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A farewell to bioinformatics (2012)

madhadron.com

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Re: A farewell to bioinformatics (2012)

#41

Post by FreeKill »

If you really want to get a feel for how deluted the Bioinformatics community is, look for a job in the field as an outsider. It's not uncommon to see requirements like:

"Must be an expert in 18 technologies" "Must have a PHD in Computer Science or Molecular Biology" "Must have 12 years experience and post doctoral training" "Pay: $30,000"

It's delusional because they apply the requirements it took for themselves to get a job in Molecular Biology (long PHD, post doc, very low pay for first jobs) and just apply it carte blanche to all fields that may be able to aid in their pursuits. Especially when it comes to software engineering where it can often be extremely difficult to explain why you did not pursue a PHD.

Re: A farewell to bioinformatics (2012)

#42

Post by [deleted] »

michaelhoffman wrote: post #23
gwern wrote: post #18

Earlier quoted context omitted.

> 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'.)…

He's not getting tenure because he doesn't have a PhD. According to LinkedIn, he has a master's degree awarded after four years of study [1], which often indicates someone who did not complete a PhD. [1] http://www.linkedin.com/pub/frederick-ross/13/81a/47

[deleted]

Re: A farewell to bioinformatics (2012)

#43

Post by droithomme »

michaelhoffman wrote: post #23
gwern wrote: post #18

Earlier quoted context omitted.

> 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'.)…

He's not getting tenure because he doesn't have a PhD. According to LinkedIn, he has a master's degree awarded after four years of study [1], which often indicates someone who did not complete a PhD. [1] http://www.linkedin.com/pub/frederick-ross/13/81a/47

According to his 2009 CV he was working a PhD in biology back then and expecting to finish in 2011.

Given that he is not a professor it is not clear why he would be expected to be seeking tenure.

Re: A farewell to bioinformatics (2012)

#44

Post by kanzure »

epistasis wrote: post #37
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…

>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…

> and if it's a good idea, it will be worth polishing the turd later,

Which of the released turds do you consider to be polished?

Re: A farewell to bioinformatics (2012)

#45

Post by epistasis »

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…

>I have seen people parsing Gigabytes-files with one line of Awk

I feel exactly the opposite. I'm suspicious of anyone that does not use AWK (or other Unix text utilities) as a standard tool for checking the integrity of multi-gigabyte files, or generating summaries. AWK is super-fast, allows highly flexible checks, and allows quick and reliable interaction with huge amounts of data in the way that a script can not.

Re: A farewell to bioinformatics (2012)

#46

Post by lemming »

This is a little discouraging - BioInformatics was my top choice for a Master's program I'm planning to start this year. The program at Melbourne Uni looks really good (accepts from three streams, Math/Stats, Biology or Computing and tailors the course based on your background). Maybe I should go for a more generic Machine Learning one and try to apply that to healthcare in some other field if things are really this bad.

Re: A farewell to bioinformatics (2012)

#47

Post by east2west »

aheilbut wrote: post #40
east2west wrote: post #36

Earlier quoted context omitted.

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.

It was initially a programming error but the Duke researchers refused to acknowledge it and reanalyze their data, because that might mean retracting their prominent paper. From there it just snowballed. It was certainly fraud after the error was pointed out to them. There might also be other elements of fraud in their paper. I watched a presentation by MD. Anderson researchers who spotted the error and spent more than two years trying to call attention to it.

Re: A farewell to bioinformatics (2012)

#48

Post by gabeiscoding »

MattRogish wrote: post #20

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 bioin…

I live in this field, as a computer scientist learning the biology, and trying to make a living with a bootstrapped company.

I wrote a post about why GATK - one of the most popular bioinformatic tools in Next Generation Sequencing should not be put into a clinical pipeline:

http://blog.goldenhelix.com/?p=1534

In terms of your ideal software strategy, I can speak to that as well, as I am actually attempting to do almost exactly what you suggesting. My team is all masters in CS & Stats, with focus on kick-ass CG visualization and UX.

We released a free genome browser (visualization of NGS data and public annotations) that reflects this:

http://www.goldenhelix.com/GenomeBrowse/

But you're right, selling software in this field is a very weird thing. It's almost B2B, but academics are not businesses and their alternative is always to throw more Post-Doc man-power at the problem or slog it out with open source tools (which many do).

That said, we've been building our business (in Montana) over the last 10 years through the GWAS era selling statistical software and are looking optimistically into the era of sequencing having a huge impact on health care.

Re: A farewell to bioinformatics (2012)

#49

Post by cmccabe »

MattRogish wrote: post #20

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 bioin…

There are companies out there that offer commercial sequencing software. DNANexus is one.

As for whether there's "a killing to be made", it's kind of unclear so far.

Re: A farewell to bioinformatics (2012)

#50

Post by tkl »

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…

I am a bit clueless here. What is bad about parsing large files with Awk?
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