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“You’re not allowed bioinformatics anymore”

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Re: “You’re not allowed bioinformatics anymore”

#21

Post by 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.

Re: “You’re not allowed bioinformatics anymore”

#23

Post by dalke »

michaelhoffman wrote: post #14
anon4 wrote: post #4

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

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

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... .

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"

Re: “You’re not allowed bioinformatics anymore”

#24

Post by hirenj »

simonster wrote: post #21

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 muc…

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.

Re: “You’re not allowed bioinformatics anymore”

#25

Post by mnw21cam »

iSnow wrote: post #22

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.

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.

Re: “You’re not allowed bioinformatics anymore”

#26

Post by 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...

Re: “You’re not allowed bioinformatics anymore”

#28

Post by ejain »

simonster wrote: post #21

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 muc…

There's a lot of data that can be collected without much knowledge of experiment design, consider e.g. all the sequencing projects.

The problem is that if the data ends up in inconsistently formatted spreadsheets or poorly conceived custom formats, the effort required to extract the data for analysis later (especially across multiple projects) can be prohibitive.

Re: “You’re not allowed bioinformatics anymore”

#29

Post by webmaven »

angersock wrote: post #18
collyw wrote: post #12

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

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

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