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A farewell to bioinformatics (2012)

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Re: A farewell to bioinformatics (2012)

#31

Post by saraid216 »

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…

As a general rule, the people on the short end of the stick are the people least capable of producing change. Worse, change that they bring about tends to be good from a strict, technical viewpoint but has huge negative side effects that go unnoticed or deliberately ignored until it becomes difficult to distinguish the resultant system as a better one.

Rants like this, and providing interviews to third parties, are actually one of the more positive things that he could bring to the table: it provides information to people who aren't aware and inspires motivation in people who aren't entangled.

Re: A farewell to bioinformatics (2012)

#32

Post by ElliotH »

That's a shame. I just finished a uni module about bioinformatics. It seemed like a cool field where progress was being made, and as an undergraduate I could generate meaningful looking results by following very recent papers. I hope the field has some saving graces even if this is all true. The idea of CompSci folk working with biology folk to solve human problems inspired me a lot.

Re: A farewell to bioinformatics (2012)

#33

Post by saraid216 »

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…

> In the realm of bioinformatics, lets ignore the work done on the human genome and the like.

He discusses this specifically in the rant. Are you saying he's wrong?

Re: A farewell to bioinformatics (2012)

#35

Post by sbassi »

OK, I agree that there are some shitty work on this field, but he can't think they we all in the same boat. For example "Irene Pepperberg’s work with Alex the parrot dwarfs the scientific contributions of all other sequencing to date put together." this is not true. Bioinformatics is not just blinding sequencing new DNA, but analyzing data and almost every new breakthrough in medicine is based in a direct (or indirect) bioinformatics analysis. I used to work in an agrobiotech company and the sequencer was the first source of data for any breeding program. Bioinformatics was used to design primers for PCR to find molecular markers. There is bad software out there? Yes, but I see this as an opportunity than a problem. And the cause is not the need to hide something, but the lack of ability of biologists with no CS background in the field.

Re: A farewell to bioinformatics (2012)

#36

Post by east2west »

michaelhoffman wrote: post #21
zerohp wrote: post #6

> the software is written to be inefficient, to use memory poorly, and the cry goes up for bigger, faster machines! When the machines are procured, even larger hunks of data are indiscriminately shoved through black box implementations of algorithms in hopes that meaning will emerge on the far side. It never does, but maybe with a bigger machine… I spent five years working in bioinformatics, and this is exactly the a…

Hi, I'm a bioinformatics researcher. Apparently I work for this guy's ex(?)-employer although I have never heard of him before. My single most limited resource is programmer time. My time and the time of other people who work with me. I have access to loads of computers that sit idle all the time, even if it is on nights and weekends. There is zero opportunity cost to me in using these computers more fully. I have en…

Well, I can call myself a bioinformatics researcher, I guess, as I have CS Ph.D working in genetics/genomics. I see your point of throwing computers at simple solutions as cheaper than throwing good programmers. I do that too. We are very fortunate in that we write run-once programs that only have to work in one environment using one inputs. However, bad programmers write incorrect programs, which give wrong conclusions that lead to faulty clinical trials (look up Duke University facing class-action law-suit). I have seen people parsing Gigabytes-files with one line of Awk. People seem to forget that good engineering practice is learned with blood. Is it any wonder academic research is looked with suspicion by the pharmaceutical companies?

Re: A farewell to bioinformatics (2012)

#37

Post by epistasis »

michaelhoffman wrote: post #21
zerohp wrote: post #6

> the software is written to be inefficient, to use memory poorly, and the cry goes up for bigger, faster machines! When the machines are procured, even larger hunks of data are indiscriminately shoved through black box implementations of algorithms in hopes that meaning will emerge on the far side. It never does, but maybe with a bigger machine… I spent five years working in bioinformatics, and this is exactly the a…

Hi, I'm a bioinformatics researcher. Apparently I work for this guy's ex(?)-employer although I have never heard of him before. My single most limited resource is programmer time. My time and the time of other people who work with me. I have access to loads of computers that sit idle all the time, even if it is on nights and weekends. There is zero opportunity cost to me in using these computers more fully. I have en…

>There can be a big opportunity cost in trying to rework a workflow so that it is more efficient and then test it thoroughly ensure correctness.

Hi, I recognize your name as a legit bioinformatician, am a huge fan of the lab that you're currently in, and others should listen to you.

I'd like to add that for many projects, general reusable software engineering is not necessarily a huge advantage. Instead of verifying a single implementation, it's often better for somebody to reimplement the idea from scratch; if a second implementation in a different language written by a different programmer gets the same results, this is a much more thorough validation of the software than going over prototype software line by line.

Also, I've seen way too many software engineers come in with an enterprisey attitude of establishing all sorts of crazy infrastructure and get absolutely no work done. If Java is your idea of a good time, it's unlikely that you'll be an effective researcher (though it's not unheard of), because it's not good at maximizing single-programmer output, and not good at maximizing I/O or CPU or string processing. In research it's best to get results, fail fast fast fast, and move on to the next idea. If you're lucky, 1 in 20 will work out. Publish your crap, and if it's a good idea, it will be worth polishing the turd later, but it's better to explore the field then to spend too much time on an uninteresting area.

The only time you worry about efficiency is when it enables a whole other level of analysis. So, for example, UCSC does most of their work in C, including an entire web app and framework written in C, because when they were doing the draft assembly of human genome a decade ago on a small cluster of computers that they scrounged from secretaris' desks over the summer, Perl wouldn't cut it.

Re: A farewell to bioinformatics (2012)

#38

Post by chewxy »

saraid216 wrote: post #31
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…

As a general rule, the people on the short end of the stick are the people least capable of producing change. Worse, change that they bring about tends to be good from a strict, technical viewpoint but has huge negative side effects that go unnoticed or deliberately ignored until it becomes difficult to distinguish the resultant system as a better one. Rants like this, and providing interviews to third parties, are a…

I don't know, but I think Fred is in a prime position to disrupt bioinformatics. He knows all the flaws, he knows all the problems. If I were him, I'd have seized the opportunity and work on a hard problem.

Then again, I am in no position to judge what Fred should or should not do

Re: A farewell to bioinformatics (2012)

#39

Post by east2west »

aheilbut wrote: post #30

I sympathize with the author, but this piece fails because many of the specific criticisms are off-base, and he's not trying to be at all constructive. For example, it isn't true at all that microarray data is worthless. The early data was bad, and it was very over-hyped, but with a decade of optimization of the measurement technologies, better experimental designs, and better statistical methods, genome-wide express…

No kidding about reinventing wheels. I once saw a manuscript based entirely on dot-product as 1-D least-square. I don't know what happened to it, but one reviewer called it a seminal event in GWAS.

Bioinformatics is hard, but too many careerists take advantage of difficulties and uncertainty to publish as many papers as they can get away with.

Re: A farewell to bioinformatics (2012)

#40

Post by aheilbut »

east2west wrote: post #36
michaelhoffman wrote: post #21

Earlier quoted context omitted.

Hi, I'm a bioinformatics researcher. Apparently I work for this guy's ex(?)-employer although I have never heard of him before. My single most limited resource is programmer time. My time and the time of other people who work with me. I have access to loads of computers that sit idle all the time, even if it is on nights and weekends. There is zero opportunity cost to me in using these computers more fully. I have en…

Well, I can call myself a bioinformatics researcher, I guess, as I have CS Ph.D working in genetics/genomics. I see your point of throwing computers at simple solutions as cheaper than throwing good programmers. I do that too. We are very fortunate in that we write run-once programs that only have to work in one environment using one inputs. However, bad programmers write incorrect programs, which give wrong conclusi…

The Duke situation to which you refer was fraud, not just a result of programmer error or poor engineering practice.
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