It is very similar question as Gustavo Rodriguez-Esteban asked (link below), but it is particulary about linux. Witch distribution do you recomend for work and for teaching of bioinformatics. What do you think about BioLinux?
https://www.researchgate.net/post/What_OS_would_you_recommend_to_use_as_a_platform_in_Computational_Biology_Bioinformatics?ev=home_person_add_comment_question_target
I would suggest you to use one of the 4 main Linux distributions, i.e. Debian, Ubuntu, Red Hat, or CentOS.
This suggestion is based on maintainability, continuity, stability, and security. All the above mentioned distributions are supported by very large communities or companies. This means that you can always count on them to fix bugs, deal with security problems, and keep developing and improving their distributions. I am not saying that BioLinux is not well maintained, or the people behind it are not good. In fact I have never used it, but all I can say is that it is based on Ubuntu with some extra software (bio software) already installed, which you can always install by yourself. You probably don't need everything they bundle with their distribution, and therefore it is just a waste of space.
When choosing a Linux distribution you must be aware that there is no difference between them in terms of what you can do or what software you can install. It is a matter of choosing the one that you feel comfortable working with and if the philosophy of the people behind it align with your own views. With that being said, I will make a brief description of the 4 distros I mentioned based on my personal experience, and why not, own point of view.
1. Debian: it is a very well maintained distribution. One of the first distributions to be created. Their focus is on stability, security, and on preserving free and open-source software. They have very serious people working on it. I would say it is probably the most successful distribution ever if you consider the number of distributions that derived from it (which includes Ubuntu). Considering scientific research, Debian is my #1 choice. In my opinion, for scientific applications you need the most stable platform you can get and the most trustworthy. That's why I would go with Debian. Note that it is not possible to achieve decent levels of stability and security if the distribution early adopts the most recent (barely tested) versions of all software. For this reason you wont find the last version of KDE or Gnome, or anything else on a Debian release. They always include in their releases versions that have been tested for a while, thus minimizing instabilities an security issues in their base releases. Despite that, you can always install more recent software by using Debian backports, or their testing packages tree.
2. Ubuntu: it derived from Debian (it uses .deb packages as well). It is maintained by the Ubuntu community and Canonical. The moto of Ubuntu is "Linux for human beings". Their aim is to provide good end user experience. For this reason they compromise security and stability in order to offer easy of use for end users. I would recommend Ubuntu in two situations, to use at home where you want to have comfort and use what is latest in terms of software (I use it for my Home Theatre PC), or for someone that wants to know Linux and is coming from a Windows environment. It is very good for the latter because it is really easy to install, easy to use, beautiful and has the power of Linux. In terms of performance it looses to Debian. I wouldn't use it for my research, and if you use it at your home for a while you will understand why. It is not as stable as Debian. Well, it doesn't freezes or anything like that (it is still Linux), but it is not uncommon that you have to fix something after an update. That is very, very, very rare to happen in Debian. Anyways it is one of the most popular Linux distributions. The open source community is a little bit mad at them because they mostly use what other develop and they don't contribute back to the community.
3. Red Hat: is maintained by the company with the same name. They are a reliable system and are the second in number of distributions that derived from them. They use .rpm packages and are as a good choice as Debian. The difference is that in general you have to pay for a support plan, which makes sense if you are running enterprise servers (their focus). Hardware vendors generally support Red Hat because they are a company with which they can have partnerships and contracts. Red Had is a good choice if you want support. Just a note, despite of the fact that Debian doesn't have a company behind them HP supports Debian in their products. In my opinion that is a vote of confidence on their serious community.
4. CentOS: or should we say Red Hat without support. CentOS is exactly the same of Red Hat. Yes, it is the Red Hat but without the support and some specific tools developed by Red Hat for their enterprise clients. If you want Red Hat but doesn't want or need the support, just go with CentOS.
No matter which Linux you choose, you will be able to achieve the same outcomes and rely on the open source community to answer your questions and help you with any problems. Just see which one you prefer.
There are many, many other Linux distributions (check http://distrowatch.com/ for the full list). It is impossible to talk about all of them. I just check distrowatch and remembered of Linux Mint, which derives from Debian, but they aim at providing more frequent releases and being a little bit more user friendly. Not a bad choice as well. There is also Fedora, which is maintained by Red Hat. Basically Red Hat's testing platform. I would avoid... if you want a Red Hat-ish distro, go with CentOS.
Please, for your own sake avoid Suse or OpenSuse no matter what other people may tell you ! :) OpenSuse is the 6th most popular distro... Windows is the #1 OS used and that doesn't mean it is good! ;o)
Well, this are just my two cents. Despite of what I said, Linux distribution is a matter of preference, it is very hard to say that one is better than the other [except for Suse ;o) ]
Hope it helps.
Cheers.
I would suggest Ubuntu Linux and its variants. It can be effectively used both as desktop and server. It has a very strong community support and pretty much any issue you may encounter you will find answers quickly. Most of the Linux software comes in a form that can easily be installed on Ubuntu (either through its Software Center, or in form of .DEB files). This answer was not necessarily specific to bioinformatics, but I am speculating that it will be applicable. I hope this helps.
No doubt Ubuntu is the classiest OS to work on, but, the other verision called "BIO-LINUX" developed particullary for computational biology and bio-info work is much useful as bio-info tools are intergrated with the OS. Please try it.
OK, am I right, that Bio-Linux is prepared on ubuntu? And do you think is it acurate for teaching - for students of biotechnology?
If you are completely new to linux, i would recomend to use the linux distribution which is most used among your friend and colleges. doing do you have a first line of support in case of any basic problem. Ubuntu is fine for desktops , for headless servers I would recommend centos
I'm not new in Linux, about 15 years ago I've started to use Unix (I don't remember the version) RedHat 5.0, next RH 7.0, after Enterprice and Fedora. I've tried Knoppix. Today I'm using Ubuntu, Mandriva, Fedora from time to time, and specialized versions as Scientific Linux, Edubuntu and PLD Linux.
I want to know your opinion, which distribution is the most friendly to install it in the class for students (for the excercises of bioinformatics). In my opinion the easiest way for both students and teachers is to use windows. Now I'm thinking (next time) if it is time to change the OS.
I would NOT recommend Ubuntu. If you are learning from scratch, Linux Mint is a good choice. If you are courageous and looking for a learning experience, I recommend debian (either stable or testing, not unstable). The good thing about debian is the large community and vast choice of packages.
Ubuntu is fine and you can always get rid of Unity. I too like Mint but BioLinux 7 is a decent distro
I love Debian too. It gives you full control and everything you want from the desktop to the server, and plenty of oportunities to learn how linux distribution works. I used to use debian unstable because i want the last versions of packages. Tons of fun, tons of learning.
IMHO Ubuntu is fine if you want that your students focus on the application and not in the details of the underlying OS. In that sense, It could be a decent choice for "the first linux" of your students. It is a good start, and it does not stop your students from explore other distributions more suited to their own interests.
Sadly, I have not tried linux mint yet but I have received good comments too.
so, in your opinion the Ubuntu is the easiest as the first Linux for students. Is there anything easier?
The reason I am not recommending Ubuntu has little to do with Unity; it is about many different factors that contribute to the overall long-term user experience. However I should also mention that getting rid of Unity is not trivial and for a beginner it would be much better to use something already 'set up' like Mint.
I my opinion ubuntu is a good start, as well as other Linux distributions like Linux mint. I strongly recommend to use the Linux distribution which is most used among the students in your department or faculty. It is possible to do a test run with a small group of students before the whole class?
I think that Linux Mint with MATE is the best choice. It's more stable than Ubuntu with Unity on my computers but in my case IPA working only under my ubuntu (and I don't know why but I assume that this is not a problem for you). I think that this is also good system for Windows users because of similarity. Mint is just a better ubuntu.
OK, I've never tried Mint - I'll try it.
About Linux most used by students in my departament - the most used Linux in my departament amoung students is ... Windows. ;)
As the second is Windows and third - Windows. That is why my question.
According to my understanding the distribution does not matter in case of linux but I would prefer Ubuntu due to three reasons 1. Excellent User Interface. 2. Good Online Support. 3. A Large User Community.
Bio-Linux is a good choice for teaching. It is pre-loaded with several day to day bioinformatics tools and programs. http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info
Ubuntu is a good enough start for the novel user, but you should try Fedora
Zorin is especially made for the Windows convert. I use Mint Cinnamon; simple menu system. I tried Ubuntu Unity, but it's not for everyone. Elementary and Bodhi are pretty. All these are Ubuntu, and therefore Debian, based.
If you are not familiar with linux, ubuntu is a good choice. If you want to run a server, debian is much better, or, if you like rpm-based distros, Scientific Linux is nice.
I strongly recommend Ubuntu. It is easy to configure and has a great community support.
BioLinux is great. It is built on Ubuntu, so has all the good features of that, but also comes with a large number of pre-installed bioinformatics tools. It is my Linux flavor of choice for home as well.
Here is a list of few good and known Linux distributions, particularly for life science researchers:
1. BioLinux (http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info)
2. BioBrew Linux (http://bioinformatics.org/biobrew/ )
3. DNA Linux (http://www.dnalinux.com/)
4. BioKnoppix (http://bioknoppix.hpcf.upr.edu/ )
5. BioLinux-Br (http://glu.df.ibilce.unesp.br/)
6. VLinux (http://bioinformatics.org/vlinux/index.html )
7. VigyaanCD (http://www.vigyaancd.org/)
8. BioPuppy (http://biopuppy.org/index.html)
9. Discovery2 (http://opendiscovery.org.in/)
10. BioSLAX (http://www.bioslax.com/)
11. BioconductorBuntu (http://www3.it.nuigalway.ie/agolden/bioconductor/version1/biocBuntu.iso)
12. phyLIs (http://www.eve.ucdavis.edu/rcthomson/phylis/)
13. Debian Med
14. Quantian Scientific Computing Environment (http://dirk.eddelbuettel.com/quantian.html)
I'm not familiar with BioLinux, but it might be convenient as, as far as I know, it comes with whole bunch of preconfigured bioinfo tools. Personally, I use Fedora for teaching, but Ubuntu is really good choice as well. And if you need a server, ScientificLinux would be my recommendation for someone preferring rpm-based distros (it's CentOS clone) and for those who like debs Debian is fine.
If you are new to Linux systems then Ubuntu is the best to start with.
I use the Debian: http://www.debian.org/ and I don't have problem with it.
Is there really any benefit to using a specialty distribution instead of just adding a few extra repositories to Linux Mint or Fedora? Do these distros use any customized kernel modules or compiler flags to better process bioinformatic workflows?
I'm not sure it would be necessary to go for a distribution that is particularly orientated towards biology. What you really want is a distribution that has a good quality, well maintained package database that includes the software you will need. The best choice depends on your Linux experience and how 'easy' you want the set up to be.
Arch Linux is a good 'bleeding edge' distribution, but will require a bit of setup/tailoring
https://www.archlinux.org/
Debian is a more 'standard' distribution, go for the Testing branch (it's actually very stable), it has the up to date packages.
http://www.debian.org/releases/testing/
If you want something nice and easy (although debian is pretty simple to setup/use) Linux Mint is a good distribution.
http://www.linuxmint.com/
A few people have mentioned Scientific Linux, I have found the package versions to be too out-of-date for my liking. Specifically the ant compiler, Python packages such as numpy and matplotlib, as well as a few other things. Ubuntu used to be the default choice for an easy life, nowadays it has rather lost that reputation as it is going in several controversial directions (making it annoying and potentially buggy). Linux Mint is an Ubuntu derivative so I would reccoment that over Ubuntu at the moment.
I'm working with Fedora distribution since 10 years, and for biotechnology, crystallography or molecular modelling it was perfect, rpm based packages as centos or scienticlinux who were all red hat based system.
I think that no particular distribution is indicated for working in bioinformatics. My particular experience is that Ubuntu appropriately fits the needs of these HPC applications.
I would suggest Fedora or CentOS, both RedHat alike. For computational applications I never had problems in particular when you need special libraries and a good development environment (even if the latest fedoras went on gnome 3 as interface which I didn't particularly like). Also the advantage is that they are reasonably updated and up-to-date. If you miss a special package it is easier to install and maintain it in these distributions then on others. My experience with Ubuntu is that it is perfect for the out-of-the-box tools but it starts to be very complicated when you need to install external packages (in particular in connection with scientific libraries/tools and drivers). I do not have direct experience with "dedicated" distributions thought. In any case if there is a couple of specific software which you cannot live without, I would check on which platform they are developed and maintained.. and consider this results..
This is just a little suggestion, in general...
If you do not like gnome 3 in fedora, I encourage you to install cinnamon in place that is a fork of Gnome 2, pretty much led
Ubuntu!
An easy customizable OS with a crowded online community to resolve (all) troubles.
I think it is better to use a standard Linux distribution and add the resources you need for your work.
Linux Mint 15 with CINNAMON works like a chaarm for computational biology
If you need a linux distribution powerful using all of your instructions' processor (for example you will have to compile the source of your graphic desktop), I recommend you Gentoo. Or if you want something more reliable but easiest : Centos Client.
I would suggest you to use one of the 4 main Linux distributions, i.e. Debian, Ubuntu, Red Hat, or CentOS.
This suggestion is based on maintainability, continuity, stability, and security. All the above mentioned distributions are supported by very large communities or companies. This means that you can always count on them to fix bugs, deal with security problems, and keep developing and improving their distributions. I am not saying that BioLinux is not well maintained, or the people behind it are not good. In fact I have never used it, but all I can say is that it is based on Ubuntu with some extra software (bio software) already installed, which you can always install by yourself. You probably don't need everything they bundle with their distribution, and therefore it is just a waste of space.
When choosing a Linux distribution you must be aware that there is no difference between them in terms of what you can do or what software you can install. It is a matter of choosing the one that you feel comfortable working with and if the philosophy of the people behind it align with your own views. With that being said, I will make a brief description of the 4 distros I mentioned based on my personal experience, and why not, own point of view.
1. Debian: it is a very well maintained distribution. One of the first distributions to be created. Their focus is on stability, security, and on preserving free and open-source software. They have very serious people working on it. I would say it is probably the most successful distribution ever if you consider the number of distributions that derived from it (which includes Ubuntu). Considering scientific research, Debian is my #1 choice. In my opinion, for scientific applications you need the most stable platform you can get and the most trustworthy. That's why I would go with Debian. Note that it is not possible to achieve decent levels of stability and security if the distribution early adopts the most recent (barely tested) versions of all software. For this reason you wont find the last version of KDE or Gnome, or anything else on a Debian release. They always include in their releases versions that have been tested for a while, thus minimizing instabilities an security issues in their base releases. Despite that, you can always install more recent software by using Debian backports, or their testing packages tree.
2. Ubuntu: it derived from Debian (it uses .deb packages as well). It is maintained by the Ubuntu community and Canonical. The moto of Ubuntu is "Linux for human beings". Their aim is to provide good end user experience. For this reason they compromise security and stability in order to offer easy of use for end users. I would recommend Ubuntu in two situations, to use at home where you want to have comfort and use what is latest in terms of software (I use it for my Home Theatre PC), or for someone that wants to know Linux and is coming from a Windows environment. It is very good for the latter because it is really easy to install, easy to use, beautiful and has the power of Linux. In terms of performance it looses to Debian. I wouldn't use it for my research, and if you use it at your home for a while you will understand why. It is not as stable as Debian. Well, it doesn't freezes or anything like that (it is still Linux), but it is not uncommon that you have to fix something after an update. That is very, very, very rare to happen in Debian. Anyways it is one of the most popular Linux distributions. The open source community is a little bit mad at them because they mostly use what other develop and they don't contribute back to the community.
3. Red Hat: is maintained by the company with the same name. They are a reliable system and are the second in number of distributions that derived from them. They use .rpm packages and are as a good choice as Debian. The difference is that in general you have to pay for a support plan, which makes sense if you are running enterprise servers (their focus). Hardware vendors generally support Red Hat because they are a company with which they can have partnerships and contracts. Red Had is a good choice if you want support. Just a note, despite of the fact that Debian doesn't have a company behind them HP supports Debian in their products. In my opinion that is a vote of confidence on their serious community.
4. CentOS: or should we say Red Hat without support. CentOS is exactly the same of Red Hat. Yes, it is the Red Hat but without the support and some specific tools developed by Red Hat for their enterprise clients. If you want Red Hat but doesn't want or need the support, just go with CentOS.
No matter which Linux you choose, you will be able to achieve the same outcomes and rely on the open source community to answer your questions and help you with any problems. Just see which one you prefer.
There are many, many other Linux distributions (check http://distrowatch.com/ for the full list). It is impossible to talk about all of them. I just check distrowatch and remembered of Linux Mint, which derives from Debian, but they aim at providing more frequent releases and being a little bit more user friendly. Not a bad choice as well. There is also Fedora, which is maintained by Red Hat. Basically Red Hat's testing platform. I would avoid... if you want a Red Hat-ish distro, go with CentOS.
Please, for your own sake avoid Suse or OpenSuse no matter what other people may tell you ! :) OpenSuse is the 6th most popular distro... Windows is the #1 OS used and that doesn't mean it is good! ;o)
Well, this are just my two cents. Despite of what I said, Linux distribution is a matter of preference, it is very hard to say that one is better than the other [except for Suse ;o) ]
Hope it helps.
Cheers.
I also like Ubuntu; however, thank you to everyone for the alternate recommendations.
I've always preferred fedora linux for research purposes and clustering. While it needs of software installation it is ideal to fit your linux to your own needs, and not to others'.
Ubuntu is the easiest and quite powerful. CentOS is what I use for most of the servers and workstations.
Try, Ubuntu 13.04 (latest version available)
1. It is simple
2. It is free to use, under certain parameters
3. It includes, most of the software packages needed for personal use, are available
4. Excellent graphics
5. Human-machine interface is fine, more than average
I like Debian and used to like Ubuntu. It was quite a ready-to-go distro some years ago when others could not recognize many drivers properly, for instance. Nowadays it doesn't make a big difference since most Linux flavors perform pretty well with newest hardware. I appreciate the great job Canonical has done with Ubuntu during last years, making it easier for beginners to approach a Linux system.
The reason I don't feel comfortable with Ubuntu anymore is the privacy concerns Canonical has introduced since version 12.10 with the Dash lens search, sending data from your searches in your own computer (and I mean your own computer files, not Internet nor Google) to private companies like Amazon (and others). It's true that this "public" search can be deactivated and that this is a desktop matter anyway, so changing from Unity to Gnome 3 or Cinnamon (just to mention a few), bypasses the problem, but I think this is contrary to GNU/Linux philosophy.
More info: https://www.eff.org/deeplinks/2012/10/privacy-ubuntu-1210-amazon-ads-and-data-leaks
As stated before by others, any Linux distribution will allow you to do same things. My vote goes for Debian or Debian-based anyway. The only problem (or advantage) with raw Debian is that it sacrifices incoming improvements in exchange of stability.
Personally I like Linux Mint with Cinnamon. This distribution is based on Debian, like Ubuntu, but out-of-the box include packages that are free but not necessarily open-source like in Ubuntu. You can install additional software through Software manager (specific Mint tool), but also through apt. All packages can be installed from source, but deb packages are right as well. Previously I have tried Mandrake/Mandriva, "pure" Debian, Knoppix, Red Hat/Fedora, Aurox, Slackware, Gentoo, but... Mint suits me best.
In fact, it depends on one's needs: some time ago the most useful for me was BSD with some special ports...:)
@Magdalena: I would like to point out the following regarding your answer: unless you were talking about LMDE (Linux Mint Debian Edition) which is indeed solely based on Debian, Linux Mint is not based on Debian just like Ubuntu, it is based on both Debian and Ubuntu, and it relies on Ubuntu repositories. So, Linux Mint mostly includes same packages as Ubuntu, which not only includes free/open-source packages but also proprietary software such as privative drivers, Adobe Flash or MP3 playback support, for instance.
I recently installed Ubuntu at home and am very happy. RedHat Enterprise is our standard scientific platform at work.
You could try Ubuntu easily by using a USB installation to try it out.
See for example http://www.ubuntu.com/download/desktop/create-a-usb-stick-on-windows
I am sure there are others you could test drive.
Good luck
Yes definitely, Ubuntu is good for basic user, which does not need any special skills to setup
For bioinformatics overview, Biolinux is good one
Depend the machine. For a notebook, perhaps Ubuntu or Debian are the best. For workstation or server, with many users in the same machine the best is OpenSuSE.
those claiming a distro is the best (or the worst) are simply wrong. they're all very much the same, and differ mainly in details which do not affect their function, such as desktop color, window manager preferences or package format. all of the mainstream distros are perfectly acceptable for most users - whether you choose to move away from the mainstream is really a strategic choice. generally speaking, distros come into existence whenever some set of people dislike the decoration/packaging choices made by the mainstream distros. you can think of them as specialized or peculiar, but in a practical sense, they're fringe. this matters because when you have a problem, you'll find more help from mainstream distros..
the traditional division among distros is by package format. debian/ubuntu/mint all use .deb files; redhat-related ones (fedora, centos, scientific linux, maybe suse, mandriva, mageia) use .rpm files. though nowadays, one would normally use, for instance, yum on RH distros and might never see an rpm file face-to-face.
of course, the background for this is that none of the distros are really adding much unique: they're all building on the same basic open-source projects, from the kernel all the way to desktop apps. this suggests the only really meaningful way to look at distros: as a mechanism for capturing a very sparse sample of the space of all possible versions of all the packages. when I say "I'm running fedora 17", it really means that the fedora organization has selected a particular set of versions and put them together in a hopefully consistent, correct-functioning way. all the packages are really the same as for some version of, say, Mint, except that particular minor versions differ, along with occasional distro-carried patches. so a distro is really a naming scheme, as well as a snapshot of versions. in fact, if we had a universal naming scheme, you would be able to install packages from one distro on another.
I vote for BioLinux or Ubuntu if you are at the first "contact" with Linux-based systems...
Hope it helps,
G.
Back Track Linux is a distribution focused on penetration testing. It is designed for IT security professionals, not for research. Specially not for bio research.
For its relative ease of use, the inclusion of several major programs, and the vastness of the Ubuntu repositories, I would suggest Linux Mint with the Mate desktop option. I've been using it as a virtual machine (Virtual Box) under Windows for several weeks now, and it runs very smoothly and reliably. For the sake of performance, I would avoid Unity, Gnome 3, Cinnamon, and KDE desktop environments. Though they are "pretty", they will impede performance. Mate is a nice compromise between performance and visual aesthetic; however, if your machine is dated, you may want to consider the XFCE desktop.
Someone mentioned BackTrack Linux; however, this distribution is completely unsuitable and does not offer the user protection from one's self that most other distributions do. Also, while Linux is Linux, distributions vary widely in the size of their repositories, ease-of-use, and stability. For all of these reasons, again, I recommend Linux Mint.
I very much doubt Ubuntu and its derivatives have any advantage in the size or comprehensiveness of their repos. Fedora, for instance, is normally run with rpmfusion add-on repos (Centos with epel as well). I strongly suspect the result is at least as "vast" as Ubuntu-ish distros.
I also would speak up in defense of KDE at least - it runs perfectly fine on even low-powered/old machines. I guess the poster is actually talking about GPU-based (GL) eyecandy, which is easy to disable. The basics of KDE (and probably Gnome) are plenty fast even on entry-level hardware. (Running in a VM, of course, is a rather special case, since the GPU is generally emulated, and often a dumb unaccelerated VGA-only model from the 1990s...
I'm not sure how meaningful this is as a measure of "vastness":
[hahn@hahn ~]$ yum list available|wc -l
31189
(That's a somewhat out-of-date Fedora 17 desktop. It is amusing to note that I've only got 1569 packages actually installed!)
I think the real message here is that if you choose from the leading distros (RHEL/Centos/Fedora/SL, Ubuntu et al, perhaps Debian), you won't go wrong. Specialty distros can be rewarding but do require greater attention and mindshare (that is "share of your mind"). Sometimes there are geographic or local-expertise reasons to use, for instance, Suse or Mandriva.
I recommand you to use a debian stable distribution for a better stability (http://www.debian.org/distrib/netinst) and add packages from Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/package-repository) and neurodebian (http://neuro.debian.net/pkgs.html).
For beginners, Ubuntu is the best. You also want for the teaching purpose, so I would recommend Ubuntu as Fedora, CentOS, OpenSuse and RedHat are complex and one requires prior knowledge of Unix for installation and execution of the softwares on these distributions.
I also work on Ubuntu. One thing to consider too is stability, and for Ubuntu I would strongly suggest that you use the LTS (Long Term Support) version as with the bi-yearly release you may get into trouble with older hard ware when it update. Also using LTS allows you to keep the same system, stable, for a fairly long time.
I believe other major distros are as good as Ubuntu. Some do not offer upgrade and you'll have to do a clean install when the next release happen, so this is also something to consider.
Although not research orientated, may I recommend you this article:
http://www.pcpro.co.uk/features/378145/which-is-the-best-linux-distro
You have to try a few and see which you like. It may seem like there are many distros, but they are very stratified. I would claim that the non-fringe systems fall into just two categories - divided roughly along Debian vs Redhat lines. This divide is reflected in the choice of package format: deb/apt vs rpm. In the first group you have Debian, Ubuntu, Mint and some smaller variants (I have trouble telling any of these apart, except that Debian tends to be a bit "purist", whereas Ubuntu and its spinoffs are semi-commercial and not afraid of, for instance, coming with non-free components.) It's also difficult to say which distro leads the RPM-based clique: perhaps Fedora, but there are plenty of people who swear by openSuse, Mageia, even Redhat itself. (For servers, Centos, the "generic" version of RH is extremely prevalent).
I use Fedora myself, partly for historic reasons, and partly because my work (HPC) is in the RPM camp. Fedora provides very up-to-date packages, a wide choice of window managers (trendy name: "desktop environments"). Fedora has been doing major-release upgrades very smoothly for many years, so is easy to maintain.
I strongly suggest that if you want to get stuff done, you shouldn't get hung up about distro features or particulars of desktop environments. Any one of the top few options (Fedora, Ubuntu, Mint, Suse, etc) will do everything anyone needs, and provide a stream of prompt updates/upgrades. They all "just work" (far more so than that fruit-based company...) If there were some reason for me to switch, for instance, I could work with any Linux environment that let me use ssh, xterm, firefox/chrome, xpdf, openoffice mplayer, multiple virtual workspaces and let me configure double-clicking on the title bar to vertical-maximize. I don't need panels or docks or file browsers or "activities" or any form of desktop integration. And I suspect anyone who just wants to get work done will be similarly uninterested in desktop bling and whiz.
I was using Ubuntu 13.04 , and upgraded to 13.1 but there is some problem with my GUI, and then the toolbar. and It takes heavy memory. So I prefer Linux Mint
I would recommond Ubuntu as it is very easy to use, recently we integrated large number of drug discovery tools in Ubuntu and created customize ubuntu for drug discovery, it was really fun see http://osddlinux.osdd.net/ (your feedback will be highly appreciated.
If you are asking this question this is my advice.
The main difference is the package manager, which takes care of installing software. Stay away from distributions like Arch, which are 'rolling' distributions with a constant update of packages, they break over time unless you pay attention to them. You want a distribution with periodic releases which update the complete system at once The two most popular package types are .deb and .rpm. Debian uses .deb; RedHat uses .rpm. Other distrubutions choose one of them or invent one themselves, stick to .rpm or .deb. I tried both and found .deb supperior. Ubuntu, been based on Debian as pointed out before, is a good choice, because is configured extensively to make it user-friendly, and it updates in frequent and reliable releases.
Personally I follow the oposite advice; I use Arch and despise Ubuntu. And I don't see the point of these custom distributions for science.
For other considerations as desktop manager, as pointed out before, forget about how it looks and think only on which saves you more time. If you are new to linux, be prepared to have things grow on you over time, to put it mildly, but its very worth it.
Yeah Ubuntu 13.04 has no issues, but I upgraded to 13.1, then it is a lot of mess. So I changed to Linux Mint. Its fine, it takes only less memory than Ubuntu and nice view
I would also suggest any of the ubuntu-related distros, mainly due to the package management. However, as Guillem says, the development of the main distro (Ubuntu) has focused on how it looks rather than on its performance. Since it shifted from Gnome to Unity, the memory requirements have increased. Fortunately there are alternative desktop environments such as XFCE, Cinnamon, Mate or LXDE.
Linux Mint can be downloaded with either Cinnamon or Mate (also XFCE, I think) integrated and the work fine in most of the cases (in my particular case I had problems with cinnamon and mint 15).
An even faster alternative and still (after some tuining) nice looking is XFCE, that in combination with Ubuntu is Xubutu. I'm currently usin this distro and works fine.
If you don't care about how it looks, Lubuntu (ubuntu+LXDE) is a good distro.
Regarding the upgrading process, in principle it is a nice feature but it is quite risky. To minimize the risks, you should be very sure that the old version is up to date and then you can try the upgrade. No matter what you do, most likely some (hopefully few) programs will stop working. I tried upgrading a couple of times but I prefer a clean install that, anyhow, is not that big deal if you have a good partitioning of the disk.
Although I use Sabayon Linux (an Italian Gentoo Like) all day, in Desktop and for Chemical Calculations (Molecular Modelling)
For an Completelly Novice in Linux, for a begginer, I reccomend Mint, because i consider it the Distro more easy to install and use.
I think you should stay within the well-know distributions like Ubuntu, Fedora, Debian or Mint. I was personally a fan of Mandriva and then Mageia, but I had to go away from these tow because of recurrent Wifi connection problems. I now use Ubuntu and I'm pretty satisfy with it. If your not a computer and operating system specialist, Ubuntu may be a good choice, as the installation and the software management are easy to do.
In any case, you can install a lot of software available in the Ubuntu repository (or adding additional ones), where you should find many things for biology.
Debian and RH derivatives both have fully-functional and entirely equivalent package systems. The choice is largely aesthetic (perhaps slightly cultural), but for most people, it hinges more on the desktop style and decor.
I think it's a huge mistake to create domain-specific distros, mainly because it creates a niche which always, inherently, seems to lag behind whatever it forked from. First find out whether the tools you want are supported in the mainline distros (Fedora, Centos, Ubuntu, etc). These provide a phenomenal number of tools, touching on almost every scientific domain. And you're hitching your wagon to a larger team of horses, which is kind of the whole point of using a distro.
I would definitely go for a well maintained and supported distro and not one of the "exotic" ones because support through forums, etc.. is going to be much better. Also, you'll get a much more stable system with less problems of common drivers, etc.. being available, and drivers problems in Linux can be a right pain to solve. Be aware however of the fast cycle of upgrade in Ubuntu and most Debian-based distribution. Upgrade should be straightforward and problem-free but in my experience is not in 90% of the case (failure, incompatible display drivers, etc..). To avoid this make sure that you go for the LTS version if you chose Ubuntu, the latest one has just been released in April this year and will be supported for 5 years... I am using Ubuntu 12.04LTS (April 2012) for a lot biomedical imaging analysis, my students use it for Matlab work, etc.. no problem even on old harware. I am not upgrading to the 14.04LTS because I fear breaking my system, I'll wait until the release of the next LTS version in April 2016, but I'll most likely change my PC at that point anyway.
Hope this is useful... happy work on Linux!
Just out of curiosity, which version did you choose and what were your experiences?
And to add my five cents: when you got used to linux and want total control and freedom to operate, but is willing to do some serious debugging from time to time, then Arch Linux is a great option. Rolling distribution, meaning you allways have the latest software at your disposal. No need to upgrade the system. Downside is that updating the system occasionally breaks it. Therefore -> debugging time is a requirement. but the very best thing with Arch linux is the community and forum. No other linux distro comes near the quality that this source of information can offer in my opinion.
Niclas Ericsson, as I said above so far I have sticked to Ubuntu 12.04 LTS (now on version 12.04.5 with Kernel 3.13.0.46). As you said the issue is that rolling distribution can still break your system, in a sense upgrade between version of Ubuntu can be seen as rolling upgrade... and they can break your system too, 50/50 chance).
My experience of Ubuntu is now about 7 years, so not that extensive, but I am comfortable tinkering with it and using command line when needed, although it's a bit of a pain.
One issue to closely watch for is the potential breaking of display driver when performing kernel update, and also when upgrading, check that your current video card is still supported (i.e. drives made to run on the new version).
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