
“You’re not allowed bioinformatics anymore” - georgeg
http://biomickwatson.wordpress.com/2014/07/21/youre-not-allowed-bioinformatics-anymore/
======
simonster
The author is right to criticize the current state of data sharing and
analysis. However, the solution is not to have experimentalists collect their
data and then pass it on to someone else. That would be good for the people
doing data analysis (provided they know enough to understand the experimental
procedures, which is not always the case), but remove many of the incentives
to be an experimentalist. Science is much less fun if you don't actually get
to make new discoveries.

The problem is that in many fields there is a weird dichotomy between people
who know how to get data and people who know what to do with it. This is not a
sustainable situation. Proper experimental design requires knowledge of how
the data will be analyzed.

My proposed solution is to require that the leaders of research groups have
expert knowledge of both experimental procedures and data analysis, because
that is the expertise required to pick an appropriate hypothesis and supervise
the corresponding scientific project from start to finish. Because students 1)
work in a lab with diverse knowledge and 2) desire to become professors
themselves, they are likely to acquire these skills as well. Aspiring
professors who have substantially greater aptitude for either data collection
or data analysis should form a joint lab with a researcher with the
complementary skill set so that their students can learn both fields.

~~~
hirenj
I had a conversation along these very lines today. The hard question is how to
fund such a thing. A lot of funding seems to be for the individual researcher
to start a group, or for large consortia to work on a project, with precious
little middle ground. My ideal lab would in fact be medical biologist, mass
spectrometrist and bioinformatician working together. I'm not sure how to do
that when each individual has a good, but not insane track record. This is to
say nothing of the difficulties in putting such a team together.

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cwyers
The end of the post:

"If you are leading a project that creates huge amounts of data, instead of
employing a bioinformatician in your own group, why not collaborate with an
existing bioinformatics group and fund a post there?"

If that's your goal, perhaps using a less derisive and incendiary tone towards
the straw man scientist in the post would've been good?

~~~
LordHumungous
As someone who's worked with micro biologists I can assure you it's not a
straw man.

~~~
benrapscallion
As someone who has worked with microbiologists, maybe you could start by
spelling microbiologist right.

~~~
LordHumungous
Maybe you could not be a cunt

------
ejain
Lost me at "we've requested funds to employ a bioinformatician for the
lifetime of the project". More realistic is "I'll have a grad student deal
with the data".

One of the local institutes just dissolved their bioinformatics group because
they couldn't convince enough research groups to hand over grant money. They'd
be part of the grant proposal in order to secure the grant, but then the money
would end up being spent elsewhere...

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chrisamiller
The field is slowly coming around. I've been very harsh when peer-reviewing
papers without proper code release and documentation. I know that I'm not
alone. Both investigators and funding agencies are starting to understand the
message. This is especially true as older folks retire and a new
computationally-savvy group of folks ascends into senior positions on
editorial boards, faculty review panels, and grant review panels.

Things may look messy in science, and they often are, but I'm optimistic about
the future.

~~~
rmcastil
I'm hoping so.

I got a MS degree in Bioinformatics and for the past three years the only role
it has served is collecting dust in my closet upstairs :)

I was the young bioinformatician in 2006 and when working in a lab it felt
very isolating. The PI and Postdocs just had me solve simple computational
problems (or even IT problems). It felt very much like I was a cog in their
grant writing machine rather than a collaborator that deserved any kind of
authorship in a publication.

And looking back there was no one to teach me about good practices of writing
software like source control, SOLID, testing, etc. Or even storage of our
microarrays.

I eventually went to work for a biotech consultancy but I discovered that
biotech software was a gimmick used to hike up the prices on software. Sure it
was a niche field but we would charge clients hundreds of thousands of dollars
for software that was barely functional.

I think a lot of Research groups were badly burned by this and eventually
started trying to do everything in house. I eventually became
disillusioned/burned out and left the field entirely.

I've been out of the field for four years now but still feel badly as I felt
I've wasted my training. I still have a retainer client as a way back 'in'
back into bioinformatics.

It would be nice to find these 'bioinformatics groups' and see how they're
successfully collaborating with other labs/research groups.

------
collyw
Most of the tasks mentioned would be better served by a software engineer,
rather than a bioinformatician.

~~~
angersock
Selling people on funding a staff programmer is a bit hard outside of a
handful of institutions, I wager.

~~~
webmaven
Thinking 'bioinformatician' is a fancy name for 'programmer' is likely part of
the problem too.

------
epaladin
And this is exactly why I'm trying to find a new place to work. I finally
realized after a few years that I need some real mentorship to be fully
competent in a research environment (even after an MS), and four years of
"trial by fire" in a lab which generates data from a ton of tiny experiments
(rather than a few larger experiments) with 100 biologists and only two of us
bioinformaticians, and a pile of ten years worth of old microarray data that
no one has any sample annotation for (but it's invaluable!)-- was less of a
constructive learning experience than it seemed like it was going to be. I
need to find/create an environment that will allow me to use the motivation I
know I used to have for this.

So for anyone from a CS-oriented background, or who is thinking of doing a
degree program in bioinformatics that isn't oriented around research- try to
help out in various labs, and find a good mentor. See what environments work
best for you, and what sort of problems you want to apply yourself to. The
field is developing far faster than most college programs can move, but by
getting out there and seeing what skills/knowledge will actually be useful,
you can work on filling in the gaps sooner.

------
aaren
It isn't just Bioinformatics. Working at the edge of a research group doing
technical work that no one else can comprehend can be very difficult and
lonely. Don't underestimate the utility of a technical mentor that can
understand what it is that you are doing.

The silver lining is that you can have a lot of freedom in what you learn and
what you do and that you can become completely indispensable.

~~~
dekhn
In general anybody who's really good at data analysis and is willing to be
collaborative need not worry about finding employment in the foreseeable
future.

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fnbr
What are best practices in data management/reproducibility? The research that
I'm involved in has typically used make & git at best, and more typically,
hacked together Matlab scripts.

------
iSnow
The worst I have seen was a systems biologist flipping between Excel cells
with the arrow keys and staring at the Excel input line to find out if
sequences are different. My jaw dropped.

~~~
mnw21cam
There is the story of course of the years of research that were destroyed
because some particular gene names looked suspiciously like dates to Excel.

Yes, I was working on a bioinformatics data warehouse a while back. Yes, we
did have to write an import filter to extract data from Excel files.

------
anon4
Is anyone else irked whenever someone uses "data" as a plural? It's an
uncountable singular for chrissake!

~~~
michaelhoffman
Honestly, I am only irked when people insist that data must be used as a
singular or that it must be used as a plural. You'll find it listed both ways
in good dictionaries:

> Both constructions are standard. The plural construction is more common in
> print, evidently because the house style of several publishers mandates it.

[http://www.merriam-webster.com/dictionary/data](http://www.merriam-
webster.com/dictionary/data)

~~~
dalke
The commentary is a subset of what's in the wonderful M-W "Concise Dictionary
of English Usage." The entry for "data, datum" starts "The word data is a
queer fish."

The most complete online version of it that Google knows about is at
[http://www-old.accademiadellacrusca.it/forum/htdocs/phpBB2/v...](http://www-
old.accademiadellacrusca.it/forum/htdocs/phpBB2/viewtopic.php%3Ft=328&postdays=0&postorder=asc&start=30.html)
.

Some key points and quotes:

\- data isn't an ordinary plural. "Ordinary plurals ... can be modified by
cardinal numbers; ... no one, it seems, can tell you how many data."

\- "To summarize, data has never been the plural of a count noun in English.
It is used in two constructions - plural, with plural apparatus, and singular,
as a mass noun, with singular apparatus. Both constructions are fully standard
at any level of formality. The plural construction is more common. If you are
an editor for a publisher whose house style insists on the plural construction
only, take care to be consistent ..."

\- "There have been more occurrences of datum in popular sources since [about
the middle 1960s]. Perhaps the insistence of many editors that data is a
plural has accelerated the tendency for datum to be used as a singular of
data"

