Re: [DIYbio] Opentrons OT-2 release

I know that the tube rack holder at least is open source, you can probably just email the OpenTrons folks to get the file

On Tuesday, June 25, 2019 at 5:10:37 AM UTC-7, Dakota Hamill wrote:

Anyone have any dimensions on the OpenTrons tube tack holders or TipOne box holder?  

On Mon, Apr 1, 2019 at 8:37 PM Koeng <koen...@gmail.com> wrote:

I have a personal repository of opentrons protocols, but they probably wouldn't be very useful to you (I'm also moving towards using all json protocols since they're easy to generate and track with an actual database). In essence, no not really.

Have you used their protocol designer software? That might be able to do what you want. Also, I'm not really sure if the pipette itself is physically able to go from 24 to 96 well plates.. do you actually have one right now?

For complicated stuff like 24-to-96, you'll probably have to roll out your own little piece of software, which shouldn't be too hard given their API. 

On Monday, April 1, 2019 at 5:30:24 PM UTC-7, Dakota Hamill wrote:

Is there a repository of Open Tron protocols outside of the main websites extremely small library?  Just got ours up and running and it looks like I'm going to need to learn to do some coding.  Have a deep well 24-well plate and there's nothing in the database for that, and no simple UI to adjust plate height.

The software also doesn't allow using an 8 span to go from 24-well spacing to 96 well spacing.  Just planning on removing every other pipette tip and doing it that way, but again looks like something that must be custom coded. 

On Wed, Sep 12, 2018 at 4:12 AM Michael Crone <crone....@gmail.com> wrote:

We're looking at getting the OT-2. I was wondering if anyone could please give me an idea of the most useful pipettes and modules for starting out. We're a synthetic biology lab (we have an Echo and Felix, but nobody uses the Felix because it is such a pain). I was thinking that the multichannel 50-300 would be good (mainly minipreps and other wash steps for RNA purification etc), along with probably all the single channel pipettes. And then the magdeck initially (for minipreps and other purification). Is the tempdeck useful? What kind of applications would you use it for? Scale transformations?

I was hoping to get someone's experience just to inform our own decision!

Thank you!

Michael

On Friday, 29 June 2018 23:39:07 UTC+1, Koeng wrote:

Last time I talked to one of the devs, they would like to get an OT port once they're more widespread. It's not here yet. 

And yep, that sounds about right for copyright situation. I'd rather write my own software and own it under MIT.

Koeng

On Friday, June 29, 2018 at 2:25:54 PM UTC-7, Cathal Garvey wrote:

It appears that Antha itself is still FLOSS and gratis: https://github.com/antha-lang/antha

However, perhaps this GUI you mention is not FLOSS, and it's possible that they are not releasing device drivers. Because they are the copyright holders of Antha, they can do that even though for someone else it would be a GPL violation. :/

I'd still expect the OpenTrons Antha drivers to be open though, because it's OpenTrons.

On 29 June 2018 16:30:45 GMT+01:00, Koeng <koen...@gmail.com> wrote:

(actually, if I remember correctly, you have to purchase actual Antha for support of running on the bots? It seemed like it was good for labs doing high throughput work but didn't want to have to think about running robots and developing code)

On Friday, June 29, 2018 at 8:29:08 AM UTC-7, Koeng wrote:

Antha is also pretty pricey per year, I think 4 times an OT cost?

That said, I met with some developers of Antha and I really like it. Their GUI is really great for management and wonderful for multifactorial optimization. Their data from optimizing GoldenGates was very impressive. It's a piece of proprietary software I would consider purchasing, if I had the money to, since mainly what you're paying for is support and the user interface supporting the bottom-level code. Also, yea it's not really vendor lock-in because it works across many platforms - but python is pretty hard to beat when working with libraries.

Here are some videos of our OT1s doing work with our codebase. When in "build-mode" we run about 3 at a time, cloning about 300 plasmids a day. 

OT doing GoldenGates

https://www.youtube.com/watch?v=-_tEMNG0I3U

OT doing transformations

https://www.youtube.com/watch?v=IQA4v-9h0W8

OT doing plating (from above)

https://www.youtube.com/watch?v=FxHn1avxR-4

OT doing plating (from back)

https://youtu.be/xXuF4v3vZ78?t=11s

(At the end of this video, you can see how we're doing the serial dilutions. Extremely important to note: you want to slowly dispense the liquid above the plate, creating a small droplet that sticks to the sides of the tip, and THEN move down to drop the droplets while stabbing the agar a little. If you do it when you're already down in the agar, you're gonna have a bad time)

Koeng

On Wednesday, June 27, 2018 at 11:30:34 PM UTC-7, Michael Crone wrote:

Antha removes the vendor "lock-in" that you are talking about and allows for cross-platform workflows (which becomes useful when you are working in a DNA foundry environment). And when you already have a $30 000 robot it's difficult to justify to your PI to buy a $10 000 one... especially when that robot is already fully equipped with all of the accessories.

I completely agree though that the opentrons is great for every day work in the lab and its programmability makes it very attractive.

On Wednesday, 27 June 2018 17:02:22 UTC+2, John Griessen wrote:

On 06/27/2018 02:42 AM, Michael Crone wrote:
> We have a Felix in my lab and I'd like to get it up and running because it is easier to justify using that than buying the cheaper opentrons.

What makes it easier to justify?  After Koeng's email on how wonderful programmability without vendor lock-in is, I don't get you.

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