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Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

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Re: Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

#111

I need to introduce my customers using Excel to the typecasting concept. :o>

> I need to introduce my customers using Excel to the typecasting concept.

I misread this as "... the typesetting concept.".

I immediately feared someone adding LaTeX support to Excel cells.

But now I'm thinking "hmmmm..."

Re: Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

#112

So let me get this straight: Scientists would rather rename genes, than to simply use a tool other than MS Excel?

> So let me get this straight: Scientists would rather rename genes, than to simply use a tool other than MS Excel? It's not that they'd rather. They understand that a trillion dollar corporation cannot supply the most basic tool they need for work, despite trying for 40 years. They just can't effect change. The real problem behind it all is that they allow themselves to be bullied. Despite holding multiple PhDs they…

> Colin still thinks Windows XP was the best thing ever and goes a funny shade of red when anyone mentions Linux (or anything else he doesn't understand)

Circa 2000 I worked in a place with such a head of IT. After some effort I managed to get my work done by bringing in my own Linux laptop. But, connecting it to the network was strictly prohibited ("everyone knows that Linux is insecure"), and data had to be transferred by floppy disk to/from the rather unreliable networked Windows PC shared by me and two other scientists in the same office. This PC used to crash after each user logged out and required a reboot pretty much every time.

Re: Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

#113
post #74
post #73

Earlier quoted context omitted.

I was also just thinking this… but really only realized it reading the grand-post. Probably the general rule is simply, “you get more bugs when expectations don’t match reality”. Example: 1. (null) This value can’t be null 2. (article) This value won’t be converted into a date 3. (misc) This API can be called frequently

> Probably the general rule is simply, “you get more bugs when expectations don’t match reality”. That's too vague to be useful. You might as well say "you get bugs when you write wrong code". Whereas framing it as a lack of type safety points towards an actionable solution.

I think this is too strong a take. The general rule, as stated, can be useful as a way to think about systems, interfaces, architecture, etc in broad strokes as a vector for expectations which might fall victim to this pitfall. Being general, it isn’t prescriptive about the solution… but then, type safety isn’t always (and isn’t the only) solution. It’s a way to think about problems where you explicitly scrutinize the expectations they promote and their corresponding realities. You might arrive at type safety as a measure to align those, but you might also consider a variety of other concerns in the same thought process. It’s only unuseful if the problem you’re applying it to is itself vague, or if you’re unprepared to do the thinking involved in understanding a more specific problem and what expectations you’re addressing in solving it.

Re: Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

#116

Earlier quoted context omitted.

We, as CS people, think computers are easy. However, for other disciplines, computers are not easy. We can try to (and do) create tools, but it's not as simple as a table editor or a simple CRUD application. Scenarios has many peculiarities and edge cases.

A fair proportion of CS is precisely oriented around the fact that computers are not easy in ways that non-CS people don't realise, and provides methods for quantifying and trying to cope with that. I refer you to https://xkcd.com/2030/

I think the reason why first two examples can say that they are safe is that in case of failure, people die. And thus there was a regulation introduced. People generally care when they can die.

In case of software, rather rarely people die and when software is being done on something human critical (a friend of mine works on pacemakers), there a great deal of care being done.

So basically it's a wide range from DIY using a cheap wrench to person rotating a torque calibrated wrench on a rocket. Because just like the hammer, there is a wide range of use cases, some critical (e.g. pacemaker), some mundane (e.g. ecommerce).

Planes and elevators always have a risk of crashing and killing humans. And it did. Software doesn't.

Re: Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

#117
post #84

Earlier quoted context omitted.

it would be so easy to just implement an opt-out function, but Microsoft doesn't want to. There doesn't have to be a tradeoff if you make it optional.

As usual, I think it's a lot more nuanced than that. An option was added last year [0] the way you propose it, but until then users already had the option to mark the columns as text. The same way we have to deal with any data where auto detection might be problematic: explicitely set a type, and potentially a format. But of course that's bothersome, sometime people forget to do it, sometimes they don't even know how…

> but until then users already had the option to mark the columns as text

This only works on Excel files though, which save a type for columns/cells. With CSV files, Excel would just auto-format them. I guess you could save everything as xls/xlsx, but I shouldn't have to use a vendors file format because they're threatening to corrupt my data if I don't.

Re: Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

#118
post #8

As a computer scientist this sounds ridiculous. Especially that they restrict themselves to Latin letters and Arabic numbers. I guess many people here will point out that they should use other tools. I think we should help them in any way. They could also prefix every gene with Gn so it cannot be confused with other acronyms (e.g., GnDEC12). It not only breaks parsing by computers but also by humans who might read of…

These gene names are human readable strings, not concept unique identifiers. We in bioinformatics / comp bio world strongly encourage the use of ncbi or ensmbl gene IDs. In general it is bad practice to use human readable “names” of things as a primary indexing key.

Yes that's true, unfortunately people do it all the time and there's really no way to stop it.

Re: Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

#119
post #101
post #89

Earlier quoted context omitted.

An opt-out doesn't solve the problem, because one person in the chain of custody if an excel file who hasn't opted out would be enough to destroy the data.

Only if the option was implemented as a user preference which isn’t stored in the file. The right way to do this would be to add the flag as a file header, and give people a UI control to set it by default. That way you’d always see spreadsheets as the person who gave it to you did, and you would create new ones with your preferred behavior.

I don't understand what's wrong with the existing solution of:

Right Click > Format Cells > Text.

Set the data type of the column and Excel will not fiddle with it. Let it stay implicit and Excel will to guess. This change is saved in the file. The article only slightly touches on this: converting to CSV and losing all the Excel formatting and then opening it in Excel again.

Re: Scientists rename genes to stop Microsoft Excel from misreading them as dates (2020)

#120

So let me get this straight: Scientists would rather rename genes, than to simply use a tool other than MS Excel?

Spreadsheets are irreplaceable because they're the only no-code software development tool that's ever succeeded. Nothing will ever replace spreadsheets, because the tech industry no longer believes in making products for power users. In modern thinking, any form of user training is an indication your product is too complicated, and any feature only used by 5% of users should be removed. The idea of a product where us…

Or any R or J user doing faster and secure stuff, even by using BioPerl/BioPython under a Jupyter instance. 1970's? This came from 2040, but brainwashed Excel users are still mentally locked in the 80's.
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