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A farewell to bioinformatics (2012)

madhadron.com

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Re: A farewell to bioinformatics (2012)

#11

Post by chewxy »

Spelling error: 'technically apt', not 'ept'.

"Ept" means effective. As in "inept"

I don't understand this part:

> No one seems to have pointed out that this makes your database a reflection of your database, not a reflection of reality. Pull out an annotation in GenBank today and it’s not very long odds that it’s completely wrong.

In fact this entire article seems to be a rant on why bioinformatics as a field is rotting. But instead of ranting, surely something can be done about it?

Shouldn't we as hackers see this as an opportunity to revolutionize the field?

Re: A farewell to bioinformatics (2012)

#12

Post by singingfish »

jmspring wrote: post #8

Sounds like a fed up academic with a stick up his backside. Sh*tty data? Comes from the community. If the data and algorithms are so poor, and the author so superior, he should have been able to improve the circumstances. This whole screed reads like an entitled individual who entered a profession, didn't get the glory, oh and yeah, academia doesn't pay well. In the realm of bioinformatics, lets ignore the work done…

Depends. Subtle corruption of institutional research processes is unfortunately far too common. It means that there's nice low hanging fruit if you know where to look and have access to funding. But that, especially the latter is a tall ask in almost every field.

Re: A farewell to bioinformatics (2012)

#13

Post by dmak »

chewxy wrote: post #11

Spelling error: 'technically apt', not 'ept'. "Ept" means effective. As in "inept" I don't understand this part: > No one seems to have pointed out that this makes your database a reflection of your database, not a reflection of reality. Pull out an annotation in GenBank today and it’s not very long odds that it’s completely wrong. In fact this entire article seems to be a rant on why bioinformatics as a field is rot…

It all begins with a rant.

Re: A farewell to bioinformatics (2012)

#14

Post by dmak »

jmspring wrote: post #8

Sounds like a fed up academic with a stick up his backside. Sh*tty data? Comes from the community. If the data and algorithms are so poor, and the author so superior, he should have been able to improve the circumstances. This whole screed reads like an entitled individual who entered a profession, didn't get the glory, oh and yeah, academia doesn't pay well. In the realm of bioinformatics, lets ignore the work done…

Perhaps the algorithms aren't within his grasps. They could very well be paying for an out-of-the-box solution.

Re: A farewell to bioinformatics (2012)

#15

Post by singingfish »

Also, yes molecular biologists with few exceptions know little more than fuck all about ecology. Hence the mostly gung-ho attitudes to GM of crop foods for example. Honestly. I've done real molecular biology work (simple commercial protein chemistry and molecular phylogenetics of mitochondrial DNA) and tried to start a PhD in ecology (failed due to funding issues and realising it was a dead end job wise).

Re: A farewell to bioinformatics (2012)

#16

Post by BioGeek »

adambratt wrote: post #4

Really makes me want to learn more about molecular biology. Any solid factual resources besides the references mentioned in this justified rant?

Biostars.org is a stackexchange-like site for bioinformaticians.

See there for answers to your question, eg:

* Best resources to learn molecular biology for a computer scientist. [1]

* What are the best bioinformatics course materials and videos (available online)? [2]

[1] http://www.biostars.org/p/3066/

[2] http://www.biostars.org/p/10766/

Re: A farewell to bioinformatics (2012)

#17

Post by gwern »

christiangenco wrote: post #7
aheilbut wrote: post #3

Earlier quoted context omitted.

Everyone is jumping on that, but (while I had to look it up too) 'ept' actually is a real word: from the OED: ept, adj. Pronunciation: /ɛpt/ Etymology: Back-formation Used as a deliberate antonym of ‘inept’: adroit, appropriate, effective. 1938 E. B. White Let. Oct. (1976) 183, I am much obliged..to you for your warm, courteous, and ept treatment of a rather weak, skinny subject. 1966 Time 30 Sept. 7/1 With the excep…

That was…surprisingly thorough.

That is the point of the OED: to be comprehensive and include real usages.

Re: A farewell to bioinformatics (2012)

#18

Post by gwern »

jmspring wrote: post #8

Sounds like a fed up academic with a stick up his backside. Sh*tty data? Comes from the community. If the data and algorithms are so poor, and the author so superior, he should have been able to improve the circumstances. This whole screed reads like an entitled individual who entered a profession, didn't get the glory, oh and yeah, academia doesn't pay well. In the realm of bioinformatics, lets ignore the work done…

> Sh*tty data? Comes from the community. If the data and algorithms are so poor, and the author so superior, he should have been able to improve the circumstances.

Why? Aren't you assuming a lot about the incentives? What if the ground truth is simply that all the results are false due to a melange of bad practices? Do you think he'll get tenure for that? (That was a rhetorical question to which the answer is 'no'.) Then you know there's at least one very obvious way in which he could not improve the circumstances of poor data & algorithms.

Re: A farewell to bioinformatics (2012)

#20

Post by MattRogish »

I have some experience working at a genomics research company and I'll broadly +1 Fred's experience about the industry, although in less negative terms. I got out before I got jaded, so my perspective is a bit more "oh, that's a shame" than his. I really like genetics, bioinformatics, hardware, deep-science, and all that but the timing and fit wasn't right.

The tools are written by (in my experience) very smart bioinformaticians who aren't taught much computer science in school (you get a smattering, but mostly it's biology, math, chemistry, etc.). Ex:

http://catalog.njit.edu/undergraduate/programs/bioinformatic...

http://www.bme.ucsc.edu/bioinformatics/curriculum#LowerDivis...

http://advanced.jhu.edu/academic/biotechnology/ms-in-bioinfo...

The tools themselves are written by smart non-programmers (a very dangerous combination) and so you get all sorts of unusual conventions that make sense only to the author or organization that wrote it, anti-patterns that would make a career programmer cringe, and a design that looks good to no one and is barely useable.

Then, as he said, they get grants to spend millions of dollars on giant clusters of computers to manage the data that is stored and queried in a really inefficient way.

There's really no incentive to make better software because that's not how the industry gets paid. You get a grant to sequence genome "X". After it's done? You publish your results and move on. Sure, you carve out a bit for overhead but most of it goes to new hardware (disk arrays, grid computing, oh my).

I often remarked that if I had enough money, there would be a killing to be made writing genome software with a proper visual and user experience design, combined with a deep computer science background. My perfect team would be a CS person, a geneticist, a UX designer, and a visual designer. Could crank out a really brilliant full-stack product that would blow away anything else out there (from sequencing to assembly to annotation and then cataloging/subsequent search and comparison).

Except, I realized that most folks using this software are in non-profits, research labs, and universities, so - no, there in fact is not a killing to be made. No one would buy it.

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