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Scientists rename human genes to stop MS Excel from misreading them as dates

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Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#221

Post by shpongled »

gundmc wrote: post #186
shpongled wrote: post #159

Earlier quoted context omitted.

I would say the number of biologists who actually understand programming is extremely small. I've been programming for fun for ~15 years, and I'm about to finish a PhD in chemical biology (e.g. I started programming in C far before I started learning biology). You might occasionally run into someone who is passable - at best - with R or Python. But most of the code they might write is going to be extremely linear, an…

To be fair, linear code is often totally sufficient for most types of data analysis. Biologists don't really need to understand design patterns or polymorphism, they just need to not make computational mistakes when transforming the data.

Absolutely. My point was more than you can't expect comp. biologists to actually be "good" programmers when compared to SWE or even web devs.

Most of the code I write to do biological data analysis is fairly linear. However, I also generally use a static type system and modularity to help ensure correctness.

I've perused a lot of code written by scientists, and they could certainly learn to use functions, descriptively name variables, use type systems and just aspire to write better code. I just saw a paper published in Science had to issue a revision because they found a bug in their analysis code after publication that changed most of their downstream analysis.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#223

Post by hairofadog »

hairofadog wrote: post #14
lvturner wrote: post #3

I think another question is that why isn't there a viable alternative to excel for this particular use case? Is there, perhaps, a market for niche spreadsheet applications that serve one particular market?

I’ve been wishing for something like this lately in the apple ecosystem: sort of a “plain text” tabular editor that can handle large data sets. Numbers feels like it’s designed for presentations more than data crunching, and Excel (or at least the price of excel) would be overkill for my needs (which largely consists of data cleanup, spot-checking, and quick calculations). I’d happily pay for an IA-Writerish spreadsh…

Thanks, I'll check these all out!

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#224

Post by otherme123 »

ellis-bell wrote: post #174
ethanbond wrote: post #91

Earlier quoted context omitted.

Also... Excel is great. What exactly is "ahead" of Excel? People on here really underestimate how great of a product Excel is because of its cultural affiliations.

LibreOffice Calc is free and doesn't corrupt data. It also has full support of UTF8

In the case menctioned in the article, LibreOffice is on par with Excel. Don't believe it? Open up LibreOffice, type "MAR-1" or "SEP-2" in any cell, and look how easy is your data corrupted.

I have meet some other glitches: identifiers in the form of "1E123" get turned into scientific numbers. The column was something like "1A123", "1B123", etc. Those things are sneaky: you can have thousands of rows, and Excel/LO doesn't mind if only the 0.1% matches its rules for smartness. They just change without notice, leaving the others intact.

I'm a bioinformatic, and this kind of stuff is a daily issue. IMO, two problems colide:

1. People with very rudimentary knowledge of computers. I've meet some people way smarter than me, with thousands of papers written, that cannot open a CSV with R with a gun to their head. They can cut you, put three robotic arms in your heart, remove a tumour, sew you and send you home in three days. But R is just too much.

2. People that needs to collect and analyze data, and Excel is the easiest tool they know, but at the same time it's no lame toy: it sorts, it sums, it filters, it makes stats, it graphs... You cannot ask this people to use SQL, specially if it involves foreign keys. They just use Excel for data collection, storage and analysis.

Excel (and LibreOffice) are to blame. This shit could be avoided if they had a "scientific mode" to not be smart with your data, and be the default mode for any file in CSV/TSV mode. Unless you explicitly turn the file into a XLS/ODT or ask "turn this range of cells into dates for me" or "this cells are scientific numbers", they should not change a single dot.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#225

Post by rorykoehler »

whatisthiseven wrote: post #206
Balgair wrote: post #178

Earlier quoted context omitted.

In grad school I had a friend that was doing olfactory (smell) research on rats with tetrode drives (wires in their brain). He was looking at the neuronal response to smells that they gave the rats and had a few signals to match up. There was the signal from the arduino running the scent gates, the amps that reported the weak neuronal currents, the nose lasers that gated the ardunio, etc. He was having a hard time ge…

I keep seeing this sentiment when it comes to those in the natural sciences, but it makes no sense. I could replace "programming" in your above little bit with "mathematics" and it would be just as weird. Our modern world runs on computers and programs, just as our modern world and modern science built itself on mathematics and required many to use it. So too the new world of science may require everyone to know to p…

Tbh I think its a case for multidisciplinary research. You wouldn’t only hire one skill set to run a company, even a tech one, so why should research be any different? That’s probably where the deep insights are.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#226

Post by LatteLazy »

owl57 wrote: post #119
LatteLazy wrote: post #26

It's honestly amazing that Excel hasn't fixed this issue. It's pisses off an enormous number of users especially in basically any non-US country (even if 01/02 is a date, it isn't the second of January in most of the world...)

I don't even know why anyone still uses this notation in today's connected world. 2020-08-06 is ideal. Russian standard (06.08.2020) is uglier (digits are not sorted by significance) but still unambiguous. But that slash horror? Why would anyone continue inflicting this on themselves and their peers!?

>2020-08-06 I've just switched to 20200806. Let it be an int and be done with it.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#227

Post by jpindar »

lvturner wrote: post #3

I think another question is that why isn't there a viable alternative to excel for this particular use case? Is there, perhaps, a market for niche spreadsheet applications that serve one particular market?

I'm sure there is, which is great for one's own use but you can't make everyone else use it.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#228

Post by jordigh »

fock wrote: post #194
acidburnNSA wrote: post #76

Earlier quoted context omitted.

I have a strong feeling that, if people really put an effort into reading and replicating more papers, we would find that a lot of what's being published is simply meaningless. In grad school I had a subletting roommate for a while who was writing code to match some experimental data with a model. He showed me his model. It was quite literally making random combinations of various trigonometric functions, absolute va…

I work in computational materials science (where ML brings funding) and a funny paper of this kind is here: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.11... - they are literally trying out 100000s of possible combinations by brute force, to build a "physical model". Then they go on conferences and brag about it, because they have to (otr they know it's bs). Datasets are soso (you can have a look at QM9…

> (otr they know it's bs).

Well, that's a new acronym for me. I wonder where it came from. Apparently it's "on the real". Sounds like AAVE?

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#229

Post by otherme123 »

mcv wrote: post #162

> "Why, exactly, in a fight between Microsoft and the entire genetics community, was it the scientists who had to back down?" Back down? Or pick a better tool. If Excel proves to be an unreliable tool for your job, use a better one. Alternatives exist, ranging from Google Docs, and LibreOffice, to simpler light-weight spreadsheets. Or possibly more specialist tools. Why does everything always have to be put in Excel…

LibreOffice AND Google Docs fall in the same exact spot than Excel here. Try it. Type "SEPT-2" or "SEPT2" in any of them and see what happens.

Re: Scientists rename human genes to stop MS Excel from misreading them as dates

#230

Post by t34saves »

meow1032 wrote: post #47
jordigh wrote: post #7

To people asking, "why do they use Excel?" that's like asking "why must we be subjected to gravity?" The whole world's data ultimately comes from or ends up in an Excel spreadsheet. Sure, we might use other intermediate data storage methods, but in the end it's going to go into some scientist's or some politician's computer, and by golly it's gonna be in Excel. Trying to rally against Excel is like trying to rally ag…

I don't disagree completely with this, but just want to point out that it's kind of a bad smell to have computational biologists who are - as someone in the article puts it - computationally illiterate. I have met lots of these types over the years, and usually their methods are kind of a gong show. If you can't properly sanitize your data inputs on your column headers, why should I trust that you've treated the rest…

Considering how Perl was chosen as the computational biologists lingua franca in 1990's - 2k's since it was good at text manipulation (since genes are represented by text) I would say they don't have a history of making good choices.
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