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Introduction to Genomics for Engineers

learngenomics.dev

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Re: Introduction to Genomics for Engineers

#21

Post by agumonkey »

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 ?

Re: Introduction to Genomics for Engineers

#22

Post by mbreese »

bsder wrote: post #11
civilized wrote: post #2

Really glad to see this, but it reminds me of the earlier HN post that said engineers don't go into genomics because it doesn't pay and requires a lot of investment in learning biology.

The reason why San Diego has such a craft brew scene is that it has a lot of underpaid microbiologists.

The people studying yeast metabolism in grad school were always the ones with the best beer (especially the ones that created mutant strains). I think the two might be related.

Re: Introduction to Genomics for Engineers

#23

Post by conradev »

civilized wrote: post #2

Really glad to see this, but it reminds me of the earlier HN post that said engineers don't go into genomics because it doesn't pay and requires a lot of investment in learning biology.

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/

Re: Introduction to Genomics for Engineers

#24

Post by dekhn »

mbreese wrote: post #22
bsder wrote: post #11

Earlier quoted context omitted.

The reason why San Diego has such a craft brew scene is that it has a lot of underpaid microbiologists.

The people studying yeast metabolism in grad school were always the ones with the best beer (especially the ones that created mutant strains). I think the two might be related.

One of my gateways into Making was during grad school when my housemate brewed beer. He wanted to make a counterflow wort chiller, went to Home Depot, bought some parts, assembled the whole thing, and it worked perfectly. I was completely blown away you could make "scientific" apparatus from Home Depot. And immensely jealous.

Re: Introduction to Genomics for Engineers

#25

Post by feet »

chairhairair wrote: post #15
yuppiepuppie wrote: post #12

Genomics is where I started learning how to program. Having worked as bench scientist in a genetics lab I understood nothing about my lab mates research when they were showing me python scripts of their analysis. Which initially got me curious. Now having been in the in the industry developing apis for large companies for the past 8 years, I’d be keen to get back into it. Any ideas where to start or find jobs in the…

I have a similar story with chemistry. I’d also like to get back into the sciences, but I’m not sure how relevant programmers are.

Very relevant and becoming moreso. Check out job postings at research institutes and universities with healthy research departments

Re: Introduction to Genomics for Engineers

#26

Post by janeway »

penciltwirler wrote: post #4

Nicee, but I feel like really the only thing you need to know as an eng is DNA -> RNA -> Protein. Sometimes RNA -> DNA via reverse transcriptase. Everything else is just normal Python scripting.

Oh no. A major flaw that kills protects; to run a valid statistical test you need to understand the underlying reality of the data. Otherwise you just run tests until you find “something”.

How do you handle one genomic variant affecting dozens of different rna transcripts and isoforms? How do you handle tissue-specific expression? LD haplotype blocks? Frequency across populations and reference choice? Sample handling affecting read depth? Mixed direction of effects in phenotype-genotype? The critical (and beauty IMO) feature of bioinfo is requiring an understanding of how your dataset can rarely be considered clean and as simple as _observation name_ and _observation value_. To succeed it is usually critical to know a lot about the observation meta data which is not collected in the dataset. Hopefully in the future it will be better curated and less esoteric.

Re: Introduction to Genomics for Engineers

#27

Post by mtlmtlmtlmtl »

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…

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 differentiate into new liver cells.

Then the implications for things like drug synthesis with the ability to programmatically control enzyme levels to compile more or less arbitrary biosynthetic pathways into fast growing photosynthetic algea, turning CO2, water and sunlight into medicine.

It's still a long way off being at that level of applicability, but man oh man it's gonna change everything.

Re: Introduction to Genomics for Engineers

#28

Post by supahfly_remix »

dekhn wrote: post #24
mbreese wrote: post #22

Earlier quoted context omitted.

The people studying yeast metabolism in grad school were always the ones with the best beer (especially the ones that created mutant strains). I think the two might be related.

One of my gateways into Making was during grad school when my housemate brewed beer. He wanted to make a counterflow wort chiller, went to Home Depot, bought some parts, assembled the whole thing, and it worked perfectly. I was completely blown away you could make "scientific" apparatus from Home Depot. And immensely jealous.

What kind of materials are food grade there? Sound like a fun project

Re: Introduction to Genomics for Engineers

#29

Post by pgayed »

ALittleLight wrote: post #20

I didn't get this from skimming the first page - but what will this let me do? If I take this course will I be able to mess with a cell or will I just learn some stuff about biology. I saw a recent Lex Friedman podcast where the guest talks about "bioelectric patterns" and somehow getting a worm to grow a second head by messing with those patterns. I would absolutely start on this course now if it was a realistic pat…

This is the worst outcome of regulation of the life sciences.

There is no REPL for the cell. No tinkering allowed.

When Marvin Minsky was growing up in New York, neighborhood pharmacists owned fluoroscopes. He said those fluoroscopes were like “great black boxes” to him and that “those kinds of black boxes don't exist for kids anymore.”

Re: Introduction to Genomics for Engineers

#30

Post by wheresmycraisin »

civilized wrote: post #2

Really glad to see this, but it reminds me of the earlier HN post that said engineers don't go into genomics because it doesn't pay and requires a lot of investment in learning biology.

You basically end up with the salary of a helpdesk person at a university.
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