Science

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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Good point, Andreas. True, shipping permit is for Agro, not for plasmid DNA.

But that poses 2 other questions:

Q1. If I do not know anyone here (I moved here recently), then why would anyone give me Agro strains as a gift? So are there DIYbio strain collections that I can request? Plus I am looking for a few different ones - LBA4404, C58C1, EHA105, GV3101.

Q2. I've only used electroporation to transform Agro, and no DIYlab in my vicinity has an electroporator. I know there is a freeze-thaw protocol, but I've never used it.

Your thoughts? BTW, do you have experience dealing with such issues? Just curious....

Thanks!

On Thursday, June 20, 2019 at 2:30:11 PM UTC-4, Andreas "Mega" Stuermer wrote:

Why do you ship agrobacterium to VA? Aren't there local sources? Just ship the plasmids. 

AFAIK, only shipping agrobacterium between States requires a permit. 

On Tuesday, June 18, 2019 at 11:23:05 PM UTC+2, Tom De Medts wrote:

Hi DIYers,

I am new to the DIY Bio universe, having worked almost exclusively in university settings.

Currently, I want to transform some plants / seedlings with Agrobacterium. But it looks like I will need a lot of paperwork approved - 

1. USDA-APHIS permit for inter-state shipping from my alma mater in CA to me in VA

2. USDA-BRS facility inspection at physical location,  for compliance with biosafety regulation

Agro is BSL-1 and RG-1 (see this UCSD link), but NIH, CDC, USDA guidelines seem pretty paralyzing for DIYers..

But what do I know? As an independent community researcher, I am new to all of this regulation. Hence this email request for help.

Can a DIYer please tell me how to convince faculty at my former university, with true facts, as to why

shipping Agro strains, containing recombinant DNA plasmids, is compliant with all policies.

Several threads on this forum refer to permit applications. Can a citizen scientist apply for one?

Could some one guide me to relevant info? Which one would it be - USDA PPQ Form 526?

How about carrying out this project in a garage lab? Is that also allowed?

Would I need permits for that as well? Which ones?

If not, then what are workarounds? DIYLab? Community Lab? Or will they need to have been already inspected and approved?

Thanks, in advance.

- Tom

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>species grown in higher  density 3D arrangements (i.e. hydroponics, etc)

I see you immediately revert to suggesting using random options with little or no safety testing... as long as they're not GM.

How many decades of actual safety testing have been done of the health effects of plants grown in unnatural warehouses, grown in a [patentable] ]nutrient broth running through [patentable] hydroponics systems, under banks of [patentable] LED's and all the random biochemical changes that leads to... compared to the safety tests applied to most GM crops? 

I'm just gonna start replying to every one of your posts with the words "ISOLATED DEMANDS FOR RIGOR"

Because it describes them perfectly.

>" in contrast to raising existing species which provide little to no ability for patents "

but which do include plant breeders rights, which are functionally equivilent except for having a longer term than patents.

It's like you spend half your post railing against patents and lack of safety testing... and your alternative is a system suffused with vastly more patents and other IP rights with basically zero safety testing.

Seems like a poorly though out and basically undefendable position.

On Fri, Jun 14, 2019 at 8:43 PM Jonathan Cline <jcline@ieee.org> wrote:

On 6/14/19, Andreas "Mega" Stuermer <andreas.t.stuermer@gmail.com> wrote:

>
> Also, I am doubtful this biosphere will stand another 20 years. If we don't
> grow our food more sustainably (that is - genetically engineered), I can
> preety much guarantte you that it will certainly not stand 100 more years

Switching to a plant-based menu of existing species grown in higher
density 3D arrangements (i.e. hydroponics, etc) would sustain the
future global population and ecology just fine, more easily in terms
of financial investment, and with less impact regardless of genetic
engineering.   Your comment is simply using fear as rationalization
for use of untested technology.  The sole reason that this legitimate
avenue is not employed in large scale is that the new technology can
be patented and thus investment returns are far higher, in contrast to
raising existing species which provide little to no ability for
patents.  The creation of a wide economic moat by applying new
technology regardless of test history is what is rewarded.  Safety and
in-depth study prior to deployment are not rewarded.


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You're right, sorry for assuming that. 

On Thursday, June 13, 2019 at 6:58:47 PM UTC-7, Kelly Z wrote:

Hi Koeng,

Thanks again for your prompt response.

There are two surveys that we are currently running, the Global DIY Biology survey which ultimately aims to capture the global landscape of the DIY Biology field and the Perception of Biorisks whereby the invites for these two surveys have been sent separately.

Please correct me if I am wrong, but I think you are referring to the Perception of Biorisks survey which aim is to analyse the perception of biorisks of the general population. Thus irrespective of whether or not the survey respondent is a DIY Biologist. It is to have an idea of how does the general population perceive biorisks of research done in a traditional lab setting (academic/government etc.) versus a non-traditional lab setting and the correlation with their STEM education.

However, I do understand your concern, which is valid and will forward to the project leads for their attention. 

In the meantime, it would be great if you could help fill out the Global DIY Biology survey (https://www.surveymonkey.com/r/diybio) and spread the word to your networks :)

Thank you!

Cheers,

Kelly

On Thu, 13 Jun 2019 at 23:35, Koeng <koen...@gmail.com> wrote:

Hi Kelly,

I prefer an open form. 

The main issue that I meant to bring up is that there wasn't a section to actually claim that you were a practitioner or how long you practiced in the field. On paper, I basically look like a random uneducated teenager that has strong opinions, when in reality I have the skill + experience + home lab to execute on many of those theoretical projects.

Ie, it would be interesting to know what normal people think vs what practitioners think.

Also, it is a bit concerning that you didn't answer Patrik's question. Where will the results be published?

Koeng

On Thursday, June 13, 2019 at 12:37:34 AM UTC-7, Kelly Z wrote:

Hi Koeng,

Thank you for your response to the thread! We appreciate it very much.

To address your questions/concerns, the survey has been designed to understand the DIY Biologists as much as possible and therefore there are 4 sections which extensively looks at 3 aspects - motivations, challenges and opportunities. There is also an open comment box section where DIY Biologists are free to express their opinions or fears if need be. I would also like to remind you that the survey is completely anonymous and therefore no personalised answers have been obtained and/or kept. 

As for the education section, you would see that there is an 'other' answer option where you can specify if there is no formal education that has been undertaken.

I personally think  (as a scientist and educator) that the DIY Bio field has tremendous potential for education and thus should be further encouraged.

I hope that this clarifies some concerns you have. If not, please feel free to email me. I would be happy to answer any other questions you may have.

Thank you!

On Tue, 11 Jun 2019 at 07:26, Koeng <koen...@gmail.com> wrote:

I think I said this in an email I sent after getting this survey, but I believe the last section is (or was) poorly created in respect to understanding the landscape of DIYbio practitioners. If I remember correctly, there wasn't a section on if you actually did work as a DIY biologist or to what capacity (which would definitely influence your opinions/ fears), and the section on education didn't have any position for those who never got a formal education but do amazing work in the field of DIY biology (David Ishee and Sebastian Cocioba come to mind), which by it's very nature has a skew towards different educational paths.

ie, it seems to me the survey isn't actually interested in practitioners opinions, which is sad to see.

Koeng

On Monday, June 3, 2019 at 8:17:03 AM UTC-7, Kelly Z wrote:

Hello fellow DIY Biologists,

I am part of a research team who is looking into the Global DIY Biology landscape. We have launched a survey today and are seeking as many participants for the survey as possible. We would really appreciate your help! Please see below for the official invitation containing the details of the survey.

 

Invitation to Participate in the Global DIY Biology Survey

 

We humbly request for your cooperation to fill out this survey on Do-It-Yourself (DIY) biology. This survey is conducted by the Global Young Academy (GYA) in collaboration with Sunway University and funded by the Volkswagen Foundation. The aim of the survey is to explore the global landscape of DIY biology and understand the challenges and opportunities in the field. We plan to use this information to inform policies that can help support the maximising of benefits and minimising of the associated risks related to DIY biology field.

 

This survey will take about 10-20 minutes of your time.

Please see below for the survey link:

https://www.surveymonkey.com/r/diybio

Global DIY Biology Survey www.surveymonkey.com A survey by the Global Young Academy (GYA) in collaboration with Sunway University and funded by the Volkswagen Foundation.

 

Please kindly fill out the survey by 11.59 PM (GMT), 1st of July 2019. 

 

Please feel free to email us if you have any queries and/or if you require more information with regards to the survey.

 

Professor Dr Abhi Veerakumarasivam         

Principal Investigator                                     

ab...@sunway.edu.my

+603-7491 8622 ext 7175

 

Dr Khalisah Zulkefli

Research Associate

khal...@sunway.edu.my

 

Please disseminate this survey to anyone who you believe should participate in the survey.

 

We thank you in advance for your participation!

 

Best regards, 

 

Khalisah Zulkefli, PhD

Postdoctoral Research Associate

Sunway University

 

On behalf of, 

Professor Abhi Veerakumarasivam 

Co-Chair, DIY Biology Working Group, Global Young Academy 

Chair, International Network for Government Science Advice-Asia
Co-Chair, ASEAN Young Scientists Network

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