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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

#131

Post by tgb »

azalemeth wrote: post #23
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…

> " 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…

Surely then the blame should go one step further back: .csv and tab-separated are poor file formats for *omics data and excel (and pandas, etc.) have no choice but to guess data types and metadata. Unfortunately I'm just not sure there's any format that's sufficiently better to ever replace them.

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

#132

Post by welterde »

hutzlibu wrote: post #36
DethNinja wrote: post #11

Earlier quoted context omitted.

What’s the alternative?

Well, everybody should set up their own, custom script powered favourite DB of course. Ok, seriously, it would be nice to te able to recommend a alternative. I heard LibreOffice Calc is not really equivalent?

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

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

#133

Post by JoBrad »

donatj wrote: post #66
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…

So much this. I work in educational software, and have a little write up about the troubles we’ve had with schools “fixing up” CSVs from their student information systems before sending them to us. The simple act of opening the CSV and hitting save loses data (Microsoft actually fixed some of the problem very recently). That said, they will use Excel, it’s not in my control. I received dozens of comments “Just use Op…

I’ve shifted to trying to get people to use the PowerBI data import function, at least. It offers the ability to import your data without managing it.

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

#134

Post by ubermonkey »

leecarraher wrote: post #24

Final Jeopardy : Trebeck: You know what, how about you just write down a number, any number at all. Could be a 1 or a 2, perhaps 3... and excel you answered; A smiley face emoji, simply stunning. Excel is no longer motivated by the original intention of a spreadsheet, and now caters to the lowest common denominator, a piece of graph paper. As such MS has shifted focus from doing calculation to text and graphics layou…

MSFT did the same thing with Project when they introduced something called "Manually Scheduled Tasks."

Project is fundamentally a critical path scheduling tool, or at least was. Task A must finish before Task B, which must complete before Task C. If A is delayed, then that delay pushes B and C out, too.

This is what it's FOR, more or less.

Manually scheduled tasks don't move. They're set with whatever dates you give them, and do not move in response to delays or whatnot from predecessor tasks.

People wanted this because some (dumb) people insisted that "well, that task CANT move because it has to be done by then!"

This is akin to asking for the arithmetic engine to be turned off in Excel, because by golly you really need 2 and 2 to sum to 17.5.

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

#135

Post by meow1032 »

gameswithgo wrote: post #100
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…

it would be nice if everyone was expert at everything, but they cant be. it would be nice if they hired experts but money doesn’t grow on trees. we often insist on a degree of excellence we refuse to pay for

It's not about being an expert at everything or hiring more people. These aren't particularly hard problems, it's not difficult to find biologists who are incredibly adept at using python, R or C. It's about thinking about how science gets funded and how it gets implemented. I've written here before about the difference between "grant work" and "grunt work", and how too computer touching tends to get looked down upon at a certain level.

If you're deciding who gets a large-scale computational biology grant, and you're choosing between a senior researcher with 5000 publications with a broad scope, and a more junior researcher with 500 publications and a more compuationally focused scope, most committees choose the senior researcher. However, the senior researcher might not know anything about computers, or they may have been trained in the 70's or 80's where the problems of computing were fundamentally different.

So you get someone leading a multi-million dollar project who fundamentally knows nothing about the methods of that project. They don't know how to scope things, how to get past roadblocks, who to hire, etc.

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

#136

Post by t-c-h »

ethanbond wrote: post #91
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.

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.

Excel is great, and generally really useful. But not so much in microbiology. Sure, if you have several dozen genes/proteins with some quantitative values and some conditional formatting to visually distinct certain properties, it's fine.

But in microbiology you usually works with very large datasets that undergo a lot of calculations through a lengthy pipeline. Larger sets and more intense ML approaches even need HPC's. Inserting Excel into this pipeline would be catastrophic.

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

#137

Post by owl57 »

spuz wrote: post #124
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!?

How is "06.08.2020" unambiguous?

Does anyone use mm.dd.yyyy?

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

#138

Post by tremon »

spuz wrote: post #124
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!?

How is "06.08.2020" unambiguous?

There are no conventions that write a date as mm.dd.yyyy, so if you encounter a date in that format, it is safe to assume dd.mm.yyyy.

Contrast this with the slash or dash notation, where both mm/dd/yyyy and dd/mm/yyyy are prevalent in the world. But 2020-08-06 is unambiguous in the same way that 06.08.2020 is: the only convention in common use is yyyy-mm-dd.

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

#139

Post by cproctor »

gameswithgo wrote: post #103
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…

isn’t the saying, 80% of everything is garbage?

We better work on making more stuff.

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

#140

Post by dijksterhuis »

jordigh wrote: post #33
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…

Excel is not fundamentally suited, but it's fundamentally used. I wish you luck, but I long ago declared defeat against Excel. I can't prevent everyone from using it. I have come to accept that whatever Excel does is what I have to live with, because someone, somewhere out there hasn't heard the anti-Excel gospel yet.

> I wish you luck, but I long ago declared defeat against Excel.

Totally relate to this.

I studied a degree because I wanted to rid the world of Excel.

Just like I wanted to rid the world of pie charts.

Turns out the rest of the world is quite happy using both of them, no matter whether I think it's right or not.

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