liquid handling for sanger sequencing

[Jeswin]

Hi all,

Is anyone familiar with the robotics used in conjunction with sanger seq. machines (specifically, Applied bio 3730xl)? I am looking at university set-ups now. The main issue is adding reagents and the purification steps for sequencing samples. They would be practically inefficient without a robot to do it.

Any advice on companies, what I should be looking for, pricing data, etc. Thanks

[Otto Heringer]

If you have the time and resources, you could try set up the automation using the OpenTrons machine:
https://www.kickstarter.com/projects/932664050/opentrons-open-source-rapid-prototyping-for-biolog

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[Jeswin]

On Thu, Nov 13, 2014 at 11:44 AM, Otto Heringer <ottowh...@gmail.com> wrote:

If you have the time and resources, you could try set up the automation using the OpenTrons machine:
https://www.kickstarter.com/projects/932664050/opentrons-open-source-rapid-prototyping-for-biolog

Yea, about that. This isn't really a DIY question b/c this is for a commercial lab so we would need a reliable machine plus good technical support behind it. I know there are some people here who are familiar with liquid handlers so I thought they would be able to point the way. So far I have looked at the Beckman Coulter Bio-Mek platform and I have heard that Tecan and Hamilton offer good systems.

[Nathan McCorkle]

On Thu, Nov 13, 2014 at 9:58 AM, Jeswin <phill...@gmail.com> wrote:
>
>
> On Thu, Nov 13, 2014 at 11:44 AM, Otto Heringer <ottowh...@gmail.com>
> wrote:
>>
>> If you have the time and resources, you could try set up the automation
>> using the OpenTrons machine:
>>
>> https://www.kickstarter.com/projects/932664050/opentrons-open-source-rapid-prototyping-for-biolog
>>
>>
> Yea, about that. This isn't really a DIY question b/c this is for a

If you aren't paying someone else to do it, isn't it DIY?

[Otto Heringer]

Is true that the OpenTrons liquid handler was build on a DIY approach, but it may be useful like any "comercial" liquid handler and with a smaller price.

Also there is the community advantage to help you program and improve your protocol. I bet that OpenTrons guys might even help you do this - since it is a interesting application of their product.

You should try speak with them.

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[Cathal Garvey]

CC'd Will, but I think he's on the list already.
Will; Any room for a special Kickstarter pledge that gets commercial
support contracts; assistance setting up and maintaining a process or
workflow? :)

On 13/11/14 19:06, Otto Heringer wrote:
> Is true that the OpenTrons liquid handler was build on a DIY approach,
> but it may be useful like any "comercial" liquid handler and with a
> smaller price.
> Also there is the community advantage to help you program and improve
> your protocol. I bet that OpenTrons guys might even help you do this -
> since it is a interesting application of their product.
>
> You should try speak with them.
>
> 2014-11-13 16:50 GMT-02:00 Nathan McCorkle <nmz...@gmail.com

> <mailto:nmz...@gmail.com>>:

>
> On Thu, Nov 13, 2014 at 9:58 AM, Jeswin <phill...@gmail.com

> <mailto:phill...@gmail.com>> wrote:
> >
> >
> > On Thu, Nov 13, 2014 at 11:44 AM, Otto Heringer <ottowh...@gmail.com <mailto:ottowh...@gmail.com>>

> > wrote:
> >>
> >> If you have the time and resources, you could try set up the automation
> >> using the OpenTrons machine:
> >>
> >>https://www.kickstarter.com/projects/932664050/opentrons-open-source-rapid-prototyping-for-biolog
> >>
> >>
> > Yea, about that. This isn't really a DIY question b/c this is for a
>
> If you aren't paying someone else to do it, isn't it DIY?
>
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[Jeswin]

On Thu, Nov 13, 2014 at 2:34 PM, Cathal Garvey <cathal...@cathalgarvey.me> wrote:

CC'd Will, but I think he's on the list already.
Will; Any room for a special Kickstarter pledge that gets commercial support contracts; assistance setting up and maintaining a process or workflow? :)

Sorry, guys, I don't think a DIY solution is possible for this lab. The bot needs to reliable with good tech support and we need it validated to conform with government regulations. So, no one wants to make the process harder than it is already. No way anyone around here would accept a diy project.

I'm just here asking for your technical expertise cause I think some of you are familiar with the commercial lab robotics equipment. No one I work with has worked with them before.

[John Griessen]

On 11/13/2014 03:15 PM, Jeswin wrote:
> we need it validated to conform with government regulations.

Opentrons can do that by getting it safety tested at UL or ETL,
which is a good way to go ultimately for anything with the potential
to pinch someone, much less mash their finger.

I am saddened by your assumptions Jeswin. There may be little
opportunity for faster innovation in lab gear if others share your
haste to judge a project like Opentrons as DIY, always was DIY,
and always will be DIY--> trash.

It's a product, not a DIY recipe.

[Alexey Zaytsev]

Dude, seriously.

He needs something that works, works reliably, and is known to work
reliably. And passed some regulation testing. And probably also
something that's available now, with tech support and professional
installation.

I really like the OpenTrons project, and I think that out of the
recent bio-related tech kickstarters, it's the only one that would
actually be useful in a "professional" lab, but it's just not there
yet, or anywhere close to, no matter how much you or I want it to
succeed.

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[Nathan McCorkle]

jcline wrote this a while ago, so you might send him an e-mail... the
only name-brands I know for this stuff are Tecan and openTrons :P
http://88proof.com/synthetic_biology/blog/archives/386

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[John Griessen]

On 11/13/2014 05:06 PM, Alexey Zaytsev wrote:
> it's just not there
> yet

He didn't say how fast he wanted it, but yes,
he wants it tomorrow, so you're right.

[Jeswin]

On Thu, Nov 13, 2014 at 5:54 PM, John Griessen <jo...@industromatic.com> wrote:
>
> Opentrons can do that by getting it safety tested at UL or ETL,
> which is a good way to go ultimately for anything with the potential
> to pinch someone, much less mash their finger.
>

It's more than about safety. There are other regulations to consider,
especially for clincal samples.

> I am saddened by your assumptions Jeswin. There may be little
> opportunity for faster innovation in lab gear if others share your
> haste to judge a project like Opentrons as DIY, always was DIY,
> and always will be DIY--> trash.
>

Well, by DIY, I just meant that it is not a widely used or known
product and it would be challenging to use it in this lab. I'm not
even sure a smaller robotics company will be considered compared with
the well known ones like Beckman or Tecan. This is a niche market and
it's better to have less issues and go with the tried and tested
product, especially if its software is flexible and the system is
easily upgradable. Nothing against new products but for companies like
this, there are many issues to consider.

On Thu, Nov 13, 2014 at 6:06 PM, Alexey Zaytsev
<alexey....@gmail.com> wrote:
>
> He needs something that works, works reliably, and is known to work
> reliably. And passed some regulation testing. And probably also
> something that's available now, with tech support and professional
> installation.
>

I met with a Beckman rep the other day to see what they offer and what
our lab is looking for. They offer those things and their system is
very open, unlike Qiagen's. I was researching by looking at the
robotics that univeristy and commercial labs are using and Beckman is
very popular.

> I really like the OpenTrons project, and I think that out of the
> recent bio-related tech kickstarters, it's the only one that would
> actually be useful in a "professional" lab, but it's just not there
> yet, or anywhere close to, no matter how much you or I want it to
> succeed.
>

I like the project but it's application in this lab is not appropriate
or suitable. For a "garage" based lab that's just doing research, it's
a very good product, especially given the low barrier of entry to own
such equipment. ("Garage" just means a really small startup or
personal endeavor, etc.)

On Thu, Nov 13, 2014 at 6:23 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> jcline wrote this a while ago, so you might send him an e-mail... the
> only name-brands I know for this stuff are Tecan and openTrons :P
> http://88proof.com/synthetic_biology/blog/archives/386
>

Tecan is the next one I'm looking into. I also was told of Hamilton Robotics.

On Thu, Nov 13, 2014 at 6:41 PM, John Griessen <jo...@industromatic.com> wrote:
>
> He didn't say how fast he wanted it, but yes,
> he wants it tomorrow, so you're right.
>

That's an issue also.

[John Griessen]

On 11/14/2014 10:01 AM, Jeswin wrote:
> Tecan is the next one I'm looking into. I also was told of Hamilton Robotics.

Mettler Toledo offers liquid handling equip also.

What are the "other" regulations on clinical samples you referred to?
Sterility and wash down related?

[Jeswin]

On Fri, Nov 14, 2014 at 3:51 PM, John Griessen <jo...@industromatic.com> wrote:
>
> Mettler Toledo offers liquid handling equip also.
>
> What are the "other" regulations on clinical samples you referred to?
> Sterility and wash down related?
>

Thanks, I'll take a look at MT.

Well, not really regulations, but we do have to get all the equipment
and processes validated to meet certain lab certifications. So, if we
work with equipment that is more familiar with our consultants, it
will be much easier to set up. There's just a lot of paper work to do
and there are time constraints.

Finally, now that I have taken a look at more products, it looks like
some systems already contain programs for use and we won't have to
design our own. Easy to use software is a big plus. And some like the
Beckman platforms are fully optimized to do the whole work from
reaction prep to sample purification.

[Will Canine]

Hi guys!

Thanks for putting OpenTrons out there -- but I have to agree that we are not the right automation solution for PhillyJ's lab. 

Current robots are like big mainframe machines. They cost a ton, break a ton, but do a ton of work for you. Plus, they are fully certified and tested, clinical studies on them, etc. As a UX person, I would say that none of them have good interfaces or would qualify as easy to work with in any way -- but thats why people hire lab techs whose whole job is to run the machines. And Hamilton, Tecan, etc are really good at what they do, once you get them up and running. 

Our focus is on being a personal lab automation platform. So instead of a workflow where researchers pass their experiments off like punch cards to a mainframe machine, individuals us an OT.One to save themselves a bunch of time and automate their own pipetting work. We give you much more flexibility as an innovator, and let you share your protocols seamlessly with peers across the world. Our focus is on rapid iteration, hardware flexibility, experiment reproducibility, protocol abstraction, avoiding human error, peer-to-peer collaboration, open-source community. We are not focused (right now) on super high-throughput or certifications. 

We dont have a separate category on our Kickstarter for a "support contract" because we plan on engaging very closely with all of our Kickstarter backers. Our early-adopters will be the backbone of our user community going forward, and I plan on establishing a personal relationship with all our new OT.One users in 2015 -- and I honestly cant wait to work with them!

After we go to live retail sales in Spring 2015 we will have performance and durability statistics as well formal support contracts available. 

phillyj, have you looked at Transcriptic? Not sure if they can do Sanger sequencing, but I am curious what a lab like your would think about outsourcing a piece of your workflow to "the cloud," as opposed to buying, de-bugging, and operating robots yourselves. 

Anyways, always happy to talk about this stuff! 

Thanks,

Will 

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