+ new. I guess they have a lot of extra features...

Scientists, Educators, Hobbyists, Clinics, Forensic Labs, and everyone interested in understanding DNA up close and personal - from Farmers to Fashion Designers - deserve a more affordable, accessible, open, and simple solution for visualizing their DNA gels.

Help us kickstart the solution. It's called Gelfoo :)

We don’t need the $500 filters, the high-powered UV transilluminator, the industrial-strength 80-pound bent-steel frame, or the “scientific-grade” cooled CMOS camera.

(But hey, If you've got one hanging around, I bet it works great. If not, when faced with the lack of affordable imaging options, I'm sure some users just build a DIY system from a point-and-shoot camera, a box, and an "affordable" blue-light transilluminator like the Syngene Ultraslim at ~$400. But stick around - I think we can sell a better version of the whole enchilada for less than that!).

All we really need to successfully image gels stained with "sybr green" style dyes is (from bottom to top) 

  • a box to keep out ambient light; 
  • a bright upward-facing array of 470 nm blue LEDs at the base;
  • a diffuser and blue acrylic pre-filter to spread and condition the blue light;
  • a frame for to cradle the gel in the optimal location above the blue light;
  • an orange acrylic post-filter to block all the blue excitation light while allowing green light from fluorescing DNA bands in the gel to pass upwards to the camera; 
  • and an affordable digital camera with reasonable low-light performance looking down from the top at the proper focal distance;

This is doable... so let's add some features to make gel imaging more fun

  • A custom 8-megapixel camera module (possibly e-CAM80_MI8825_MOD w/ Omnivision OV8825 sensor) and board specifically designed for... 
  • a single-board computer like the Tessel.io, raspberry pi, or beaglebone, running...
  • a local mobile-friendly webapp that controls the camera, manages saved images, and optionally shares them via dropbox, email, and a simple API (for all those fancy new digital lab notebooks out there), and
  • An on/off switch for the transilluminator, and
  • A physical button to trigger the camera shutter, and
  • A warning flash of the transilluminator if the captured image was not high quality, and
  • a commitment to innovation-friendly open-source software and hardware

Gelfoo! - a $300 open-source web-connected gel transilluminator and imager. Gelfoo rounds out the basic molecular biology toolchain with its affordable price, cutting-edge features, built-in connectivity and extensibility, and innovation-friendly open source licensing!

Stretch goals:

  • $55k - Colony counting via additional ambient white LEDs (possibly RGB, if this would help with certain types of sorting) facilitated by OpenCFU.
  • $65k - add-on actuated cassette tray to facilitate integration with eGels and automation platforms
  • $75k - add-on Battery for mobile convenience!
  • $85k - lightsaber noise module

Concept Development

Early concept based on Raspberry Pi + raspcam.
Early concept based on Raspberry Pi + raspcam.
A rough prototype based on an a $200 refurbished iPod touch for camera and connectivity
A rough prototype based on an a $200 refurbished iPod touch for camera and connectivity

Timeline

1/15: Organize project, initiate outsourced EE feasibility analysis; start recruiting design talent. 

2/15: iterate on industrial design (hopefully with prototype at KS + ITP), materials, identify manufacturing technique for first 100-500 chassis (2.5d flatpack laser or vacuum forming?) ; recruit EE, backend dev, ID. Finish outsourced EE feasibility analysis

3/15: Select Camera, SBC, begin design of adaptor board; Finalize ID; design blue LED board; get high-quality rapid prototype for demo unit; begin server software dev

4/15: Get in front of potential "earlyvangelist" customers, see if they want the demo unit; iterate; if possible, Launch Kickstarter campaign. Keep working. Start figuring out manufacturing.

5/15: finish KS campaign and regroup...

6/15: If we're still here... start manufacturing!

7/15: oh boy!

Camera, Interface Board, and Single Board Computer

Tessel.io, otherwise rpi.

Alternatively, image processing techniques such as frame stacking may significantly improve the rpi 5MP camera.

WebApp

  • Ideally node (express or meteor) app on Tessel.io
  • automated alert if poor image capture
  • automated band calling
  • live stream mode 
  • images sent to dropbox, evernote, email? Network folder?
  • Images available via REST? For Benchling etc?
  • OpenCFU for colony counting (where does data go?)

Manufacturing

try to make the first 10 units locally, lasercutters, 3d printers, possibly vacuum forming.

Shipping

Oh please, can we just use amazon fulfillment?

Design Considerations

RPI & RPI camera: The camera's low-light performance and resolution was terrible compared to the ubiquitous phone cameras we all have. The WiFi configurator was an unexpected pitfall - how would the user configure the wifi for an enterprise university network? No screen or keyboard out of the box to make it simple. Best idea was a config file that the user edits in the root of the SD card. This concern, coupled with the ballooning cost from the USB hub, wifi card, rpi camera, and case, and the poor performance of the camera, was enough to motivate looking into using a refurbished ipod touch

Refurbished ipod touch : Pros: Awesome interface, everyone knows how to connect it to networks, adds lots of nice interface hw that was missing w/ the SBC. Camera performs better than RPI. Cons: $200 / unit. Uncertain supply. Feels like a give-up solution. Not sure a native app could perform all the desired duties of the webserver. Perhaps an android tablet would be a better idea...

RPI & logitech c910 or SLR w/ gPhoto: c910 support was iffy. For $90, mind as well get a point-and-shoot and use gphoto2. Cons: hard to stream camerea video via gphoto over web, can't do live-positioning. Pros: camera (esp SLR) images are the highest quality. Note: can we add mount-points for the SLR in case customers want to retrofit after the fact?

Earlier Designs

The first prototype
The first prototype
Poor LED - filter matching inside the first prototype.
Poor LED - filter matching inside the first prototype.
A 3D-printable design of a tower w/ logitech c910 integrated into cap
A 3D-printable design of a tower w/ logitech c910 integrated into cap

About Mac & Genefoo

Hi, I'm Mac
Hi, I'm Mac

 Kickstarter 2015

     I'm a biologist who was always more interested in the tools and techniques than the research itself. With experience, after cofounding diybio.org in 2008 and the Boston Open Source Science Lab (bosslab.org) soon after, I began to believe overpriced lab equipment and complex methods presented a huge, but pointless barrier to entry. I've focused a lot of time since then on eliminating that barrier. I'm a huge supporter of openPCR and open qPCR; I started the miniPCR project (then called PersonalPCR); and developed a $25 PCR reagent kit with Josh Perfetto called GeneLaser. I run Genefoo LLC, a biotech consulting and design company in San Francisco. In 2014 I developed an interactive exhibit for the Tech Museum of Innovation in San Jose that invited visitors to construct and then interactively measure hundreds of uniquely-colored bacteria grown in the museum.

    In 2015 I received a SynBioLeap fellowship to develop common benchmarks and software connections for the new wave of automation platforms, connected lab devices, and “cloud” lab service providers that have recently launched.

Extended Science Details

With these tools and some inexpensive reagents, you can check your own genome for thousands of known mutations; test food for GM genes; explore paternity; create a unique genetic fingerprint of yourself, and design experiments to detect the genome of many different plants, animals, and microbes.

A basic DNA extraction, amplification, and sequencing (mail-order) workflow, from the SNParty / GeneLaser
A basic DNA extraction, amplification, and sequencing (mail-order) workflow, from the SNParty / GeneLaser

Add an incubator, freezer, culture media, glassware, an autoclave, lab-grade k12 E. coli, and some more reagents (perhaps $500-$1000 of stuff) and you basically have everything you need to do modern molecular biology: you can use PCR to hunt for and isolate specific DNA sequences from the environment; restriction enzymes to cut-and-paste DNA sequences together or apart; gel electrophoresis to check your work; transformation to transfer plasmids into your e. coli; and minipreps to get the plasmids back out again. 

All of those components are available at more-or-less reasonable prices new... except the gel imaging system! Basic submarine gel tanks and power supplies can be found on eBay for less than $100, but imaging towers and transilluminators are far less common and much more expensive.

They don't need to be.

Help kickstart Gelfoo, the affordable, open-source, web-connected digital gel imager, and reduce the pricetag of the basic molecular bio toolchain from $6500 to less than $1800.

  • Handheld variable pipette set - for moving and mixing precise volumes of fluid. $80 / $160 / $600  (used/ebay / low-end retail / high-end retail)
  • PCR Thermocycler - for amplifying specific short DNA sequences with the polymerase chain reaction and precise temperature control. $200 / $600 / $1500 
  • Gel Electrophoresis tank + power supply - for casting and running agarose gels to sort DNA by size. $100 / $500/ $800 
  • gel imager + transilluminator - for viewing and imaging the stained DNA in the gel under specific lighting. (DIY $100) $800 / $600 (iorodeo) / $5000+

For pete’s sake, Petcube raised $100k on their kickstarter for their sleek $200 aluminum-shrouded motorized 5-megapixel CMOS camera + LASER telepresence *pet toy*! We’ve got this! For Science!

Risks and challenges

First of all, congratulations, everyone! We made it! Now we just have to worry about post-launch management.

At this point, it's too early to speculate about the manufacturing strategy and consequent logistics.

Assuming we succeed in manufacturing a working product and getting it shipped to customers, and they like it, this product will be in good shape. As an open-source project, I hope gelfoo brings together a community of contributors and users to offer improvements and support. If the launch goes well, I will definitely put a significant amount of the profit into engineering improvements and manufacturing a larger batch two.

Ultimately, I would like Genefoo to grow into a product development company with a special talent for designing and building products that support not just the expected customer base of technical experts and scientists, but through excellent attention to industrial design and user experience, successfully engage and draw in non-experts alike.

I think Gelfoo is positioned to be the first small step towards that vision, and I can't wait to see what suggestions and critiques the Kickstarter community has for it.

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Support

  1. Select this reward

    Pledge $49 or more About

    DIGITAL DNA PORTRAIT - Receive a unique image of a DNA fingerprint created from your geneome. We'll ship you a saliva sample collection kit and a pre-paid return envelope. Ship it back to us, and we'll use one of the GelFoo prototypes to capture the image.

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    Pledge $99 or more About

    PHYSICAL DNA PORTRAIT - Receive a unique image of a DNA fingerprint created from your geneome. We'll ship you a saliva sample collection kit and a pre-paid return envelope. Ship it back to us, and we'll use one of the GelFoo prototypes to capture the image.

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    Pledge $299 or more About

    Get an one of 10 GelFoo Prototypes extra early! We are making this by hand in San Francisco, so they'll be a little different from the final units.

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    Pledge $299 or more About

    Get your GelFoo imager, fresh from the second batch

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    Pledge $299 or more About

    Get your GelFoo imager, fresh from the third batch

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    Pledge $325 or more About

    Get one of the first GelFoo units, hot of the production line!

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