On microfluidics & data

There have been some ideas floating around on a new possible avenue of research for the Open Insulin project. Anthony and me got in touch with Federico from digi.bio, who are developing an open source microfluidic device. I only got to writing a summary of the conversation now.

It boils down to this. There is someone in CCL planning to generate a bunch of genetic sequences that could be potentially interesting as linkers for bringing the insulin A and B chain together more effectively. Hopefully this would result in many viable options, that have to be tested in lab experiments.

Testing many options would be very resource intensive, and this is where the microfluidics chips come in. A small demo at one of the Digi.bio events can be found here (cool video!). If optimized, the chips would allow for much cheaper and automated testing of the generated sequences.

The optimization part is something that we could work on here in Belgium. Federico is based in China/Amsterdam, so he is around close enough to help us get started and betatest his chip. This would give a new dimension to replicating the work previously done by CCL, if we could test culturing the bacteria on the chips. If it works, it would even be pretty valuable step towards opening up biotech research in general.

This is getting more and more interesting... Any thoughts @ritavht | @stevenvv90 ?

I dug up some specs of the device (approximates) that Federico shared:

  • Up to 20 liquids in- and output
  • Run program to get a droplet from the liquid: 300nl-2µl depending on size of device
  • Temperature goes from 4°C to 95°C, so you could run a PCR and anything in between (eg. cell incubation at 37°C)
  • Magnet to do purification (unsure about this)
  • They're planning to add fluorescence detection (months in the future)
  • It should be possible to do everything on the chip: transformation, cloning, selection, screening, ... Also planning to add electroporation.
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In other news

WinniePoncelet's picture

@ritavht is collecting the consumables we will need for receiving the samples and starting our culture, based on an older version of the CCL protocol from December. We will proceed with this as a starting point until we get the latest protocols, as differences are expected to be minor.

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Mindblowing, though...

Alberto's picture

... with @WinniePoncelet we had a conversation about this. I absolutely love this stuff, and yes, it will make tests much simpler and faster. But I doubt you will be able to bruteforce combinatorics problems, at least in the foreseeable future. The numbers explode too quickly. 

That does not mean Open Insulin should not deploy digi.bio stuff. After all, it as much for the learning journey as it is for producing insulin. But you guys will still need to apply domain expertise to figure out which sequences are most promising, before testing. 

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Building an OpenDrop

WinniePoncelet's picture

Today I met with Michiel, Bram & two students of UGent who were interested in teaming up to develop this further. We think the first step is to build an existing device ourselves to familiarize with it: the OpenDrop of GaudiLabs (http://www.gaudi.ch/OpenDrop/). Asking around for a fablab to host us and then find a date in the coming weeks.

Next up is trying to culture some E.coli on it and prepare for the Biohackathon in Waag (Amsterdam) on 7-8-9 July.

Who else wants to join in for preps/experiments/biohackathon?

ping @ritavht 

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preps/experiments/biohackathon?

ritavht's picture

Count me in!

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Where to begin?

WinniePoncelet's picture

The repository link for OpenDrop is here and the website is here. I'm kind of new still, been learning about the tech behind it, so I can't seem to wrap my head around where to begin from the Github files. Can anyone pitch in on the materials we need etc.?

Also a warm welcome to @Rpelicae and @Michielstock ! There's a manual on how to use the platform here, if you should need it.

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Greetings

Rpelicae's picture

Hi to you all,

I saw one of Winnie's presentations where he mentioned the Open Insulin project. This seems a very interesting and important subject. I'm a PhD student in bioinformatics in food microbiology. I have been reading about insulin production in E coli and I will check this OpenDrop device because I'm not familiar with it.

Regards,
Rudy

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Let's make some plans

WinniePoncelet's picture

Hello and welcome @Rpelicae ! Also welcome to @atilla | @BramDeJaegher & ping @ritavht and @Michielstock

I'm ill, hence the radio silence. Some updates: I was in touch with the creator of the OpenDrop and documentation is limited to what we have on the GitHub. We could buy a finished one for €500 though. Else, we are welcome to build at the Fablab of the UGent on weekdays from 9:00-16:00 (except Tuesdays). From looking over the documentation and talking to people I realise we really need some electronics expertise to get going.

For meeting up I propose we join the Open Insulin meetings we have every two weeks. The next one is planned for June 7 at 8 pm at ReaGent.

Some things that need to be done:

  • Translate the documentation into some concrete steps to get started (probably electronics expertise needed)
  • Gather the necessary materials

Is anyone up for doing one of these tasks?

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Let's make some plans indeed

BramDeJaegher's picture

Allright, I'll join the meeting June 7.

In the mean time I'll browse through the documentation of OpenDrop trying to figure out how complex it is and to what extend we need additional electronics expertise.

Regards,

Bram
 

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OK, I will join as well the

Michielstock's picture

OK, I will join as well the 7th and will also go through the documentation of OpenDrop.

Wim Van Criekinge is planning to also join. He made quite some promotion for the open insulin project in his lecture today.

M

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Techniques

WinniePoncelet's picture

Happy to hear Wim is coming!

Apart from getting the device together, we can start thinking about what to do at the biohackathon in July. Federico shared some interesting techniques like Loop Mediated Isothermal Amplification (LAMP) and Recombinase Polymerase Amplification (RPA) that are convenient to use in microfluidics, as they are isothermal reactions. We already discussed culturing bacteria on the chip. We could add a detection step or try to do a transformation, or do cloning.

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Documentation OpenDrop

Rpelicae's picture

Hello all,

What is actually the documentation document of the OpenDrop device? I don't understand anything from all these files on the GaudiLabs Github account

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Re: documentation OpenDrop

BramDeJaegher's picture

The documents on the Github are schematics for the circuit board itself, CAD-files for the electronic components, SVG-files of the carrier...

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Things to get

WinniePoncelet's picture

So we need to make a circuit board, get electronic components & laser the carrier?

I can do the lasering at Timelab next week, I'm a member there so it's cheaper than other places.

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