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Author Topic: mswin vs linux in academia  (Read 3101 times)
kalos
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« on: August 02, 2012, 08:18:24 AM »

hello!

i know there are numerous mswin vs linux topics, but in a new workplace i am in (computational chem, biology, etc), they use mainly linux
is there anything in general (or particularly in specific sciences like these) that we cannot do it in mswin and can do it in linux?
i mean, okay, there maybe copyright issues that make linux definately more attractive, but practically do they have differences in abilities?
for example, vi, tex, etc are very much used in academia. arent there mswin counterparts that are the same or even better?

thanks!
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40hz
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« Reply #1 on: August 02, 2012, 11:08:51 AM »

An OS is an OS is an OS to paraphrase the Bard.

It's not so much a question of technology as application software availability. Nix environments are legally and culturally more "open" which encourages the cooperative and collaborative efforts educational and research institutions naturally gravitate towards.

If more is available in the Nix environment, it's mainly because it's a better fit for the way things get done in those settings. It's not for any technical reason. And since these users tend to be very bright, learning a new OS doesn't really pose a significant challenge to most academics.
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« Last Edit: August 02, 2012, 12:17:31 PM by 40hz » Logged

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mahesh2k
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« Reply #2 on: August 02, 2012, 11:10:58 AM »

Some of the softwares like say - Matlab and similar other academia softwares are commercial and they are on apple or windows. They don't usually have linux port for many reasons. So commercial academia applications on the apple and windows are better if more people are using it and it makes sharing of files easy without any file format conflict. That doesn't mean there are no applications on linux. There are and mostly they are ignored or not brought for many reasons.

I have seen nothing better in windows after using linux. I found windows to be more productive if the applications that you use are not buggy. Many of the open source and free software on *nix and linux world are made with keeping power users in mind and that's why there are very few apps which are more powerful on windows and don't exist on linux. Most of the apps which are in demand on windows are largely due to the popularity of applications, not because of the usability and features.

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Renegade
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« Reply #3 on: August 02, 2012, 11:23:35 AM »

Wow. I think abortion, legalizing drugs, euthanasia, and why all <insert religion here /> are going to hell are all much calmer topics. smiley

Ok, jokes aside...

I think on Linux that you really need to be much more willing to drop down to the command line/shell. If you like typing, then Linux is great. If you want a GUI, then often Windows is more appropriate.

For what you can actually do? Well, again, that kind of depends. If speed and ease are important, and you don't want much of a learning curve, then often Windows is better. If you want infinite flexibility everywhere and are willing to spend more time and energy, well, you can even compile Linux from source, so that's pretty hard to beat.

So basically, I blathered on without saying much. cheesy

Probably the best thing to look at is the variety of software packages for computational chemistry and biology, then see which suits you better. I don't know much about them, and can't comment.

If you're interested in vi and whatnot, well, again, it boils down to preferences. Once you get used to vi, it's great as you can ditch the mouse, which helps with speed. However, it has a steep learning curve. Notepad++ or Editplus might be more to your liking. Depends mostly on you. I use Editplus mostly, but also use Notepad++ when I need to. (Editplus doesn't handle one specific case that I require every once in a while.)

One of the problems is illustrated by the fact that any complete language can do what any other complete language can do, with the only difference being in speed and hair loss/frustration. smiley
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« Reply #4 on: August 02, 2012, 11:53:14 AM »

with the only difference being in speed and hair loss/frustration.

I was actually sitting here trying to figure out what hair frustration was...

Mind = Lost; send brightly colored string.
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40hz
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« Reply #5 on: August 02, 2012, 12:42:22 PM »

If speed and ease are important, and you don't want much of a learning curve, then often Windows is better.

But only if you ignore the fact that most people already have a significant amount of Windows learning under their belt whether they realize it or not.

One advantage Microsoft has being the desktop 'standard' is that millions get exposed to it early and often.

All operating systems and system tools need to be learned. You're not born knowing how to use a command line - or a GUI for that matter. You learn them. But when you're exposed to something as often as you are a Windows desktop and mouse, you forget just how much you've actually have learned over the years in order to use it effectively.

Since most people's Nix exposure often comes well after they've become proficient in Windows, they're more consciously aware they're learning something new. And occasionally they also find themselves needing to "unlearn" Windows conventions which they had previously assumed were the only "correct" way to do things on a computer. Small wonder Nix can seem "hard" to someone who's conceptual framework and workflow has been strongly shaped and influenced by Microsoft's vision of how to do things.

Linux is no harder to use (on the desktop level) than Windows. And beneath the hood, it's not really any harder to master either. (If you don't believe it, try tackling the Windows Registry, Group Policies and Objects, or Active Directory components before you say Linux is difficult to understand or work with. Especially when something goes wrong. Or when you start getting into serious shell scripting. ) Linux doesn't, however, hide its underpinnings and clockwork like Windows does. You can get into much deeper levels in Linux than Windows will allow. But that doesn't mean it's more complex. It just means the complexities are more accessible. Underneath the pretty GUI, Windows is every bit as complex - or possibly even more complex - than Linux is. But that's only to  be expected. Operating systems are complex beasts. No getting around that. No matter who wrote it.

How deep into it you need to go, and how much complexity you need to deal with, will be determined by your individual interest and needs.

It's no different than anything else that's "technical" when you think about it. smiley




« Last Edit: August 02, 2012, 01:43:53 PM by 40hz » Logged

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« Reply #6 on: August 02, 2012, 02:06:08 PM »

If speed and ease are important, and you don't want much of a learning curve, then often Windows is better.

But only if you ignore the fact that most people already have a significant amount of Windows learning under their belt whether they realize it or not.

One advantage Microsoft has being the desktop 'standard' is that millions get exposed to it early and often.

All operating systems and system tools need to be learned. You're not born knowing how to use a command line - or a GUI for that matter. You learn them. But when you're exposed to something as often as you are a Windows desktop and mouse, you forget just how much you've actually have learned over the years in order to use it effectively.

Since most people's Nix exposure often comes well after they've become proficient in Windows, they're more consciously aware they're learning something new. And occasionally they also find themselves needing to "unlearn" Windows conventions which they had previously assumed were the only "correct" way to do things on a computer. Small wonder Nix can seem "hard" to someone who's conceptual framework and workflow has been strongly shaped and influenced by Microsoft's vision of how to do things.

Linux is no harder to use (on the desktop level) than Windows. And beneath the hood, it's not really any harder to master either. (If you don't believe it, try tackling the Windows Registry, Group Policies and Objects, or Active Directory components before you say Linux is difficult to understand or work with. Especially when something goes wrong. Or when you start getting into serious shell scripting. ) Linux doesn't, however, hide its underpinnings and clockwork like Windows does. You can get into much deeper levels in Linux than Windows will allow. But that doesn't mean it's more complex. It just means the complexities are more accessible. Underneath the pretty GUI, Windows is every bit as complex - or possibly even more complex - than Linux is. But that's only to  be expected. Operating systems are complex beasts. No getting around that. No matter who wrote it.

How deep into it you need to go, and how much complexity you need to deal with, will be determined by your individual interest and needs.

It's no different than anything else that's "technical" when you think about it. smiley

Mostly yes. A little bit of no. smiley

The No Part:

Windows is really GUI-centric. Everything is in a GUI. And GUIs are simply much easier to learn than the command line because everything is laid out in front of you to see in 1 glance. I think that accessibility is the thing to look at. i.e. Is it possible to use the functionality easily? If not, well, then it might as well not exist unless you're willing to put in a massive amount of effort.

Now, if you really, really want to see just how unholy Linux is... Look into distribution packages... On more than a superficial level. It's ungodly. It's an abomination against humanity. Really. I think I'm actually understating it... It's worse than the 9th level of Hell. Even Apple hasn't screwed things up that badly. Windows on the other hand is pure simplicity. However, that's just one small thing -- how to distribute software sanely. It isn't a reflection on the rest of the OS.

The Yes Part:

Yeah. Pretty much. (Unless it's Ubuntu's new way to obfuscate everything. What do they call it? Oh, yeah... "Unity". tongue Grin )

-- I LOVE the Enlightenment desktop... oh god... It's just divine! Best one I've ever seen.

However, the real question is about a given purpose. My example of the mutilation of software distribution on Linux is hardly relevant to computational chemistry. The important thing there is what software packages are available to get the job done.

I don't think the OS really is all that important for any given specific task. The software used to complete the task is the real question.
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mahesh2k
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« Reply #7 on: August 02, 2012, 06:16:19 PM »

Quote
Windows on the other hand is pure simplicity.

I have to disagree on that part. Windows 8 anyone? cheesy

That Said I personally found enlightenment the ugliest manager ever. tongue

Besides linux distro options are not that bad. I mean having 1k or 10k distro doesn't change the fact that you have to select the window manager of your choice and move on with it. What's wrong with having 10k or more distros? nothing. It's just that people are bombarded with options and they feel wrong about it. As for apple, it is getting way worst hell. Restriction is hell, packaged in sugar candy. Not even windows is that bad. I must say, between windows, apple and linux, the percentage of hell quota is increasing on apple's side.
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Renegade
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« Reply #8 on: August 02, 2012, 10:17:06 PM »

Quote
Windows on the other hand is pure simplicity.

I have to disagree on that part. Windows 8 anyone? cheesy


I meant that exclusively in relation to creating software distribution packages, i.e. installers, setup files, packages, whatever anyone wants to call them.

If you know something I don't about how to sanely create a package for Linux, please, do tell me~! smiley


That Said I personally found enlightenment the ugliest manager ever. tongue


I can see why some people wouldn't like it. I really liked the availablity of everything everywhere.
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40hz
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« Reply #9 on: August 02, 2012, 10:19:26 PM »

I LOVE the Enlightenment desktop... oh god... It's just divine! Best one I've ever seen.

Gotta agree with mahesk2k in saying I really don't like it. Even Bodhi, which did Enlightenment better than anyone else, was still annoying. I felt like I was sitting in front of some 80s era researcher's notion of what the "Desktop of the Future" would look and work like. It seems funny (to me) how the Enlightenment developers think they're so forward looking when the whole Enlightenment environment strikes me as actually being rather retro. And not in a good way either.

But that's me. I like fairly boring desktop/windows managers that have a minimum of pyrotechnics and eye candy. And I truly dislike anything resembling a widget, or that uses a widget paradigm. Think I'll stick to my old favorite: Xfce. thumbs up

Actually, this Bodhi desktop doesn't look half bad:



Hmm... Grin
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jgpaiva
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« Reply #10 on: August 03, 2012, 04:05:24 AM »

Here's my opinion as a phd student in the systems area:
I believe it has absolutely no relation with ease of use of the operating system. As 40hz mentioned, at this level everyone could learn any of the OSs with ease.
For the guys around me, it seems to be a combination of several factors:
1 - there's a significant larger body of work for unix/linux (more people are using it, which makes others change too). example: my experience is that the software available from recent years of the Symposium on Operating Systems Principles (the top conference in the Systems area) is mostly prepared to be ran in linux (despite much of it being cross-platform).
2 - we do much stuff that builds on industrial work (I'm thinking of Apache Cassandraw or red hat infinispan) for which it is easier to find support for the linux platform.
3 - we build some stuff for the industry, which prefer to receive stuff for their platform, typically linux.
4 - our processing grids are in linux (using Condor High-Throughput Computing Systemw). I don't even know if there's anything comparable in windows.
5 - I have this notion that for those who work lower on the stack (kernel level?), it's either harder or impossible to do it in Windows due to being a closed platform (I have no experience in this and may be wrong, though).
6 - much of our experience during the university is directed at linux/unix.
7 - the availability of the tools we use (gnuplotw and graphvizw are the only ones that occur, but there are many others): almost everything is an apt-get away from being installed, and if necessary we can install them in the servers to run with larger datasets. In windows, they are either harder or even impossible to install.

For the reasons above, frequently people use either linux or mac for their desktops, and linux for the servers. It is also frequent to go to meetings with other universities and find the whole room filed with macs. Last year's SOSP was here in Lisbon and I attended it, and my experience was that in general mostly only the people working at MS research use Windows and the percentage of people using mac is much larger than in the general population.

Having some kind of unix on the desktop simplifies the interactions with the servers (in our case, we have about 28linux and 1dual-boot (linux+windows), without taking into account the computing grids which are all linux). I have in the past used windows with cygwin to achieve a similar result, but felt that I was trying to "patch" windows making it look more like linux instead of using the real thing, and eventually had to change.

There's a notable exception to everything I said above: there are a few guys in our research group who had a few microsoft scholarships some years ago. Those guys have built stuff for windows for those projects and are still using it today as their main desktop.
Also, this applies only to the Systems area. There are other areas which I suppose are not as tied-in to linux since their tools are more windows-centric. (I'm thinking of the people-machine interface guys or information management. But I may be wrong tongue )
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« Reply #11 on: August 03, 2012, 04:57:29 AM »

Virtually all GNU software - and even some BSD software - has been ported to Windows. There is no reason to prefer Linux just for its applications.
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mahesh2k
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« Reply #12 on: August 03, 2012, 09:51:06 AM »

Quote
I meant that exclusively in relation to creating software distribution packages, i.e. installers, setup files, packages, whatever anyone wants to call them. If you know something I don't about how to sanely create a package for Linux, please, do tell me~! smiley

How build system has to do with simplicity of the OS? Software on linux is routed via repository and software center these days, installers are hardly needed in these cases for popular programs as community takes care of it. And this method is much easier and better than windows software installation. Hell, I am sure they'll start with repository concept soon. Again, You're comparing build package system for multi-distro linux to that of single standing windows. I am sure you do know that there are formats specific to the distribution and then there is build from source method. Software like gDebi helps in any case and user has to do nothing other than downloading the archive. To get to your point about better packaging system, there was Installjammer, for both windows and linux(or *nix) which is now discontinued and then there are some commercial installers and free like installanywhere and autopackage.




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« Reply #13 on: August 04, 2012, 09:59:52 PM »

...
If you know something I don't about how to sanely create a package for Linux, please, do tell me~! smiley

Mahesh2k is right, most distros use repository + package management for installing and the like, so you'll have to get comfy with the workings of Apt and Rpm to target the majority of those systems.

The only other ways I've seen:
-Plain compressed package (tar + gz or bzip2) that unpacks to the most common default locations for executables and config files.
-Shell script that contains a binary payload, which is probably the closest thing Linux has to Windows stand-alone installers.
-0install. Never did figure that one out...

That said, I've gotten pretty cozy with the Apt package management system, and made a few packages that actually worked, so maybe I can give a few pointers.  It's not that hard, just the documentation makes it seem like it.

As far as Linux in academia, jgpaiva has the best comments on that; Linux was basically born out of Unix in an academic setting, so it doesn't surprise me at all that the tradition continues with Linux.
I would expect more Windows usage in a setting where the focus was development for the platform.
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