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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

#401

Post by TeMPOraL »

pintxo wrote: post #373
TeMPOraL wrote: post #368

Earlier quoted context omitted.

I'd say that in general, we need to get rid of locales in computing. They're an unending source of bugs and annoyances. It's not "techies know best" whining. We've been increasingly computerizing the economy for the past 50+ years; it's past time for societies to adapt to that reality, instead of wasting time and money on dealing with dozens of date formats, number separators, currency notations, etc.

We are going to get rid of locales as much as we are going to get rid of local languages, tradition and culture. The US switched to the metric system in the 60s and there is a shitload of benefits in doing so. Has it worked? Not really. Still using the old system everywhere. So the solution cannot be to get rid of locales, but to actually use them properly: - Always use the right locale for the job (the OS or browser…

If you program in C++/Java and all your libraries handle locale correctly, it's doable. A bit more difficult in languages and libraries written by people who aren't even aware of the concept - of which there's plenty. Impossible if you're dealing with customers or managers who don't understand the concept of "data type". The latter is, for example, why the problem from TFA exists in the first place - i.e. Excel being stringly typed, and eagerly converting data into your system locale.

And then, there's the problem of users - whatever locale they have set in their system were most likely not set by them, and are often misaligned with what they're naturally using.

There's a lot of bugs and issues happening to people every day that could be removed if major software vendors said, "sorry, the only allowed input format for date is ISO8601, and dot is the only valid decimal separator; take it or leave it".

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

#402

Post by mjevans »

sneak wrote: post #311
reportgunner wrote: post #220

Earlier quoted context omitted.

yes, YYYY-MM-DD HH:MM:SS is the only proper format. It is sorted from the greatest unit (year) to the smallest unit (second). If you treat them as text and sort alphabetically they still get sorted from oldest to newest. Other formats don't sort properly. writing dd.mm.yyyy is like writing time ss:mm:hh writing mm/dd/yyyy is like writing time mm/ss/hh If I really have to put YYYY at the end of the date I use the 'dd-…

I suggest a literal T instead of a space, and don’t forget the timezone offset (or a literal Z). ISO 8601 is great.

I agree with and independently also use the parent's modification to ISO8601 with that respect; though I do frequently call the format string that contains whatever magic cookies get that output something similar to iso8601mod. (The modifications: Emit a string rather than a T, and (if included) use the email like +/-OFFSET to indicate the current timezone offset rather than specify a timezone. No offset implies UTC for system times and local time for human-facing times.)

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

#403

Post by kergonath »

thaumasiotes wrote: post #392
bad_user wrote: post #152

Earlier quoted context omitted.

"01/02" does not translate to Jan 2nd in most of the world, because DMY is much more popular than MDY. Excel is biased for US users.

> "01/02" does not translate to Jan 2nd in most of the world, because DMY is much more popular than MDY. This doesn't follow. There's no year in 01/02. MD is more popular than DM.

In which country do people use DMY, but also MD? This just sounds wrong, and my (admittedly limited) sampling shows that when DMY is abbreviated it becomes DM. 01/02 is still the 1st of February everywhere I went except in the US.

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

#404

Post by goatlover »

importantbrian wrote: post #350
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…

Whenever people ask me about getting into the field and if they should learn Python or R or Scala or whatever else, I always respond with you need to get really good with excel/Google Sheets and SQL. Then worry about everything else. I can't tell you how many times I've done an analysis I'm really proud of in something like R Markdown only to have the end user say that's great now can I get it in an excel? I just del…

> good with excel/Google Sheets and SQL

Those aren't very good for cleaning and wrangling data, even if the output for analysis ends up being a spreadsheet.

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

#405

Post by TeMPOraL »

stjohnswarts wrote: post #383
TeMPOraL wrote: post #368

Earlier quoted context omitted.

I'd say that in general, we need to get rid of locales in computing. They're an unending source of bugs and annoyances. It's not "techies know best" whining. We've been increasingly computerizing the economy for the past 50+ years; it's past time for societies to adapt to that reality, instead of wasting time and money on dealing with dozens of date formats, number separators, currency notations, etc.

What computer programmer can't handle locales? I mean that's 1st year comp programming 101 stuff. I've never had an issue. Sure I've had to fix other's work but it was usually old stuff that never knew it would be leaving the factory floor where it was being originally written, but still.

Almost all of them, judging by software I've been dealing with on both Windows and Linux systems, as well as the web. Even the big companies full of smart people get it wrong - as evidenced by Excel, and the problems like those described in TFA.

The problem doesn't even have a correct solution, because the locale settings in the OS and the browser aren't often set by end users (a regular person probably doesn't even know that they exist) and the defaults depend on many random factors (like which store you bought your computer with preinstalled Windows from).

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

#406

Post by vikramkr »

rolph wrote: post #394
vikramkr wrote: post #387

Earlier quoted context omitted.

They're tags and you end up with multiple names for the same gene. They might as well be replaced with an arbitrary string of numbers- those are equally easy to do a quick Google scholar or pubmed search with. You don't lose anything of value by changing the name. In chemistry amd organic chemistry, the proper IUPAC name of the compound also tells you its structure. It tells you what the compound is in a real physica…

this does not negate the fact that these tags or lables actually do have meaning they are not arbitrarily made up. if you do not have any understanding of rust and you read the source code it seems like meaningless tags but if you understand the idea of syntax you can see there is some underlying principle to the combinations of characters. being unfamiliar with the scheme doesnt make it meaningless hash. the failure…

Since when is the universal way to identify a gene its locus? The locus is just the position of a given gene in a particular chromosome. The function of a gene is not exclusively tied to chromosomal location. If I take the sequence for SHH and move it to a different location in the genome under the appropriate promoters, it will still express sonic hedgehog. If I go and shove some other gene sequence into where SHH is otherwise located on the genome, that new insert will not serve as a ligand in the hedgehog signalling pathway. The entire field of synthetic biology is predicated on moving bits of DNA to new locations.

The point is that there is no concrete, universal, IUPAC style scheme to naming these genes. I don't know what the comparison to a program language is supposed to imply. The syntax when programming has meaning beyond a meaningless hash. The syntax in gene naming barely has more meaning that a meaningless hash, because at least occasionally its related to a phenotype or function or keeps the same silly scheme for multiple members of the (e.g. hedgehog) pathway. That's not much.

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

#407

Post by gmfawcett »

stjohnswarts wrote: post #379
owl57 wrote: post #245

Earlier quoted context omitted.

Human readability sometimes matters.

what human can't parse that? Sure it might take a half a second longer but it's hardly confusing.

For those of us whose professional lives sometimes require staring at directory listings full of filenames like "output-200003021342"... for the love of God, please just put the dashes in.

I have an infinite number of dashes, I'll send you a lifetime supply!

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

#408

Post by zuno »

hermitcrab wrote: post #398

Excel is an amazing tool. But it also has some significant shortcomings: * A well known tendency to mangle date and gene data under the guide of being 'helpful'. * Easy to making mistakes when cutting and pasting cells. * Difficult to see what is going on in a spreadsheet. * Poor handling of CSV files. Some of these shortcoming are inherent to spreadsheets. Others are specific to Excel, but hard to overcome due to th…

Thanks. I just checked the video. Looks neat! Excited to try it out.

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

#409

Post by gmfawcett »

LatteLazy wrote: post #226
owl57 wrote: post #119

Earlier quoted context omitted.

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.

A beautiful property of using ints to represent dates is that you can manipulate them using simple arithmetic. For example, if you want to refer to noon-time on 20200806, you can simply divide the day in two and write it as 10100403. An elegant, DRY solution to a perennial problem.

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

#410

Post by rolph »

vikramkr wrote: post #406
rolph wrote: post #394

Earlier quoted context omitted.

this does not negate the fact that these tags or lables actually do have meaning they are not arbitrarily made up. if you do not have any understanding of rust and you read the source code it seems like meaningless tags but if you understand the idea of syntax you can see there is some underlying principle to the combinations of characters. being unfamiliar with the scheme doesnt make it meaningless hash. the failure…

Since when is the universal way to identify a gene its locus? The locus is just the position of a given gene in a particular chromosome. The function of a gene is not exclusively tied to chromosomal location. If I take the sequence for SHH and move it to a different location in the genome under the appropriate promoters, it will still express sonic hedgehog. If I go and shove some other gene sequence into where SHH i…

do you know why HH is named such ?

>>the function of a gene is not exclusively tied to chromosomal location"Since when is the universal way to identify a gene its locus" since molecular genetics...and gene mapping.

this whole thing started with the idea that gene lables are arbitrary meaningless tags by extension not a problem to change labels to stop a spreadsheet program from mangling data. so now that we both know that genetic labels or tags or whatever you prefer to insert, are far from arbitrary thats the end of that.

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