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Introduction to Genomics for Engineers

learngenomics.dev

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Re: Introduction to Genomics for Engineers

#51

Post by ArchD »

ramraj07 wrote: post #33

Starts with “ This Guide is written specifically by and for computer scientists and engineers” And yeah it shows - contrived example after another, and honestly not a great description of anything. If you want to truly understand genomics you have to understand how biology works. And honestly it’s great info for anyone even if you’re not getting into genomics or whatever.. why would you not want a working model of ho…

Do you have an example of a contrived example and explanation of why it is contrived, for the non-biologist to see why it is contrived?

I once tried reading a few chapters of a bioinformatics book explaining DNA, RNA, protein creation, etc. The basic idea seems very simple but to my mind they explained it non-systematically with too many words. There seems to be an internal information structure in these RNA- and DNA- related processes that was not being concisely presented and it seemed that if the writers presented the material in terms of computer-science concepts, so much time could be saved.

Re: Introduction to Genomics for Engineers

#52

Post by feet »

zelphirkalt wrote: post #38
feet wrote: post #25

Earlier quoted context omitted.

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

How does one know, whether they are healthy or not?

Generally if they are producing consistent, high quality research

Re: Introduction to Genomics for Engineers

#53

Post by noipv4 »

ArchD wrote: post #51
ramraj07 wrote: post #33

Starts with “ This Guide is written specifically by and for computer scientists and engineers” And yeah it shows - contrived example after another, and honestly not a great description of anything. If you want to truly understand genomics you have to understand how biology works. And honestly it’s great info for anyone even if you’re not getting into genomics or whatever.. why would you not want a working model of ho…

Do you have an example of a contrived example and explanation of why it is contrived, for the non-biologist to see why it is contrived? I once tried reading a few chapters of a bioinformatics book explaining DNA, RNA, protein creation, etc. The basic idea seems very simple but to my mind they explained it non-systematically with too many words. There seems to be an internal information structure in these RNA- and DNA…

e.g. https://learngenomics.dev/docs/next-generation-sequencing/ne...

There's nothing about sequencing by synthesis, how blocking nucleotides are added one after another, pictures of the fluorescent nucleotides on the flow cells are image analysed, etc.

This site looks like an ELI5 kind of treatment.

Re: Introduction to Genomics for Engineers

#54

Post by User23 »

ramraj07 wrote: post #33

Starts with “ This Guide is written specifically by and for computer scientists and engineers” And yeah it shows - contrived example after another, and honestly not a great description of anything. If you want to truly understand genomics you have to understand how biology works. And honestly it’s great info for anyone even if you’re not getting into genomics or whatever.. why would you not want a working model of ho…

H-bonds! It's totally h-bonds all the way down.

Amusingly that's literally like 80% true. Water is just a really big deal in biochem.

Re: Introduction to Genomics for Engineers

#56

Post by gravelc »

ArchD wrote: post #51
ramraj07 wrote: post #33

Starts with “ This Guide is written specifically by and for computer scientists and engineers” And yeah it shows - contrived example after another, and honestly not a great description of anything. If you want to truly understand genomics you have to understand how biology works. And honestly it’s great info for anyone even if you’re not getting into genomics or whatever.. why would you not want a working model of ho…

Do you have an example of a contrived example and explanation of why it is contrived, for the non-biologist to see why it is contrived? I once tried reading a few chapters of a bioinformatics book explaining DNA, RNA, protein creation, etc. The basic idea seems very simple but to my mind they explained it non-systematically with too many words. There seems to be an internal information structure in these RNA- and DNA…

You can't present it as computer science concepts because it's not computer science.

For example, the central dogma of DNA transcribed to RNA translated to protein seems simple, but it's not.

In almost every instance, there are vague 'rules' and many many exceptions to these rules. For example, often coding regions in genes start with an ATG, but sometimes they don't. Sometimes splice sites (where the non-coding parts of transcripts called introns are chopped out) can be predicted, but a portion of the transcripts are not spliced at predicted sites for no obvious reason. Sometimes the predictions are just wrong. Sometimes the generated proteins are modified at specific locations which impacts their function, but again, sometimes not. Even whether the gene itself is 'switched on' (i.e. able to be transcribed) is impacted by many many things, such as unidentified transcription factors, or whether the chromosomal location itself is accessible or not. There are many many other things that impact the process.

There is no simple underlying concept as the system is not designed, it evolved and is quite different among different organisms, and even in different tissues or timepoints in the same organism. As long as it works and provides enough benefit to avoid negative selection, that's enough.

It's a mess, which makes it interesting.

Re: Introduction to Genomics for Engineers

#57

Post by f6v »

lordofgibbons wrote: post #50

I find the field extremely interesting, but I wish the pay in genomics was better. Compared to fang/unicorn type companies, their pay is way below market and it's really hard to justify the massive pay cut.

> their pay is way below market

The pay is exactly where market is. There’re ton of wet-lab people wanting to get into “data”. And the industry is less lucrative than showing ads like Google does.

Re: Introduction to Genomics for Engineers

#58

Post by f6v »

ALittleLight wrote: post #42
dekhn wrote: post #39

Earlier quoted context omitted.

Many modern bio experiments are almost exactly a repl. You build a system and then repeatedly interrogate it inputing some data using a Read (IE, you pass in some DNA), which is then Eval'd by the cell (warning: there will be side effects), "printed" in the form of some signal like a fluoresence, and then you loop back to the beginning. This is often called "closed loop laboratory." Unfortunately, each step ends up b…

What is the minimum it would take to run such a REPL at home? What hardware, life form, and knowledge would you need, at a minimum, to start making changes and seeing results?

You’d need to build yourself a generic molecular biology lab. The investment is huge.

Re: Introduction to Genomics for Engineers

#59

Post by ramraj07 »

ArchD wrote: post #51
ramraj07 wrote: post #33

Starts with “ This Guide is written specifically by and for computer scientists and engineers” And yeah it shows - contrived example after another, and honestly not a great description of anything. If you want to truly understand genomics you have to understand how biology works. And honestly it’s great info for anyone even if you’re not getting into genomics or whatever.. why would you not want a working model of ho…

Do you have an example of a contrived example and explanation of why it is contrived, for the non-biologist to see why it is contrived? I once tried reading a few chapters of a bioinformatics book explaining DNA, RNA, protein creation, etc. The basic idea seems very simple but to my mind they explained it non-systematically with too many words. There seems to be an internal information structure in these RNA- and DNA…

It starts by defining a cell as a bakery. First of all, what exactly is more systematic in comparing a cell to a bakery? Other than the fact that both things produce crap the analogy has no real substance. And there are so many wrong facts in that one paragraph (many of our genes are present as more than two copies in our genome, for one).

You are absolutely correct, there’s an information theoretical underpinning of genomics and systems biology that’s rarely if ever tackled in text books but (a) neither does this course tackle it, and (b) you can’t just skip on biochem basics and Jump to that. That’s like trying to become a physicist without learning math.

Re: Introduction to Genomics for Engineers

#60

Post by nextos »

f6v wrote: post #57
lordofgibbons wrote: post #50

I find the field extremely interesting, but I wish the pay in genomics was better. Compared to fang/unicorn type companies, their pay is way below market and it's really hard to justify the massive pay cut.

> their pay is way below market The pay is exactly where market is. There’re ton of wet-lab people wanting to get into “data”. And the industry is less lucrative than showing ads like Google does.

I think Calico (Alphabet) pay is not too far from a SWE at Google. However, this requires a PhD and much more experience.
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