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Introduction to Genomics for Engineers

learngenomics.dev

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Re: Introduction to Genomics for Engineers

#61

Post by tetris11 »

firstplacelast wrote: post #8
tetris11 wrote: post #5

Earlier quoted context omitted.

Thats why you stay though, the people are interesting and the work is meaningful and you directly see the fruits of your labors whilst contributing to a codebase that is by default open source.

People aren’t anymore interesting than anywhere else. Work is no more meaningful than anywhere else. It’s a big “selling point” for the industry, but it’s just a way to get people to get paid less (yay you’re making the world better than all those garbage people serving coffee or healing sick people or keeping your lights on or optimizing the routes of the goods you have delivered). If you want sustainable systems, t…

On I assumed we were talking about being a software eng in academia. It's a spiritually rewarding experience, with none of the blackholes you've described at pharma

Re: Introduction to Genomics for Engineers

#62

Post by ackbar03 »

glofish wrote: post #40
conradev wrote: post #23

Earlier quoted context omitted.

If you want some personal motivation to get into genomics, you can get your whole genome sequenced for a few hundred bucks and play around with the raw files yourself. I used Dante Labs[1] and they are great. You can even ask them to delete your data and samples! [1] – https://dantelabs.com/

and you will learn almost nothing from sequencing and studying your own genome at best you waste your time, at worst you will find all kinds of things that are not there it is the Silicon Valley hacker mentality that thinks the life is some sort of computer where you can fiddle with parameters learn some biology first, then you can marvel at it and realize just how absurdly simplistic is to think you can read anythin…

> and you will learn almost nothing from sequencing and studying your own genome

But Dante labs sure will!

Re: Introduction to Genomics for Engineers

#63

Post by Ultimatt »

glofish wrote: post #32

Those looking for a proper and comprehensive introduction into genomics from a programmer's perspective should try the Biostar Handbook: https://www.biostarhandbook.com/ I have learned so much from it. It is an introduction into what is like to do genomics in a scientific environment. The content at the link the OP posted appears to be an oversimplified, high level and naive overview

The opening paragraph of this resource states its absolutely not about being a comprehensive introduction to genomics. I strongly disagree with the sentiment its naive or oversimplified. It's trying to give someone with no knowledge a working mental model to begin to dig into building a comprehensive view. A framework of analogy for many people is an extremely helpful device for learning, frequently left out by comprehensive scientific or engineering texts.

Re: Introduction to Genomics for Engineers

#64

Post by Ultimatt »

gravelc wrote: post #43

Don't want to be too disparaging, but this to me doesn't seem to be an 'Introduction to Genomics', but more an introduction to read mapping and variant detection in human (or more broadly diploid) genomes. Genomics stretches vastly beyond this - assembly and annotation to start with. I'd argue the most interesting problem space for software engineers is outside of what is covered in the document.

The space of startups cashing in on genomics but making shiny web apps that software engineers need to understand something about human diploid genetic variation is far higher though. Thats where the money and engineers are, not in fundamental algo development for slimemould assembly.

Re: Introduction to Genomics for Engineers

#65

Post by nosianu »

glofish wrote: post #32

Those looking for a proper and comprehensive introduction into genomics from a programmer's perspective should try the Biostar Handbook: https://www.biostarhandbook.com/ I have learned so much from it. It is an introduction into what is like to do genomics in a scientific environment. The content at the link the OP posted appears to be an oversimplified, high level and naive overview

Actually, I would throw this into the ring instead:

https://www.edx.org/course/introduction-to-biology-the-secre...

by Professor Eric Lander

> Introduction to Biology - The Secret of Life

> Explore the secret of life through the basics of biochemistry, genetics, molecular biology, recombinant DNA, genomics and rational medicine.

It's really well done and genomics is the focus. I took many dozens of edX and Coursra courses over the years, this is one of the top 5% of the courses there I would say.

I don't understand the phrase "from a programmer's perspective", or "for Engineers" in the title on top.

As a programmer whos studied CS but also took numerous life science courses throughout my life. You want to learn biology you study biology, what does a "programmer's view", or an engineer's, have to do with it? You use the correct tool for the job, and having a background in both, I don't see this working out well, more like the opposite actually.

The point of looking at biology for an engineer or programmer should be to broaden ones horizons, not to use ones internal models build for a completely different field in another one that really is not like that at all. IMO it's best to forget all computer metaphors here.

----

By the way, since there was something about this yesterday, there also is this course: https://www.edx.org/course/principles-of-biochemistry - it too is very good. A good knowledge of organic chemistry is a prerequisite, but there are plenty of equally interesting course resources for that available too, including even Khan Academy (https://www.khanacademy.org/science/organic-chemistry), or to give a(nother) random link, https://ocw.mit.edu/courses/5-12-organic-chemistry-i-spring-...

Biology becomes a lot more fun with this foundation already established in ones head.

Re: Introduction to Genomics for Engineers

#66

Post by dekhn »

tombakt wrote: post #41
mtlmtlmtlmtl wrote: post #27

Earlier quoted context omitted.

The thing I'm most excited about long term is biocomputing. Having Turing complete programmatic control over biological systems has an absolutely endless list of transformative applications. Imagine being able to program bacteria that can "infect" the patient and attack tumor cells, or act as fodder to keep autoimmune disease in check. Or let's say we could program stem cells into "liver repair mode" to go and differ…

Sounds great until natural selection kicks in, and because DNA replication is largely a lossy process, suddenly the thing you programmed the organism to do mutates to do something else a whole lot more problematic. Imagine a software heisenbug, but instead it's a life form that you can't kill -9. The idea of tailor-made medicines in a vat is awesome, but as far as creating a bacteria to "specially target" certain cel…

Polymerase without error correct has error rate of 10**-6. With error correct it's 10**-9 to 10**-12.

Re: Introduction to Genomics for Engineers

#67

Post by mtlmtlmtlmtl »

dekhn wrote: post #66
tombakt wrote: post #41

Earlier quoted context omitted.

Sounds great until natural selection kicks in, and because DNA replication is largely a lossy process, suddenly the thing you programmed the organism to do mutates to do something else a whole lot more problematic. Imagine a software heisenbug, but instead it's a life form that you can't kill -9. The idea of tailor-made medicines in a vat is awesome, but as far as creating a bacteria to "specially target" certain cel…

Polymerase without error correct has error rate of 10**-6. With error correct it's 10**-9 to 10**-12.

Considering the current treatment in the worst cases(where more targeted treatments don't exist) is to blast the pasient with radiation and poison(chemotherapy) and hope it doesn't kill them, I'll take those odds.

Re: Introduction to Genomics for Engineers

#68

Post by DrScientist »

mtlmtlmtlmtl wrote: post #67
dekhn wrote: post #66

Earlier quoted context omitted.

Polymerase without error correct has error rate of 10**-6. With error correct it's 10**-9 to 10**-12.

Considering the current treatment in the worst cases(where more targeted treatments don't exist) is to blast the pasient with radiation and poison(chemotherapy) and hope it doesn't kill them, I'll take those odds.

Except a rogue bacteria won't just kill you, it could escape beyond you and kill millions.

Chemo/radiation only kills the patients it was given to ( not entirely true - if the treatment caused mutations in the germline and the patient subsequently had children, the effects of the treatment might be passed on - but still very limited ).

Re: Introduction to Genomics for Engineers

#69

Post by mtlmtlmtlmtl »

DrScientist wrote: post #68
mtlmtlmtlmtl wrote: post #67

Earlier quoted context omitted.

Considering the current treatment in the worst cases(where more targeted treatments don't exist) is to blast the pasient with radiation and poison(chemotherapy) and hope it doesn't kill them, I'll take those odds.

Except a rogue bacteria won't just kill you, it could escape beyond you and kill millions. Chemo/radiation only kills the patients it was given to ( not entirely true - if the treatment caused mutations in the germline and the patient subsequently had children, the effects of the treatment might be passed on - but still very limited ).

Bacterial infections are generally very treatable though. Even when the bacteria aren't engineered. And especially when they are, because why would you leave any antibiotic resistance in an engineered bacterium?

Bacteria are the scariest when they've had the time to develop resistance to multiple different antibiotics.

Additionally, a bacterium that's engineered to be almost completely harmless evolving into a deadly strain in vivo is fairy unlikely in itself, especially if transcriptional errors can be reduced several orders of magnitude like GGP suggested.

Adding to that the option of hospitalisation or even home isolation to reduce risk of transmission, the risk of this resulting in some huge lethal epidemic must be pretty miniscule.

Re: Introduction to Genomics for Engineers

#70

Post by jghn »

agumonkey wrote: post #21
dddiaz1 wrote: post #17

I have absolutely loved working in genomics. I am a huge believer that genomics will be a huge part of healthcare in the future, and i have two examples to motivate that point that I think may be interesting to the reader. 1) The Moderna vaccine was made with the help of illumina genome sequencing. They were able to sequence the virus and send that sequence of nucleotides over to moderna for them to develop the vacci…

what kind of math/cs/algorithmic skills do you think one should work on to get a job in this kind of company ?

There are two main flavors of jobs. For one you’ll want to be a phd in something like physics or math. For the other Amy standard software engineering background will do.
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