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Consider working on genomics

claymcleod.dev

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Re: Consider working on genomics

#181

Post by rleigh »

harles wrote: post #162
bluejellybean wrote: post #153

Earlier quoted context omitted.

Molecular Biology of the Cell got me extremely excited about genetics and bioinformatics, highly, highly recommend this book to any software person I meet who is interested in biology. As to the work environment, it seems to be extremely varied depending on the lab and team your on. I came from a number of years doing web development in marketing and finance before joining an R1 university research lab, and in many w…

Any particular edition of Molecular Biology of the Cell you’d recommend? I just looked up the 7th edition on Amazon (seems like the latest) and it’s $300 USD. Oof.

I've still got my 3rd edition copy (from 1999 when I was an undergrad molecular biologist). Most of the basic biochemistry and molecular biology will be exactly the same--it hasn't changed much if at all. While there have been lots of additional details added over the last two decades, the fundamentals are unchanged for the most part.

This wouldn't apply to other fields such as Immunology (Janeway's Immunobiology) where I have purchased multiple copies of the years due to the field changing so fast.

Re: Consider working on genomics

#182

Post by jghn »

boppo1 wrote: post #174
maximus-decimus wrote: post #151

Earlier quoted context omitted.

The fact they renamed human genes because they were importing it in Excel in a way it thought they were dates and was changing them says a lot. Can you really trust the scientific results if they depend on software made by people who don't care about code quality?

>renamed human genes because they were importing it in Excel in a way it thought they were dates Just at your shop, or the field in general?

Field in general [1]

[1] https://www.theverge.com/2020/8/6/21355674/human-genes-renam...

Re: Consider working on genomics

#183

Post by somedudetbh »

harles wrote: post #162
bluejellybean wrote: post #153

Earlier quoted context omitted.

Molecular Biology of the Cell got me extremely excited about genetics and bioinformatics, highly, highly recommend this book to any software person I meet who is interested in biology. As to the work environment, it seems to be extremely varied depending on the lab and team your on. I came from a number of years doing web development in marketing and finance before joining an R1 university research lab, and in many w…

Any particular edition of Molecular Biology of the Cell you’d recommend? I just looked up the 7th edition on Amazon (seems like the latest) and it’s $300 USD. Oof.

Go on ebay and by the "international" edition

Re: Consider working on genomics

#185

Post by elric »

Would love to, both out of interest and out of a belief that it might one day improve the world. But it's not happening. I have 20+ years of experience as a software engineer, but I don't have a degree, so anything that has even a whiff of academia rejects me outright. Not to mention that it would involve a big paycut over fintech.

Re: Consider working on genomics

#186

Post by tonto »

the_only_law wrote: post #78
anonymous_bio wrote: post #36

The author completely neglects the downsides: - The compensation absolutely do not match the workload and education required. - The sheer number of disreputable PIs and their unrealistic goals for software. - The data is likely questionable and often underpowered. - Institutional politics. everywhere. - Marketing ("Curing Cancer"). The role is actually just juggling various bioinformatics file formats.

> The role is actually just juggling various bioinformatics file formats. I need an advanced degree for that?

it is a meme that bioinformatics is just about converting different file formats but it's a shallow take

Re: Consider working on genomics

#187

Post by tonto »

teekert wrote: post #168

I work in genomics, this is very true. I know of some modernization efforts, ie by companies working with new file formats, like GenomSys [0] with mpeg-genomics [1]. It feels like it’s going very slowly though. The field just really depends on their Unix philosophy tools, there is a lot of gzipped text files that are piped through bash scripts and tool like awk and grep. It works, mostly, but there is a lot of weirdn…

mpeg-g to me is probably bad for the field. sam/bam/cram is the way of the present and mpeg-g offers little over these formats and is patent encumbered. xref samtools developer blog http://datageekdom.blogspot.com/2018/09/mpeg-g-ugly.html?m=1

Re: Consider working on genomics

#188

Post by AlbertCory »

pclmulqdq wrote: post #143
clmcleod wrote: post #46

Earlier quoted context omitted.

> That said: a lot of the comments are spot on. You're working in a field where the hard scientists and business people rule and you're a helper This definitely was the culture when I started working in the field 6 years ago. However, the culture has shifted (at least where I work) to where biologists and engineers are equal partners that work together on solving these problems. For those organizations that are not t…

That may be the case for engineers with PhDs and scientific credentials, but I'm not so sure that is true of normal developers who did not play the academic game. I'm not going to take a job based on the eventuality of a culture shift, and I don't think you should either. This isn't just genomics, by the way. Scientific computing folks are very similar.

That's always been my impression, but it does sound like "software eats the world" has had some effect. At least in some places.

Looking at it from their point of view: CS people tend to think that "everything is just information, and now that we're here you're all going to be working for us."

You can see why a PhD in mol bio would resent that. Everything is not just information.

Re: Consider working on genomics

#189

Post by AlbertCory »

boppo1 wrote: post #72
AlbertCory wrote: post #27

20 years ago I got interested in "bioinformatics." I loved learning something about molecular biology, after all those years of hearing about DNA and not understanding it. And "Molecular Biology of the Cell" is, hands down, the greatest textbook ever written. That said: a lot of the comments are spot on. You're working in a field where the hard scientists and business people rule and you're a helper. Maybe they're gr…

>Molecular Biology of the Cell Tangential, but what are the chemistry prereqs to grasp this book?

I did get a book or two out of the library, plus I had Chem 101 in college, but really, not very much.

Re: Consider working on genomics

#190

Post by rleigh »

boppo1 wrote: post #174
maximus-decimus wrote: post #151

Earlier quoted context omitted.

The fact they renamed human genes because they were importing it in Excel in a way it thought they were dates and was changing them says a lot. Can you really trust the scientific results if they depend on software made by people who don't care about code quality?

>renamed human genes because they were importing it in Excel in a way it thought they were dates Just at your shop, or the field in general?

The whole field! This was actually a thing(!)
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