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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

#251

Post by throw_m239339 »

throwaway936482 wrote: post #187
rkachowski wrote: post #80

My mind is blown that Excel's usability is so bad that the representation of the human genome itself has to adapt around it's undesired behaviour. As in, the history of genetics research is now irreversibly linked with the shortcomings of this one software product, which just happens to be incapable of describing the genetics of the organisms that created it.

Excels usability isn't bad though. Which is why everyone uses it. It falls down in this (and lots of other cases) but if you want to see what good usability looks like, look at what people use.

Everyone uses Excel because it's a tool everybody learned at University or even highschool, nothing more, it's not because it's good at all.

It's a terrible app but Microsoft managed to shove it everywhere in education. Same for Words.

Unfortunately Libre Office and co tried to reproduce the terrible UX of both software, while coming up with inferior functionalities because they had to try to maximise compatibility with these MS tools, time not spent on providing actual useful stuff.

Access is a bit better and I wish more non programmers learned basic SQL instead of Excel.

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

#252

Post by pbhjpbhj »

Cactus2018 wrote: post #155
yardstick wrote: post #123

Earlier quoted context omitted.

Same here, but with IMEI numbers. Excel silently truncates them, it’s frustrating. Why can’t the auto format detect and just store them in text format?

Why can't there be a flag (defaulted to off) to control auto formatting

I was thinking that perhaps the autoformat options could be explicitly shown in the column headers

    number date currency
    A      B    C
and you could click on the format to change it. Italics could show assumed formats, bold could show user set formats.

I'm newly returned to (very minor) Excel use and assumed formats with no feedback seems wrong. My situation is dates _not_ being picked up as dates and it not being obvious that it hasn't; I'm using ISO format (eg 2020-06-17), I guess you have to create a new date format or use USA-ordering before it will recognise dates.

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

#253

Post by lifeisstillgood »

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…

Nah, I plan on having HDF5 or Apache Arrow be the portable table of data and then build WASM based viewers - it's the excel killer but the war of attrition will be long !

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

#254

Post by s800 »

t34saves wrote: post #230
meow1032 wrote: post #47

Earlier quoted context omitted.

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.

Why?

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

#255

Post by pbhjpbhj »

FabHK wrote: post #195
BurningFrog wrote: post #79

Earlier quoted context omitted.

If the gravity metaphor doesn't reach you, maybe this will: The world speaks English. It's an illogical and absurdly spelled language. Esperanto is miles ahead on all logical measures. Yet we will never switch, both because the cost of switching is enormous, and because there is no way to coordinate/organize such a move.

> The world speaks English. It's an illogical and absurdly spelled language. Man, the extent the aviation world has to bend itself to avoid the pitfalls of English.... "to" and "two" sound alike, and so does "for" and "four". "Turn left t(w)o four zero" or "Climb t(w)o eight thousand" To avoid that, the lingo is: "Turn left heading two four zero", "Climb and maintain two eight thousand" (or, "Climb flight level two e…

Don't they say "turn left heading two four zero" which disambiguates this? Not knowledgeable here, just that sticks in my brain.

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

#256

Post by meow1032 »

Balgair wrote: post #178
meow1032 wrote: post #47

Earlier quoted context omitted.

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…

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…

> To the larger point, scientists are not programmers. They got into their programs to do research.

I would say most research, to an ever growing degree, is so heavily dependent on software that it's tough to make that claim anymore. It makes no sense to me. It's like saying Zillow doesn't need software engineers because they are in the Real Estate business, not the software business.

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

#257

Post by zw123456 »

There is a super simple work around for this and it is all over the web if you search for it. Open a blank sheet, go to data, click on From Text, that allows you to import data identifying the type for each column. Yes, it is a couple more clicks but for 99% of people the auto-formatting is probably nice. I have shown this to people a million times at work and they are always amazed. But honestly a quick google search provides the solution.

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

#258

Post by rolph »

vikramkr wrote: post #199
azalemeth wrote: post #23

Earlier quoted context omitted.

> " To people calling, "why do they use Excel?" that's like asking "why must we be subjected to gravity?"" I respectfully disagree with this. Excel is fundamentally not suited to analysing *omics data. It's often the default program affiliated with a .csv filetype on people's computers, but trying to get an entire field of scientific research to rewrite itself based on its glorified bugs is...wrong, in my opinion. If…

But we didn't accept them as they are. We looked at two options, change excel or change gene names, and picked the one most likely to solve the problem. Gene names mean nothing anyway. We're going from random letters that mean nothing to humans and computers to still random letters that mean nothing but at least don't get confused for dates.

there was a time when a gene was named to facilitate search through a bookshelf full of laboratory notes. you could look at a genes lable and know exactly where to find reference to the gene, the lable would indicate the stack number the shelf, the section the volume the page[s] and paragraph....lables such as Sonichedgehog dont do that anymore.

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

#259

Post by dgb23 »

jrott wrote: post #88
lordnacho wrote: post #44

The problem is that your average business user of Excel thinks type safety is a bug, not a feature. If Excel enforced types instead of guessing on your behalf, a lot of people would complain. And it would be really hard to explain why it is sometimes useful to have constraints to someone who normally sees Excel's flexibility as its main strength. I don't think I've ever seen a non coder use Excel in a sensible way: m…

Yeah excel produces hairballs so easily. From a coder perspective I've only seen excel workbooks that are bad or terrifying. On the other hand a ton of people that don't write software for a living and have no interest in code manage to produce things that help them do their job and automate a ton of tedious stuff.

> From a coder perspective I've only seen excel workbooks that are bad or terrifying.

I think this might be a type of bias:

The Excel sheets I usually look at as a programmer are from customers who want me to write an application for them. Typically because the conventional means (Excel sheets, directory structures, emails etc.) become unmaintainable.

So we end up seeing the stuff that is bad for w/e reason. Often a combination of complexity, inconsistency, usability and sheer mass.

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

#260

Post by throwaway_pdp09 »

acidburnNSA wrote: post #76
meow1032 wrote: post #47

Earlier quoted context omitted.

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…

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…

Not my area at all but isn't this genetic algorithm type stuff?
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