[DIYbio] Does anyone have an epoxy resin surface?

They're pretty heavy, so shipping is more of a pain than I realized. I was wondering if anyone on the list knows of any (either used or new) that are available here in the bay area. Thanks for your time!

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[DIYbio] Re: Freedom Evo Tecan Troubleshooting - HELP!

Hi everyone - I was recently given two surplus Tecan Miniprep systems, a 60 and 75, of unknown condition and without software. The both power on but I've no way of testing. They both have their software dongles. Is anyone familiar with these systems and how to determine if they are functioning?
Thanks
Richard

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Re: [DIYbio] Re: Making Money Out of a Home Bio Lab?

Get some or design some library prep kits for DNA sequencing, a thermal cycler, and some DNA purification beads and prep sequences for people.

It'll take you some start up cost.

-SG

On Tue, Nov 28, 2017 at 11:48 AM John Griessen <john@industromatic.com> wrote:
On 11/28/2017 03:47 AM, André Esteves wrote:
> A bioterium? There's always need for laboratory animals. FRogs for
> school dissection. Zebra fish for labs, rats etc
> Some care would be needed on husbandry and registry of germ lines but
> it is often a forgotten area in research...

bacteria-cafeteria.com?
With barcoding level of species verifying, it might become a go-to thing...

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[DIYbio] Re: Freedom Evo Tecan Troubleshooting - HELP!

HI Ana, did you get a solution for your problem. It seems that we are encountering a similar problem with our device and I was curious whether you find a solution. best regards, Ugur 



Am Montag, 5. Juni 2017 19:30:19 UTC+2 schrieb Ana Santos:
Hi diybio community!

I was wondering if anyone out there has experience with the Freedom Evo Tecan Robot. 

We have ours for a few years (>5) and no one has good memories of working with it. And basically, we're just trying to use it to read 96 well plates (between 8 and 12) for 24h.

Everything starts out OK, it runs for about 6h and afterward it just stops working showing messages like "Your run has been stopped" or "Your run was aborted". No red light blinking. No alarm. 

However, if we hit the recover bottom, it re-starts working, as if nothing had happened. If we're really lucky, the run then proceeds until the end, but normally it keeps crashing systematically afterwards.

The only pattern we've been able to detect is that the robot normally stops working when the plate is inside the plate reader.

The technicians from Tecan are now almost part of the lab, because of all the problems we have with the Robot, but they never manage to tell us exactly is the problem. Whatever they do (switch a cable, tweak the software, plug/unplug all machinery) works for a couple of hours but we then go back to the same original problem.

We're just desperate to know if someone else has faced the same problem or if it is a problem with our machine.

I look forward to your feedback.

Best regards and DO GREAT SCIENCE!

Ana

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Re: [DIYbio] Re: Making Money Out of a Home Bio Lab?

On 11/28/2017 03:47 AM, André Esteves wrote:
> A bioterium? There's always need for laboratory animals. FRogs for
> school dissection. Zebra fish for labs, rats etc
> Some care would be needed on husbandry and registry of germ lines but
> it is often a forgotten area in research...

bacteria-cafeteria.com?
With barcoding level of species verifying, it might become a go-to thing...

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Re: [DIYbio] Re: Making Money Out of a Home Bio Lab?

Making money with a DIY Lab?

A bioterium? There's always need for laboratory animals. FRogs for
school dissection. Zebra fish for labs, rats etc
Some care would be needed on husbandry and registry of germ lines but
it is often a forgotten area in research...

Cheers,

Andre Esteves

2017-11-28 5:26 GMT+00:00 Skyler Gordon <skgor1@gmail.com>:
> I'm not a teen, but would be willing to discuss what I think the direction
> of the at home / small start-up Biotech and DIYBio groups are taking. Feel
> free to reach out.
>
> -SG
>
> On Mon, Nov 27, 2017 at 8:22 PM InstantLife <xthechallengerx@gmail.com>
> wrote:
>>
>> Hey Emily, I just shot you an email. I would love to chat :)
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Re: [DIYbio] Re: Change blood type



On Tue, Nov 28, 2017 at 12:24 AM, Skyler Gordon <skgor1@gmail.com> wrote:
Your most likely better off trying to find a way to convert A, B and AB blood types into O outside of the human body so they can be used as universal donor blood.

There is also more to the cell signaling than just A, B and O.

-SG

        Apparently, it's been done:
https://www.nature.com/articles/nbt1298

August Pamplona

 
On Sun, Nov 26, 2017 at 6:28 AM August Pamplona <cosmicaug@gmail.com> wrote:
        Not sure if trolling or not.

        D'Adamo is a crank. Changing blood types is not an "upgrade". You are not suffering from a "recessive condition" (indeed, "dominant" and "recessive" might not mean what you think it means). In any event, without changing your entire immune system you can't do it. If you could do it, maybe it would kill you. You could presumably engineer some of your RBC stem cells so that one or the other AB antigen is expressed. It would be as if you had a built in blood transfusion of the wrong type so if the rest of your blood stem cells were not switched out (bone marrow transplant) it might be bad news for you.

August Pamplona


On Friday, November 24, 2017 at 5:35:12 AM UTC-5, Bruce Almighty wrote:
The oldest blood type on earth are the recessive O type, which is my type. I'm a fan of D'Adamo and I believe the things he said because I experienced them myself as a O'er. Secondly, from a medical perspective, we are only allowed to receive our own blood type in an emergency which requires transfusion. O IS OBSOLETE. As with our ever-changing environment, we are the minority to more dominant blood types like A, B and AB. Having suffered from this recessive condition that the mainstream medical community gives no sympathies about, it is my dream to upgrade to at least one of the newer blood types. This is not so difficult as those undergoing a bone marrow transplant will adopt the donor's blood type. However, the severe risks and side effects are not something a healthy person wants to go through, whether allowed by medical science or not. So is there a possible option to change blood type?

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Re: [DIYbio] Re: Making Money Out of a Home Bio Lab?

I'm not a teen, but would be willing to discuss what I think the direction of the at home / small start-up Biotech and DIYBio groups are taking. Feel free to reach out.

-SG

On Mon, Nov 27, 2017 at 8:22 PM InstantLife <xthechallengerx@gmail.com> wrote:
Hey Emily, I just shot you an email. I would love to chat :)

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Re: [DIYbio] Re: Change blood type

Your most likely better off trying to find a way to convert A, B and AB blood types into O outside of the human body so they can be used as universal donor blood.

There is also more to the cell signaling than just A, B and O.

-SG

On Sun, Nov 26, 2017 at 6:28 AM August Pamplona <cosmicaug@gmail.com> wrote:
        Not sure if trolling or not.

        D'Adamo is a crank. Changing blood types is not an "upgrade". You are not suffering from a "recessive condition" (indeed, "dominant" and "recessive" might not mean what you think it means). In any event, without changing your entire immune system you can't do it. If you could do it, maybe it would kill you. You could presumably engineer some of your RBC stem cells so that one or the other AB antigen is expressed. It would be as if you had a built in blood transfusion of the wrong type so if the rest of your blood stem cells were not switched out (bone marrow transplant) it might be bad news for you.

August Pamplona


On Friday, November 24, 2017 at 5:35:12 AM UTC-5, Bruce Almighty wrote:
The oldest blood type on earth are the recessive O type, which is my type. I'm a fan of D'Adamo and I believe the things he said because I experienced them myself as a O'er. Secondly, from a medical perspective, we are only allowed to receive our own blood type in an emergency which requires transfusion. O IS OBSOLETE. As with our ever-changing environment, we are the minority to more dominant blood types like A, B and AB. Having suffered from this recessive condition that the mainstream medical community gives no sympathies about, it is my dream to upgrade to at least one of the newer blood types. This is not so difficult as those undergoing a bone marrow transplant will adopt the donor's blood type. However, the severe risks and side effects are not something a healthy person wants to go through, whether allowed by medical science or not. So is there a possible option to change blood type?

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[DIYbio] Re: Making Money Out of a Home Bio Lab?

Hey Emily, I just shot you an email. I would love to chat :)

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Re: [DIYbio] Re: Making Money Out of a Home Bio Lab?

Emily, are you looking for a type of DIYBio where people "modify" their bodies or where people do genetic engineering?

On Mon, Nov 27, 2017 at 9:24 PM Emily B <emilybaumgaertner@gmail.com> wrote:
Hey there! I'm a new york times reporter writing about teens who are jumping into the DIY Bio movement. If you'd be willing to chat, please let me know! Thanks!

On Monday, October 2, 2017 at 9:24:32 PM UTC-4, InstantLife wrote:

Hi there, I am InstantLife

I have been doing amateur DIYBio for the past few years and I recently decided that my bedroom was just not sufficient for a functioning lab space. So I bought a 10x5 grow tent some cheap shelving units and a metal table along with the parts to make a bigger and better tabletop laminar flow box. I love the space and I am spending every day in there doing whatever I can to further my experiments. All my projects are going way smoother.

The problem here is I am 17 without a drivers license, working car, or job. I am running out of my savings and I want to be able to make my lab even better. I don't have any connections in Vermont and no luck getting donations or free used equipment locally. I sank $1500 into my lab and I was wondering if there was a way to make up for that? Especially so I can buy/build things like a PCR machine or Electroporator

All I can think is use extra space to grow micro greens or gourmet mushrooms and try to sell them to local restaurants.

Anyone else had any luck with turning a small profit from a home lab?

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[DIYbio] Re: Making Money Out of a Home Bio Lab?

Hey there! I'm a new york times reporter writing about teens who are jumping into the DIY Bio movement. If you'd be willing to chat, please let me know! Thanks!

On Monday, October 2, 2017 at 9:24:32 PM UTC-4, InstantLife wrote:

Hi there, I am InstantLife

I have been doing amateur DIYBio for the past few years and I recently decided that my bedroom was just not sufficient for a functioning lab space. So I bought a 10x5 grow tent some cheap shelving units and a metal table along with the parts to make a bigger and better tabletop laminar flow box. I love the space and I am spending every day in there doing whatever I can to further my experiments. All my projects are going way smoother.

The problem here is I am 17 without a drivers license, working car, or job. I am running out of my savings and I want to be able to make my lab even better. I don't have any connections in Vermont and no luck getting donations or free used equipment locally. I sank $1500 into my lab and I was wondering if there was a way to make up for that? Especially so I can buy/build things like a PCR machine or Electroporator

All I can think is use extra space to grow micro greens or gourmet mushrooms and try to sell them to local restaurants.

Anyone else had any luck with turning a small profit from a home lab?

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[DIYbio] Re: Change blood type

        Not sure if trolling or not.

        D'Adamo is a crank. Changing blood types is not an "upgrade". You are not suffering from a "recessive condition" (indeed, "dominant" and "recessive" might not mean what you think it means). In any event, without changing your entire immune system you can't do it. If you could do it, maybe it would kill you. You could presumably engineer some of your RBC stem cells so that one or the other AB antigen is expressed. It would be as if you had a built in blood transfusion of the wrong type so if the rest of your blood stem cells were not switched out (bone marrow transplant) it might be bad news for you.

August Pamplona

On Friday, November 24, 2017 at 5:35:12 AM UTC-5, Bruce Almighty wrote:
The oldest blood type on earth are the recessive O type, which is my type. I'm a fan of D'Adamo and I believe the things he said because I experienced them myself as a O'er. Secondly, from a medical perspective, we are only allowed to receive our own blood type in an emergency which requires transfusion. O IS OBSOLETE. As with our ever-changing environment, we are the minority to more dominant blood types like A, B and AB. Having suffered from this recessive condition that the mainstream medical community gives no sympathies about, it is my dream to upgrade to at least one of the newer blood types. This is not so difficult as those undergoing a bone marrow transplant will adopt the donor's blood type. However, the severe risks and side effects are not something a healthy person wants to go through, whether allowed by medical science or not. So is there a possible option to change blood type?

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Re: [DIYbio] Protein Unfolding Algorithms?

Yeah, the computing requirements will be enormous, I'm planning on starting a small 10GPU 4coreCPU server and playing with similarly small proteins to test/debug anything I come up with.

On Thursday, November 23, 2017 at 12:42:37 PM UTC-5, Skyler Gordon wrote:
The idea of 'reverse engineering' a protein is interesting, but most likely a fruitless venture. People often modify existing proteins (I.e. protein engineering) due to the fact that the 'shape' you are looking for does not necessarily have much to do with your final catalytic result.

While the folding of a protein is critical, the shape does not necessarily define the catalytic functions of the active site. Your program would essentially rely on guessing a shape based on other known proteins, getting a 'best fit' shape, and then try to produce it via 'self learning' reassembly of trillions of different protein combinations. You're going to need a distributed framework or your own server network.

That being said. Best of luck.

-SG
On Wed, Nov 22, 2017 at 11:07 AM Bryan Jones <bryan...@gmail.com> wrote:
People have used Rosetta both ways. For example, the "game" foldit uses rosetta + human intuition to figure out how proteins fold given the sequence. However, the bigger goal of Rosetta is to design new proteins. You start with a desired function/reaction -> define a topology or active site geometry to catalyze the reaction -> find an overall protein fold that can accommodate the active site -> optimized sequence -> make and test the new protein.

" it seems the only thing really missing (aside from likely lots of computing power to compile anything) is the ability to go from a desired structure to the DNA which codes for that structure"
It's even less than that. It's very straightforward to go from desired protein sequence -> DNA sequence, although you might need some optimization in terms of promoters and the like to optimize expression levels. So the only really hard step is going from desired docking or structure to protein sequence. That's exactly what Rosetta is for. I think it's the best there is for doing this, however, it's still not that great. It typically requires trying dozens of designs to find one protein that does the desired job even very poorly.

Here's a good paper that discusses how to use Rosetta to design new enzymes: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019230 

On Wed, Nov 22, 2017 at 12:11 PM Cory J. Geesaman <co...@geesaman.com> wrote:
To put it another way, think of the arbitrarily stupid use case: sharks with laser beams coming from their eyes.

You would need a way to create proteins which either are covered in quantum wells, or which assist in the construction of a planar surface of quantum wells, with the required metallic traces to power the thing, in addition to cells designed to get the electricity needed to power it (forgoing the possibility of chemical or dye lasers for this example even though they might be easier.)  Then you would need new amino acids (think things like Selenocysteine which replaces a stop codon in some organisms to create an AA with a Cysteine-like structure replacing a Sulfur atom with a Selenium atom) to allow for the structure of the actual quantum wells.  At that point (assuming you've worked out the building blocks required to get the desired elements into side chains) you could seed the cell with the appropriate mRNA components and conceivably build it, but you still have the really big problem of going from "this is the structure I need" to "this is the DNA which codes for the protein which will fold into that structure, given the prerequisite materials."

I'm trying to build an IDE which lets you use abstract concepts ("replicate N times, differentiate into these cell types, take on this superstructure, etc") to compile DNA, ultimately to compile complete chromosomes and organisms.  Awhile back I was trying to tackle this from the standpoint of semantic search type methodologies against DNA as a whole, but after learning a bit more about the structure of DNA and the way it functions within an organism it seems the only thing really missing (aside from likely lots of computing power to compile anything) is the ability to go from a desired structure to the DNA which codes for that structure, everything else is either already built (e.g. DNA printers) or a relatively straightforward adaptation of computing (e.g. the abstractions involved, creating a system of compatible docking sites without overlap, etc.)


On Wednesday, November 22, 2017 at 10:22:55 AM UTC-5, Bryan Jones wrote:
Cory, I'm not sure if I completely follow your logic, but it sounds like you might be describing something like Rosetta, which can be used to design proteins from scratch based upon a given fold/topology or desired active site. It's far from perfect but keeps getting better. There are lots of people working on it, but the Rosetta project is spearheaded by David Baker at the University of Washington. I'm not sure if it is open source, but it is at least free to use for personal or non-profit uses.
You can check it out here: https://www.rosettacommons.org/software
Here's one recent paper that used Rosetta to design a new TIM barrel protein:

On Wed, Nov 22, 2017 at 3:11 AM Cory J. Geesaman <co...@geesaman.com> wrote:
So this might seem outright insane given the computational requirements of protein folding, but I had a though I'm not able to locate any existing resources on, but could be the basis for an actual biotech boom (i.e. not just copying and pasting stuff, but creating things.)

The concept would be, to start: take a desired topology, stick it in the computer, have the computer generate a matching docking profile, then run a sort of protein unfolding algorithm to generate a best fitting protein for that docking profile.  Eventually add in things like active sites, inhibition sites, any special functionality (e.g. what part of the protein should flex when something is docked in some arbitrary site, which direction should it flex, should it just change shape, or open another site for access to some thing to dock in it, or eject something from another site, etc.)

I figure starting with the topology --> docking site --> protein --> DNA piece would be a really good start and would likely be pretty useful, but then adding in the other stuff would be the basis for a code --> DNA compiler (or one of the smaller units of a really powerful biological IDE which could let you build complete systems from proteins on up through organs and transmitters and such.)

Any thoughts on this welcome (especially if some or all of this already exists in an open source manner I can hack on.)  Decided to heat my house this winter by running Folding@home but the curecoins generated are still $3/day in the hole for electricity so I might as well play with other computationally intensive genomics.

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