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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

#211

Post by reportgunner »

acid__ wrote: post #189
mcv wrote: 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…

Excel may have failed in this specific task, but let’s not pretend like its functionality doesn’t run circles around Google Docs and LibreOffice. Excel is a “pretty darn good” tool for 95% of tasks. If your work has highly varied workflows, then that flexibility more than makes up for its failures on the last 5%. If you have very specific workflows on the other hand, you may find value in replacing Excel with a speci…

From my point of view Excel hits a sweet spot between 'very simple tasks' and 'very complex tasks'.

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

#212

Post by oneplane »

gundmc wrote: post #186
shpongled wrote: post #159

Earlier quoted context omitted.

I would say the number of biologists who actually understand programming is extremely small. I've been programming for fun for ~15 years, and I'm about to finish a PhD in chemical biology (e.g. I started programming in C far before I started learning biology). You might occasionally run into someone who is passable - at best - with R or Python. But most of the code they might write is going to be extremely linear, an…

To be fair, linear code is often totally sufficient for most types of data analysis. Biologists don't really need to understand design patterns or polymorphism, they just need to not make computational mistakes when transforming the data.

It does get rather problematic when you have large quantities of...stuff. You can't run linear stuff in parallel so now you're bound to whatever single CPU core you have lying around.

I'd say that getting some basic data science computing skills should be more important than the silly SPSS courses they hand out. Once you have at least baseline Jupyter (or Databricks) skills you suddenly have the possibility to do actual high performance work instead of grinding for gruntwork. But at that point the question becomes: do the people involved even want that.

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

#213

Post by jpindar »

FabHK wrote: post #195
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.

> 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...).

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

#214

Post by [deleted] »

meow1032 wrote: post #47
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…

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…

[deleted]

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

#215

Post by goatlover »

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?

Yeah, but one would hope that science has a higher standard. 80% garbage results in science sounds catastrophic to our understanding of the world, and in particular when it comes to making policies based on that science.

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

#216

Post by jpindar »

ethanbond wrote: post #198
t-c-h wrote: post #136

Earlier quoted context omitted.

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.…

Excel excells at being already installed on most computers. That's it.

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

#217

Post by rorykoehler »

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…

Excel should belong to the commons at this stage

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

#218

Post by rat_1234 »

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…

This calls to mind a quote from Cormac McCarthy's Blood Meridian:

  It makes no difference what men think of war, said the judge. 
  War endures. As well ask men what they think of stone. War 
  was always here. Before man was, war waited for him. The 
  ultimate trade awaiting its ultimate practitioner. That is 
  the way it was and will be. That way and not some other way.
Just swap our war for Excel! "It makes no difference what men think of Excel, said the judge. Excel endures. As well ask men what they think of stone."

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

#219

Post by oneplane »

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'm actually having a lot of scenarios where Excel is banned except for some managers, C-level and board type stuff.

If you produce, touch or directly act on data, Excel is no longer allowed. On the other levels the people that still use it (because they think they have the skill - which they often don't) can't do meaningful direct-action on those files anyway so that solves part of the problem of acting on bad data or bad data processing.

We do allow web-based spreadsheets, that has the benefit of limiting what you can do and drives people to either put a request in with the correct team or take internal courses on how to do it right.

Some people hate it, but then again, some people hate Excel. The difference is that the people that don't hate it now have an empowered skillset that they didn't have before. In theory you could do the same with Excel-oriented internal courses, but we didn't want to do Excel because a lot of us think it's stupid (often simply for emotional reasons but the push was based on hard data like process metrics and user input).

To add to this: it's probably because I find myself attracted to data-driven organisations where using Excel didn't help the workforce much anyway, and the positions I'm in allow for a certain degree of influence on the tools that we support and how much explicit allow/deny we apply on them.

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

#220

Post by reportgunner »

owl57 wrote: post #119
LatteLazy wrote: post #26

It's honestly amazing that Excel hasn't fixed this issue. It's pisses off an enormous number of users especially in basically any non-US country (even if 01/02 is a date, it isn't the second of January in most of the world...)

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!?

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-mmm-yyyy' format which excel translates based on client locale:

- 13-mar-2020 in enUS

- 13-bře-2020 in czech

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