# Finally Got This New Toy!



## xkm1948 (Aug 4, 2017)

What you are seeing here is called Oxford MinION Nanopore Next Generation DNA Sequencing Machine. To put it simply, get a few piece of your cheek swap cells and extract genomic DNA, put it into this thing. Within 24 hrs I will be able to tell your entire genetic secrets----like your ancestry, your genetic mutations, possible chance of getting cancer, immune system strength and even predict your life span.  


Pretty insane that within that last 10 yrs of biotechnology we went from this






To this size:






The sequencing machine by itself doesn't have have computation power. So it HAS to rely on some extremely powerful PC to handle the real time data generation. From the manufacture they highly recommend a large SSD specifically for data processing.

For people interested in Nanopore technology here is a short description video






















So yeah, maybe in a few months (if everything goes well) I may actually purchasing my own private MinION for actual "business" work.  TPU members get discount for submitting their DNA sample, ya know, FOR SCIENCE!


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## Nuckles56 (Aug 4, 2017)

That was really interesting, thanks for sharing that @xkm1948


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## notb (Aug 4, 2017)

How precise is this? Is it certificated for medical / forensic usage?

BTW: how much does it cost per measurement? I mean: the reagents, the replaceable parts etc.


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## XiGMAKiD (Aug 4, 2017)

That reminds me of comparison about going from getting 1TFlops of x86 compute power from this





to this


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## Vayra86 (Aug 4, 2017)

Having watched a few seasons of Orphan Black I gotta say this tickled me ALOT.

Want this for Christmas. Thanks for sharing this man


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## FreedomEclipse (Aug 4, 2017)

I thought it was a new mouse made by corsair for a second


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## R00kie (Aug 4, 2017)

Heh, poor Jeremy Kyle is gonna be losing his audience


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## Frick (Aug 4, 2017)

I don't think I want you to have my DNA. You'd just do something to it.


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## xkm1948 (Aug 4, 2017)

notb said:


> How precise is this? Is it certificated for medical / forensic usage?
> 
> BTW: how much does it cost per measurement? I mean: the reagents, the replaceable parts etc.



The quality of reads has improved drastically over the past 2 yrs. It is way overkill for regular medical or criminal investigation usage. This is more for scientific research, which requires even higher precision than commercial/civilian usage.

Reagents wise I am not sure. Haven't exhausted the first batch of free stuff yet.   




Vayra86 said:


> Having watched a few seasons of Orphan Black I gotta say this tickled me ALOT.
> 
> Want this for Christmas. Thanks for sharing this man



Yeah for Christmas! Then would probably want a RyZen Thread-ripper and a molecular biology PhD student to decipher all the data for you. 




Frick said:


> I don't think I want you to have my DNA. You'd just do something to it.



People will start to get a lot paranoid in the future. In lab we have used as little as 0.5mg of skin tissue to get both genomic DNA and mitochondrian DNA from the donor. It is kinda scary that some stranger may bump into you and a day later your entire DNA information is no longer private.  I imagine there will be more regulations in the future. Some agiculture giants, like Monsanto, has already begun encrypting their GMO crops with protection bar codes. As soon as a DNA sequencer read those bar codes during sequencing the process will be halted and the sequencer will tell you that patent genes are being sequenced.


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## qubit (Aug 4, 2017)

Cool, so apply gadget, get inhuman powers!


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## blobster21 (Aug 4, 2017)

How much is it ?


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## xkm1948 (Aug 4, 2017)

blobster21 said:


> How much is it ?



Emm, I cannot disclose this information. It is confidential.  Same as a lot of other lab equipments.

But I can guarantee you this is NOT paid by tax payers' money


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## Papahyooie (Aug 4, 2017)

Really cool gadget. One question I have, which you may be able to give an unbiased answer, being a student of the science: 

I hear really conflicting information about DNA sequencing. On the one hand, I hear that the human genome is only like... 1% mapped. Like we only know what 1% of our genetic code actually *does.* (I'm just making up the 1% number as an example... point is, I hear it's a very small amount that we do know.) 

On the other hand, I also hear things like this that make it sound like we can predict every single detail about a person and their history. As if we intimately know the encoded data in the humane genome. When I hear claims like this from businesses like ancestry.com and all those, it makes me think it's snake oil. 

And yet you, as a real molecular biology scientist, say we can find out several things from this, so that makes me a little more optimistic. 

So, if you've got the time and wouldn't mind sharing some knowledge, what's the 10k meter view on the status of DNA science? Are we closer to unlocking the secrets of the human genome and DNA in general? Or is it more of a vast sea of potential, which we are only beginning to scratch the surface of? And what of the claims of companies like ancestry.com that can claim to know your descent, history, racial makeup, etc? I assume it's pretty much settled science if you are planning on starting a business. (Unless of course you're a wily conman. If that's the case, carry on lol. )


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## Divide Overflow (Aug 4, 2017)

Fascinating stuff, thanks for sharing!  The tester is amazing, but what really interests me is the analytics that can be run on the data it produces.  Are there openly available reports you can run your sample against or do you have to have that team of molecular biologists on hand to analyze the information and give you meaningful results?


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## JalleR (Aug 4, 2017)

blobster21 said:


> How much is it ?



It says on the hp that a start pack is 1000$, so less top of the line gaming stuff   and you get a membership aswell...


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## Frick (Aug 4, 2017)

xkm1948 said:


> People will start to get a lot paranoid in the future. In lab we have used as little as 0.5mg of skin tissue to get both genomic DNA and mitochondrian DNA from the donor. It is kinda scary that some stranger may bump into you and a day later your entire DNA information is no longer private.  I imagine there will be more regulations in the future. Some agiculture giants, like Monsanto, has already begun encrypting their GMO crops with protection bar codes. As soon as a DNA sequencer read those bar codes during sequencing the process will be halted and the sequencer will tell you that patent genes are being sequenced.



And it's Gattaga IRL, where we trade urin and hair with each other. This combined with metadata and machine learning/good ol' statistics things will get really interesting.


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## Chaitanya (Aug 4, 2017)

Is this the same sequencer used by NASA at ISS? I do remember watching a tiny DNA sequencer with regards to ISS in this video:


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## the54thvoid (Aug 4, 2017)

Papahyooie said:


> Really cool gadget. One question I have, which you may be able to give an unbiased answer, being a student of the science:
> 
> I hear really conflicting information about DNA sequencing...... your descent, history, racial makeup, etc?



I'm not @xkm1948 but I do believe that such characteristics as race and ethnicity are quite readily mapped in the DNA.  It can be used to age things as well, given what we an extact from archaeological evidence (https://phys.org/news/2017-04-dna-extinct-humans-cave-sediments.html).  Evolutionary studies are massively advanced by DNA science.

Your DNA cannot predict what you will become though it may predict your likelihood of certain traits.


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## xkm1948 (Aug 4, 2017)

I can ramble on for a whole day regarding the human genome research progress, so here is my super short version.

1. We have sequences of >95% of all chromosomes. That is just  the ATCG sequences. And each and every cell of yours have 3 billion of those base-pairs.
2. About 1% of those sequences codes for protein, which goes on to make your hair, your eye, your muscle and etc.
3. About 10%~50% of those sequences codes for RNA that DO NOT code protein, they serve as regulators of protein coding sequences.
4, The rest of the sequences servers as structural regulation of your genome,

Contrary to previous "popular news media" claim that most of human DNA are junk, almost ALL human genomic DNA have functionality. For example the field I am studying is epigenetics, which links environmental factors to impact on gene expression.

And it may sounds crazy, but current computational power is still far from good enough to decipher those genomic data along with their complex multilayer interactions.

As for how much can be obtained from current molecular biology technology, pretty much we can already play god. All that scientists need is a few cell from someone, we can map out the genome(DNA), transcriptome(mRNA) and proteome(protein). With those information we can quickly predict say life span expectancy, metabolic state and etc.

A lot of crazy science is already good to go from labs, it may not be ready for commercialized that is all.




the54thvoid said:


> I'm not @xkm1948 but I do believe that such characteristics as race and ethnicity are quite readily mapped in the DNA.  It can be used to age things as well, given what we an extact from archaeological evidence (https://phys.org/news/2017-04-dna-extinct-humans-cave-sediments.html).  Evolutionary studies are massively advanced by DNA science.
> 
> Your DNA cannot predict what you will become though it may predict your likelihood of certain traits.



Actually you can. Each and every single person's neural network fundamentally is built upon the codes burried in the genome. There are already studies teasing apart the correlation of how gene expression can relate to human neural network patterns. That is how to get different personality types.

Everything boils down to the wonder of ATCG(and also modified version of those nucleotides).


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## Papahyooie (Aug 4, 2017)

xkm1948 said:


> I can ramble on for a whole day regarding the human genome research progress, so here is my super short version.
> 
> 1. We have sequences of >95% of all chromosomes. That is just  the ATCG sequences. And each and every cell of yours have 3 billion of those base-pairs.
> 2. About 1% of those sequences codes for protein, which goes on to make your hair, your eye, your muscle and etc.
> ...



That's actually great to hear. There are a lot of naysayers out there who claim that genetic science is still far behind what it claims to be. It also makes perfect sense that we don't have the computational power available, since there are several distributed computing platforms for such research. (Folding, human genome project, etc.) It makes me curious, are those folding/crunching projects making any significant impact on the field, that you know of? I've been told that the medical research side (cancer, ALS, etc) have made great strides in computational power due to these projects, so I'm curious as to whether it has the same effect on your field. 

I heard the other day that molecular biologists had successfully eradicated the gene sequence that causes hypertrophic cardiomyopathy in human embryos for the first time. I am excited for this news, even if it is just a proof of concept, because it means it is indeed possible. My goddaughter has a heretofore unknown genetic mutation. It manifests much like Down's syndrome, but the specific mutation is the first that has ever been recorded in the world. She is constantly being taken in for tests and research. The idea that one day we might be able to completely eradicate such complications from the human race is extremely exciting. So all that to say, thank you for your work! I don't imagine your specific field has much to do with her, but it's all research and all those fields tie in together to effect each other. Your work may very well contribute somehow to that goal, so thank you for what you do!


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## xkm1948 (Aug 4, 2017)

Molecular genetic has advanced quite a lot thanks to the improvment of semiconductor industry. HPCs helped a whole lot for data analyze. As a matter of fact we are generating more data for trained scientists to analyze. We just don't have enough computation power and good PhD brains to properly analyze the generated data.

Another exciting new field is programmable endonuclease, or in other words: precision genome editing(CRISPR). So we not only knows what is inside human genome through sequencing, we can also precision editing genomic sequence for live cells.  

For most people those scientific research will translate to better life in the future. For some people it means huge potential to make more money. As for us scientists, it is simply because doing cutting edge research feels awesome.


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## Norton (Aug 4, 2017)

xkm1948 said:


> _*We just don't have enough computation power*_ and good PhD brains to properly analyze the generated data.


That's why a lot of us crunch and fold- distributed computing like World Community Grid and Folding@Home contributes to a lot of important research


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## xkm1948 (Aug 4, 2017)

Norton said:


> That's why a lot of us crunch and fold- distributed computing like World Community Grid and Folding@Home contributes to a lot of important research



At one time I thought about harnessing the awesome computation power of TPU community for my research. Then my higher ups informed me that there would be tons of problem when I try to publish the data generated from those source, So project canceled.  Legal issues always holds back science.


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## Solaris17 (Aug 4, 2017)

xkm1948 said:


> I can ramble on for a whole day regarding the human genome research progress, so here is my super short version.
> 
> 1. We have sequences of >95% of all chromosomes. That is just  the ATCG sequences. And each and every cell of yours have 3 billion of those base-pairs.
> 2. About 1% of those sequences codes for protein, which goes on to make your hair, your eye, your muscle and etc.
> ...



Thank you for taking the time to write this.


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## natr0n (Aug 4, 2017)

Who needs doctors when you have this, blood pressure machines,digital scales and blood glucose testers.

Diets are just a click away as well.


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## Papahyooie (Aug 4, 2017)

xkm1948 said:


> At one time I thought about harnessing the awesome computation power of TPU community for my research. Then my higher ups informed me that there would be tons of problem when I try to publish the data generated from those source, So project canceled.  Legal issues always holds back science.



That's a bummer. I guess all the established folding/crunching systems get passed that because they have already established and proven means of validating the information gained from the distributed computing, huh?

Edit: Though, if you ever got a project approved for crunching on WCG be sure to let us know so we can all make sure to join the project lol


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## notb (Aug 4, 2017)

xkm1948 said:


> The quality of reads has improved drastically over the past 2 yrs. It is way overkill for regular medical or criminal investigation usage. This is more for scientific research, which requires even higher precision than commercial/civilian usage.


What I meant is: you've mentioned "business work", so I thought that maybe you're hoping to turn this into a (side-)job.
If so, I'd think that working for a medical company or as a forensic expert would be the best idea. But I'm pretty sure a sequencer would have to be certificated for that.

For scientific work - sure, here only the measurement precision matters.


> Reagents wise I am not sure. Haven't exhausted the first batch of free stuff yet.


I've checked their website and it seems OK. I'd say that reagents are the cheap part, because you have to replace the flow cell from time to time (how often, though?).
The wash kit for the flow cell is $190 and they say it's enough for 12 procedures - that looks fairly OK.

Experiments aren't cheap, as most people that had some exposure know very well. This is far from the more expensive stuff that I've ruined during student labs...



Norton said:


> That's why a lot of us crunch and fold- distributed computing like World Community Grid and Folding@Home contributes to a lot of important research


This isn't very accurate, to be honest. Distributed computation platforms have way more PR / education significance than actual scientific importance.

If you want to contribute to important research, get a job at a research facility. And if you can't do anything useful to science, you could simply donate the thousands USD that you've spent on your WCG rigs to one - they'll buy their own computers, flasks, pencils... whatever.[/QUOTE][/QUOTE]


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## Norton (Aug 4, 2017)

notb said:


> This isn't very accurate, to be honest. Distributed computation platforms have way more PR / education significance than actual scientific importance.
> 
> If you want to contribute to important research, get a job at a research facility. And if you can't do anything useful to science, you could simply donate the thousands USD that you've spent on your WCG rigs to one - they'll buy their own computers, flasks, pencils... whatever


Our hardware/Our decision on the _value_ and _usefulness_ of what we do. You donate the way you want to and we'll do the same- OK?

Additional discussion of this subject is off topic of the OP- stay on topic please


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## notb (Aug 4, 2017)

Norton said:


> Our hardware/Our decision on the _value_ and _usefulness_ of what we do. You donate the way you want to and we'll do the same- OK?


This is a very anti-scientific approach in a fundamentally scientific thread, i.e. it's your choice to believe in what you want to believe.

I could argument on how pointless WCG is and how easy it is to access a 1 PF computer for scientific purposes in 2017 - more or less what WCG offers.
I don't. I merely mention that what you've said (that WCG "contributes to a lot of important research") is not true.


> Additional discussion of this subject is off topic of the OP- stay on topic please


Because you don't agree? Like the moderator that removed my posts (in my topic) because he didn't care about the question asked?
*You're the one that mentioned WCG first.*


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## xkm1948 (Aug 4, 2017)

Relax folks. Science should be fun and exciting. As Norton has said, the contribution from gaming rig towards massive proteomic studies has been tremendous. Besdies, not everyone is willing to say donate their tissue sample for research.  

I for one wouldn't mind having samples donate to me from TPU members. The more the merrier. They will definitely be put to good use.


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## R-T-B (Oct 10, 2017)

xkm1948 said:


> Relax folks. Science should be fun and exciting. As Norton has said, the contribution from gaming rig towards massive proteomic studies has been tremendous.



Yeah, I'll defer to you as being the one "in the know" on that, moreso than most here.


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## StrayKAT (Oct 10, 2017)

Very cool. Although I expect no surprises from my DNA readout. I think people with a lot of immigration history probably have the most interesting results (I'm not one of them).


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