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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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Things to get (2)

BramDeJaegher's picture

Hi Guys & Girls

So, I browsed through the files and checked the schematics for the openDrop. As far as I understand there are 3 important hardware parts to the opendrop.

The hardware:

  1. The printed circuit board (PCB): I found a list of electronic components with prices and suppliers, I checked this list with the OpenDropperV2 schematics and everything seems to be there
  2. The carrier: there is also a carrier which is also a PCB without any components (Current status (WIP): I'm not sure what the function is of this part, I can't find it in the list of electronics and I can't find it on the pictures of the OpenDrop)
  3. The protective acrylic base plate with bolts, nuts: there is also an acrylic baseplate which needs to be lasercut, this protects the electronic components at the bottom of the openDrop. (Current status (WIP): I haven't found the correct measures of the bolts nor the base plate, yet)

Now, the cost of all the hardware components is about €90 and includes the cutting and the etching of the PCB.
With respect to the assembly of the openDropper, it has about 90 unique components to solder so it is going to be a lot of work to assemble this manually, the other option is to buy it assembled but I fear that is going to add about €200 to the pricetag (Maybe some advice of an electronics expert could come in handy here, @Michielstock maybe you could ask Francis' opinion).

The software
The OpenDropper uses an arduino shield as microcontroller and there is already code available on the github, so this is not an issue

Remaining questions

  1.  What is the function of the carrier board?
  2.  What is the difference between OpenDropV2-ESP01 and ESP201?
  3.  Is it feasible to solder all the components manually?
  4. Dimensions and size of Protective base plate?

I'm currently enjoying a 3 day holiday in den haag so my responses can be delayed.

Bram out! :D

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Good stuff! Some thoughts

WinniePoncelet's picture

Good stuff @BramDeJaegher !

ESP 01 and ESP 201 are modules with Wi-Fi connectivity. So my thinking is those folders are two versions of the device with different modules. Can this be?

I've had a search for those carriers and they are shown in these videos: part one and part two. Shortcut to 6:20 of part two to see both being combined.

When I was in touch with the fablab @ UGent and also Fyxxilab, they told me they have a machine we can use to etch the PCB. Would this affect the price?

Have fun in The Hague!

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Open repository for fluidic systems

WinniePoncelet's picture

I came across this today, may be useful for further research on the possibilities: Metafluidics, an open repository for fluidic systems.

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Re: Open repository for fluidic systems

BramDeJaegher's picture

Thanks, useful stuff!

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Short updates

WinniePoncelet's picture

Some updates:

  • @Michielstock has met with Noel Carrascal to help out with molecular modelling
  • After the last meeting it became clear the microfluidics avenue of research is currently outside the main focus of Open Insulin (developing insulin vs optimizing a lab-on-a-chip device to develop open insulin). However, some of us are going to go further with the microfluidics with a broader goal in mind. At some point it may help the insulin research (or vice versa), but it is not the goal.
  • The biohackathon in July is on, yet the purpose has shifted: Bram and Michiel are joining with a broader microfluidics project idea in mind, others are welcome to tag along as it will be fun, interesting and nice to visit Waag Society & Amsterdam. More here.
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