Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • A_Morozov
    replied
    Are those specialised bioinformatics distros any good? I mean, you can print something like "sudo apt-get install bioperl" (which by the way drags lots of basic tools like aligners, blast and some more as dependencies) whenever you like. And you do not litter your bin with random stuff that does God knows what and is definitely unnecessary for you.

    Leave a comment:


  • sklages
    replied
    Originally posted by Daniel Fernandez View Post
    1) Is Scientific Linux any good for bioinformatics? If yes, why?
    No, a good bioinformatician is who know how to analyze the sequences and interpreted the results, not who know Linux, Linux is only a good system to work. And depends of the area, for example I know a lot of people workking in phylogeny and they don't use Linux, they don't need, maybe other lab in phylogeny used, but not all, and both are very good in that, in my case I work in functional genomics, expression, so I need to know Linux. And I know other people that know a lot of Linux but they are not good bioinformatician.
    hmm, you are probably right if the linux system is centrally administered.
    If you run it on your "personal" machine or your labtop you do need to know a bit of linux. Having happily installed your own linux on your notebook, you are probably happy, if you find your software of question in the distro's repos without having to think about how to compile that stuff.
    And finally you are right, that a bioinf should know how to analyze his/her data/sequences ;-)

    2) Do we need Enterprise level Linux???
    No, you don't need enterprise level, I explain that above.
    Enterprise level? Voluntary? No. But if you are dependent on commercial software it may happen that this piece of software require sth. like CentOS (RedHat) or Suse (SEL) to get support.


    3) What Linux distribution are you using???
    Well, if you decide work in Linux, you can choose the distro that you prefer, in which you feel most comfortable. Don't confuse the most popular, with the best or the most stable, the most populra is Ubuntu and is very good for work, if you are a beggining I think Ubuntu is the best option, but Fedora is the most stable and Fedora is 6 months more current than Ubuntu, about the kernel, usual softwares (not bioinfo softwares). Both are the most uses you choose any that you like. In the beggining I used Ubuntu (deb packages) now I use Fedora (rpm packages) but most bioinformatic tools are in .tar.gz or .zip for any distro in Lunix.
    If you are a beginner you can use BioLinux, Open Discovery or other special softwares for bioinformaticians.

    The first question must be, what do you do in bioinformatics?
    Here I totally agree. Use whatever linux you feel comfortable with or what your environment is using (if so). On the other hand, for linux beginners (with bioinformatic focus) Ubuntu is probably NOT the best choice. I have worked with quite a few distros, but things are sometimes harder to get running on Ubuntu than e.g on a RedHat-based distro like Fedora or even CentOS. E.g. Ubuntu uses 'dash' as the system shell; though dash is POSIX compliant and should have no problems with sh-shellscripts, it turned out that quite a few sh-shellscripts are NOT POSIX compliant and as a consequence installation of program ABC fails. This is not a problem for a single shellscript but may be annoying for larger packages containing more shell scripts (e.g. Roche's 454 software suite).

    This is even worse when compiling packages on your own; compiling Roche's gsMapper on Ubuntu is really a hard job, whereas on Fedora it compiles like a charm. This is mainly due to available gcc versions (in the repos) and availabilty of the dev packages ..

    just my 2p :-)

    Sven

    Leave a comment:


  • Daniel Fernandez
    replied
    1) Is Scientific Linux any good for bioinformatics? If yes, why?
    No, a good bioinformatician is who know how to analyze the sequences and interpreted the results, not who know Linux, Linux is only a good system to work. And depends of the area, for example I know a lot of people workking in phylogeny and they don't use Linux, they don't need, maybe other lab in phylogeny used, but not all, and both are very good in that, in my case I work in functional genomics, expression, so I need to know Linux. And I know other people that know a lot of Linux but they are not good bioinformatician.

    2) Do we need Enterprise level Linux???
    No, you don't need enterprise level, I explain that above.

    3) What Linux distribution are you using???
    Well, if you decide work in Linux, you can choose the distro that you prefer, in which you feel most comfortable. Don't confuse the most popular, with the best or the most stable, the most populra is Ubuntu and is very good for work, if you are a beggining I think Ubuntu is the best option, but Fedora is the most stable and Fedora is 6 months more current than Ubuntu, about the kernel, usual softwares (not bioinfo softwares). Both are the most uses you choose any that you like. In the beggining I used Ubuntu (deb packages) now I use Fedora (rpm packages) but most bioinformatic tools are in .tar.gz or .zip for any distro in Lunix.
    If you are a beginner you can use BioLinux, Open Discovery or other special softwares for bioinformaticians.

    The first question must be, what do you do in bioinformatics?

    Leave a comment:


  • andreitudor
    replied
    I use Bio-Linux 6. It is based on ubuntu, but is developped specifically for bioinformatics by NEBC. It has a lot of software already installed. Of course you have to update some of the tools, but everything works out of the box. You just install it and you have some 300 bioinfomatics programs and scripts.

    Leave a comment:


  • ulz_peter
    replied
    Originally posted by TonyBrooks View Post
    Yes, the 454software is a bit of a pain to get installed and Roche won't support anything other than Redhat, Fedora or CentOS. There are posts on SeqAnswers on how other people have managed to install on Ubuntu though.
    I actually ended up changing one of my computer's operating system to Fedora, before the solution was published on Seqanswers. As it runs Gnome as well the changes are minor, mostly only affecting directory structure...and bwa and samtools are in the Fedora repositories as well

    Leave a comment:


  • TonyBrooks
    replied
    Yes, the 454software is a bit of a pain to get installed and Roche won't support anything other than Redhat, Fedora or CentOS. There are posts on SeqAnswers on how other people have managed to install on Ubuntu though.

    Leave a comment:


  • ulz_peter
    replied
    I personally prefer Ubuntu as well (just found out that bwa and samtools is available in Ubuntu repositories), just because it is easy and getting help is facilitated by the great amunt of people using it. However I had trouble installing the Roche software.
    Does anyone use the Bioinformatic Ubuntu distribution biolinux?:


    For file sharing with PIs, I think OpenOffice is sufficient as it can handle all the Ms office data formats.

    Leave a comment:


  • TonyBrooks
    replied
    There is no best option specifically for bioinformatics. As mentioned previously, software can be compiled on any Linux system. More important is to find one you are comfortable with for the other functions that you may find useful.
    Ubuntu is probably the most user friendly Linux distro. Most things work out of the box regardless of hardware and pretty much all non bioinformatics software is included in the repositories for easy install (OpenOffice, Filezilla etc). I just think there's less of a learning curve with Ubuntu for those who are comfortable with Windows or OS X (which constitute almost all of our collaborators).

    Leave a comment:


  • simonandrews
    replied
    Originally posted by danny0085 View Post
    No doubt that the best option is ubuntu linux.
    Because....?

    Leave a comment:


  • danny0085
    replied
    No doubt that the best option is ubuntu linux.

    Leave a comment:


  • mrawlins
    replied
    I describe Linux distributions as pre-selected dish combinations at an all-you-can-eat buffet. The differences between distribution X and distribution Y are:

    which packages, and which versions they come with as a standard
    how they prioritize performance, stability/maintainability and functionality
    what options are available for technical support (i.e. forums only, or call-in help desk)
    which personal preferences/aesthetic considerations are enabled by default

    Use what works. If your IT department has a preference, go with that. If your colleagues have a preference, go with that. If you have a preference, go with that. If you really don't know (and hence have to ask on this forum), go with Ubuntu. It's not my favorite distribution, but it emphasizes making it easy to pick up and learn.
    In the end, there's so little difference between the distributions that if you don't *know* what you want, it doesn't much matter which one you choose. All distributions will allow you to install and use almost all bioinformatics software (some Windows-only programs could be challenging, but there are alternatives).

    Leave a comment:


  • ymc
    replied
    What about CentOS? What is its advantage over Ubuntu???

    Leave a comment:


  • robertorun
    replied
    I use Fedora,but the Fedora is updated so fast and only surpport server about 1 half year, so wang to use RedHat AS or CentOS.

    Leave a comment:


  • jmw86069
    replied
    I recommend Ubuntu but agree with others' points about Fedora for IT support. If you get your IT support's buy-in early on for Ubuntu then you're all set. I run Ubuntu on my laptop and if you're adventurous enough to do something like that, hands down Ubuntu would be your choice. For me the reason is that if you Google for almost any Linux related problem, the discussion and solution is typically found on ubuntuforums.org. It has the most active and vocal community of people using it and mutually helping each other support all the bleeding edge stuff we really want to use.

    RedHat is by far the most IT supported, but when we tried to use it in a controlled environment we couldn't install many core tools due to older versions of various libraries which couldn't easily be updated without impacting other tools. That may happen with any Linux flavor, that after a couple years some tools basically drag down the Linux advances due to their specific (old) needs.

    MacOS is based upon Linux and has an Apple scientific group supporting some aspects of it. For R they compile with all the little flags that make it the fastest possible, twice as fast as default Linux builds without some tweaking. But clearly not every tool builds smoothly, evinced by the number of tools with separate Mac compile directions. The problem is that you probably don't really want to build Mac clusters or buy a bunch of Mac servers. They'd perform well but not notably better then Linux boxes, and they'd be darn pricey. But due respect, they're good boxes. :-)

    Leave a comment:


  • nilshomer
    replied
    We use Cent OS 5 on our servers. For Desktops/Laptops, each person has their own preference (Ubuntu or Fedora). Also, for Laptops, consider Mac OS X laptop as it has Word (good for interacting with the PI) and Unix under the hood.

    Leave a comment:

Latest Articles

Collapse

  • seqadmin
    An Introduction to the Technologies Transforming Precision Medicine
    by seqadmin


    In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
    01-27-2025, 07:46 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 09:30 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-05-2025, 10:34 AM
0 responses
22 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-03-2025, 09:07 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Started by seqadmin, 01-31-2025, 08:31 AM
0 responses
33 views
0 likes
Last Post seqadmin  
Working...
X