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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

#292
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…

The hyperbole here is amazing. You're saying that a 40 year old computer program that runs exclusively on windows is as un-changable as a _law of nature_. The english comparison made in a peer comment is more apt, but wow. The tech industry is so self-centered we think that Scientists should change their fields because of our bugs.

Excel is older than many of us, so yeah, having it around for our whole lives does really make it seem like a law of nature. Sooner or later, all data ends up in Excel. I don't like it at all, but that's what happens.

As for this being an Excel bug: many, perhaps most people don't think it is. That's why it's so permanent: almost everyone likes it.

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

#293

Excel isn't the program of choice for most scientists and computational biologists, who typically use R, python, or command line tools. However, we often get data from other scientists or reanalyze data from other groups that can have these errors. It's so frequent of a problem that there are scientific papers about it [1]. [1] https://genomebiology.biomedcentral.com/articles/10.1186/s13...

I feel that excel should still do the right thing which is annoying, but the change also helps people avoid confusing the names with dates, for example, in the excel sheet has dates in it well.

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

#294
Research software dev here. This came as a huge shock to me when I started at my job. I work with very smart, dedicated people performing cancer research, why would they put up with this affecting their productivity? Humans really are adaptable creatures.

After a few months of working there my boss handed me 3 or 4 Excel spreadsheets to compare to ensure a recent change I made hadn't affected our data (we don't have much in the way of automated tests either). As a software developer, this was a deeply troubling request.

One option was to load them in to database tables so that I could perform SQL queries against the data (Postgres has COPY that works with CSVs), which isn't hard and probably the path most people should take, but I didn't want to write table definitions.

I ended up using https://github.com/BurntSushi/xsv (I am not affiliated with the project in any way). It's a command-line tool written in Rust that performs queries/joins/manipulation/basic analysis against CSV/TSV files. While not as analytically powerful as Excel or Postgres, I was able to verify the data was good and pipe out results into another file without writing any custom code, and without opening a single file.

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

#295
post #171

Earlier quoted context omitted.

Not at all There is tremendous competition in the spreadsheet business, and anyone is free to use Julia, R, whatever they like.

But they don't, and that's a problem. It's an education problem: everybody automatically defaults to Excel, even when it's not the proper tool. People need to learn about better tools.

I just don't see it being a big deal. You can't just force people to use something they don't like.

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

#296
post #192

Earlier quoted context omitted.

python+pandas [1] is probably quite an easy choice for most common things people would use excel for. And being in the python ecosystem offers lots of libraries for statistics, machine learning, signal analysis, plotting etc. [1] https://pandas.pydata.org/docs/user_guide/10min.html

People like real time feedback it's why word is more popular than tex, all these tech folks pushing code solutions to wysiwyg software issues are missing the point.

Ipython/jupyter notebooks fill that niche quite nicely.

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

#297
post #17
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…

True in every sense. We shifted from google sheets to O365, there's just no way to go around excel. Its efficient and every one from a novice to expert can find their way around it.

Pray tell, why did you switch from Sheets?

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

#298
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…

Better tools for managing genomic information are probably out there, but if everyone picks Excel (or workalikes that all do automatic date formating too), then hoping people switch is tilting at windmills.

Unilaterally declaring you will not use names that confuse Excel will fix the problem (until we get new month names, anyway), and not require anyone outside their sphere of influence to comply.

I had the same situation at work, as an aquired company we had servers named devX, the new parent had servers named devX and pushed ssh config files to our laptops that made it impossible to connect to our servers; we asked them to fix it the first couple times, but eventually renamed our servers to vedX to avoid the issue. It wasn't the right solution, but it was a stable solution and let us get on with our lives instead of fighting with IT.

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

#299
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…

Excel is a wonderful tool and a type of programming that is very accessible to many people. I use it all the time.

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

#300
post #195

Earlier quoted context omitted.

> 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…

I'm surprised people don't use other words for digits, as they do for letters (alpha, bravo, charlie...).

Most of the digits sound distinct enough that they don't get confused- except "nine", which can sound like "five" over a bad radio link, and is therefore pronounced "niner".
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