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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

#191

Post by leecarraher »

jkaptur wrote: post #58
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…

The date parsing being discussed has been the behavior for at least 20 years, probably more like 30. Your comment about graph paper echoes a comment from a former Excel PM: "The gridlines are the most important feature of Excel, not recalc." https://www.joelonsoftware.com/2012/01/06/how-trello-is-diff...

Nice, well there you go.

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

#192

Post by vxNsr »

welterde wrote: post #132
hutzlibu wrote: post #36

Earlier quoted context omitted.

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

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.

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

#193

Post by benhurmarcel »

baddox wrote: post #179
epistasis wrote: post #77

Earlier quoted context omitted.

It's not usually computational biologists who are using Excel. What if you want to share data with a wetlab biologist who want to explore their favorite list of genes on their own?

If people are just looking at the spreadsheets then wouldn’t the cells interpreted as dates not be a problem? It seems like it would only be a problem if you’re doing computation on the cells.

Excel changes the displayed text when it interprets the text as date. You store "MARCH1", it displays "1-Mar".

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

#194

Post by fock »

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…

I work in computational materials science (where ML brings funding) and a funny paper of this kind is here: https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.11... - they are literally trying out 100000s of possible combinations by brute force, to build a "physical model".

Then they go on conferences and brag about it, because they have to (otr they know it's bs). Datasets are soso (you can have a look at QM9...) and for more specialized things, people generally don't bother trying to benchmark or compare their results on a common reference. It's just something new...

And with all that: even without doing fancy statistical methods without knowing too much about it, your theoretical computations might not make so much sense (at least in the sheer number which is pumped out and published)...

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

#195

Post by FabHK »

BurningFrog wrote: post #79
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…

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 eight zero").

At any rate, switching to metric would be much better (If I'm 2000 metre high, and I have a glide ratio of 1:10, I can glide 20,000 metre or 20 km. If you're 5000 feet high, and you have a glide ratio of 1:10, how many nautical miles can you glide?), but for the reasons you mentioned, it won't happen anytime soon.

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

#196

Post by epistasis »

FabHK wrote: post #168
epistasis wrote: post #92

Earlier quoted context omitted.

That doesn't solve the analysis problem downstream when a non-expert is getting started, doesn't know about Excel's anti-features, and starts doing analysis using the only tool that the world has ever told them is acceptable for tabular data. Ideally excel would change, but since we know it won't, and we want to work with lots of people with minimal problems, we must adapt.

Why should Excel change? Most people mean March, the first, when they enter march1. Researchers should use other, more appropriate tools, or at the very least specify the column type when importing data into Excel. It's not that hard.

Do they mean March 1 when they import data from a text file?

It's one thing to change typed in user text in real time. That's not causing any problems. It's another to randomly mutate cells amongst tens of thousands of rows. I don't think that has ever helped anyone.

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

#197

Post by david422 »

dr_orpheus wrote: post #69
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…

Having Excel be the default for .csv files has caused me problems in the past as well with Excel automatically changing data when you open it. The unfortunate thing I have come across multiple times is a csv file that has some values with a lot of significant figures, i.e. 123456789876, 987654321234 After opening in Excel it will convert these to: 1.23E+11, 9.87E+11 Then resaving the file (as a csv) will store the va…

Yes, and then compound this problem by transferring files with people that.... are somewhat technically illiterate and it turns into a nightmare.

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

#198

Post by ethanbond »

t-c-h wrote: post #136
ethanbond wrote: post #91

Earlier quoted context omitted.

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 HP…

Oh yeah, I'm totally aware. My day job is designing and building software to construct/maintain exactly those pipelines.

What I'm saying (which is not news to you) is that clearly Excel is excelling along some dimension that people really care about. Even if it is lacking along other dimensions, the goal ought to be figuring out what makes Excel so good, then figuring out how to reconcile that with the needs of e.g. a high scale genomics pipeline.

But to make even an inch of progress against that, we need to get rid of this "haha Excel is for plebes" attitude that many in the software community adopt.

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

#199

Post by vikramkr »

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…

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.

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

#200

Post by FabHK »

takluyver wrote: post #125
DarkWiiPlayer wrote: post #109

Earlier quoted context omitted.

YAML offers a simple solution though: just quote all one-word text and, more importantly, quote all text you don't manually write into the YAML file. Also, the main problem is that excel changes your input instead of just misinterpreting it. The difference being, the original will be gone.

You could also start every Excel cell with ' . But it's really convenient not to quote stuff, so that's what everyone does, both in Excel and in YAML.

Exactly. Excel offers the same "simple" solution.
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