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  • bio-knoppix bioknoppix

    I just found this:




    alas, the last update was from 2008

    is there a more actual similar project ?

    -------------------edit 2015/12/10-------------------

    bioknoppix is 688MB for download as an "iso" file
    but none of the 5 mirror sites were available

    > For those who have slow internet connections you can buy a bioknoppix-0.2.1beta cd for a
    > nominal fee at http://cheapbytes.com. It is also available at http://linuxcd.org.

    none of these links work for me


    > Bioknoppix is a customized distribution of Knoppix Linux Live CD. With this distribution you
    > just boot from the CD and you have a fully functional Linux OS distribution with open source
    > applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesn't
    > touch the host computer, being ideal for demonstrations, molecular biology students, workshops, etc.

    the Spanish mirror may have changed to ftp://ftp.rediris.es/mirror/
    but I didn't find it there either
    Last edited by gsgs; 12-10-2015, 07:19 AM.

  • #2
    There is: http://environmentalomics.org/bio-linux/

    You may also find it easier to run ubuntu or other unix distro in virtual box on Windows. That said make sure you have beefy enough hardware available. STAR will require lots of RAM no matter where it runs (in virtual box/or natively).

    Comment


    • #3
      I can just buy a new notebook with lots of RAM and Linux (will the knoppix - USB - stick work ?)
      No problem.
      (can't we use micro-SDs as RAM ? or is it too slow)

      But how long will it take me to get familiar enough with Linux ?

      And then, I still have to export everything back to Windows-cmd.exe=DOS,
      since I have all my utilities there

      maybe I should have switched to Linux long ago

      Comment


      • #4
        No you can't use SD cards as a replacement for RAM. They are probably too slow to be used for computation also.

        If you are reasonably computer savvy you could bring yourself up to speed on unix in less than a week. I will include this link in case you feel inclined to do this.

        What sort of utilities do you have/need on windows side? We can perhaps suggest unix equivalents so you could just stay in the unix world.

        Comment


        • #5
          ahh, I spent another 3h this morning to get Linux running on my other notenook to no avail.
          I have 2 knoppix USB-sticks, and ~5 DVDs to boot from but all that I could get was freedos,
          and then, later, when I gave up, even that didn't work.The originally installed Windows is also
          no longer available and it takes so long to boot and wait until I decide that there is no progress.
          Or long tedious licences ("openSuse") which I won't read.
          And sorting cables ...

          It has 3.6GB RAM and 2 CPUs with 2.4GHz each.
          I got 20 Computers running simultaneously without keyboard,monitor, HDs, and shared RAMs
          and floppies, but that was 15y ago and I'm probably no longer "computer savvy")

          Also, "in a week" is much time for a software that costs nothing and what I don't even know yet
          whether it will work for me.

          My software is mostly self-written over the years, adapted to my needs,
          so there is no good replacement.

          ----------edit--------------
          I ordered "Linux Fedora 23" USB-stick now from the UK, let's see ...
          And also "Ubuntu" DVD, since someone mentioned Ubuntu here.
          And also 4 more Knoppix "bootable" DVDs, several versions.
          Last edited by gsgs; 12-03-2015, 12:09 AM.

          Comment


          • #6
            What are you expecting?
            What are your plans with "biolinux"? What are you trying to achieve?

            Didn't get it ..

            Comment


            • #7
              one thing that recently became more and more necessary is fast alignment
              of large datasets. This occurred in another thread here : the "Star" software
              was available only for Linux.
              But it's a general problem, almost all the Universities only use Linux/UNIX,
              so the research software is often not available in Windows.
              It's particularly true for the field of interest here, which is Bioinformatics.
              Bio-Knoppix could be viewed as an attempt to make this available to
              Windows Users - the large majority in non-Education-life


              So, I want to be able to compile,run,download,edit,convert .... the Linux software

              Comment


              • #8
                @gsgs: If you want to stay in windows you could use BBMap, which is a great NGS data suite (multiple tools, more info in this thread: http://seqanswers.com/forums/showthread.php?t=58221). It is written in java so will run on windows without need for any changes.

                BTW: 3.6 G of RAM is not going to take you far with pretty much any software that is related to NGS. STAR requires ~30GB of RAM for mapping to the human genome (could be reduced to 16GB in the "sparse" mode with some speed loss). Not sure what kind of data you are going to be working with.

                A "week" was a very rough estimate of how long it would take to gather the basics of unix. It sounds like you certainly know your way about hardware/software, so it may take you a day or less. Just depends on how serious you are going to be about making the switch. You don't need to let go of windows. Many of us do use windows on our primary desktops. Just add linux to your repertoire. It will serve you well over time.

                Comment


                • #9
                  So there is some need for you to get linux running. If you want to compile, run, download etc. "bioinformatics" software you should at least understand the basics of a linux system.
                  So "in a week is much time for a software that costs nothing and what I don't even know yet whether it will work for me" makes no sense IMHO when you want to efficently use such software.

                  As already mentioned by GenoMax, trying to start with Ubuntu/Mint is not a bad option.
                  If you have problems installings such linux on your device(s), you should probably post your issues on the approbiate forums. As a (german) starting point for Ubuntu you might want to check e.g. https://wiki.ubuntuusers.de/Einsteiger ..

                  Comment


                  • #10
                    ok, I spent another 2h to figure out linux ...
                    The knoppix actually did boot before just that I didn't realize it had finished booting.
                    I had interpreted the screen as some "booting art".
                    Some other CDs or one usb-stick didn't boot, though. Displaying errors about CPU or missing "grab.exe"
                    I also could boot "fedora". Booting from usb=stick takes ~70s, booting from CD/DVD takes ~160s.
                    You have to press F12 permanently on switching on to enter the boot-menu and then
                    choose USB or CD/DVD respectively, but wait 30s for CD/DVD, until there are no more
                    CD-read-noises, before you press enter. Took me a while to figure that out.
                    Then in knoppix choose the screen-symbol on the bottom bar to enter "bash" commandline-mode,
                    and then use the linux equivalents for DOS/Windows , e.g. "ls" for "dir" etc.
                    There are probably lists on the internet for all the commands.
                    However, there doesn't seem to be a C++ compiler included in knoppix or fedora ?!
                    So, which compiler will compile star under knoppix-linux or fedora-linux or what linux and what
                    compiler do I need ?

                    I still think in such cases a whole computer with the software installed should be sold.
                    Or at least a booting micro-sd card or usb-stick, that runs the software automatically from
                    batch and writes the result back to the sd-card.
                    Aligning the sequences in a file with default name.

                    I would be interested to read other Windows-->Linux switchers' experiences with bio-(linux)-software

                    Comment


                    • #11
                      thanks for the replies above. (I didn't get an email about that, as usual)
                      GenoMax,
                      I don't know about Java. Also, I can't entirely switch to Linux, I still need my DOS/Windows tools,
                      so I have to use both. Why is 3.6 GB not enough for human DNA ,
                      you do one chromosome after the other ?! Or 10000 flu sequences with 2000 nucleotides each
                      And why can't it use SD-card or HD as RAM, even if it is slower ?
                      I do feel that it's the algo that gives much more improvement (over MAFFT) than the hardware

                      For Linux ... in commandline modus it should be almost the same as DOS. I wouldn'r be surprised
                      if there is an easy tool that converts DOS-commands to the corresponding Linux commands ?!
                      ---------------------------------------------------
                      sklages,
                      I just feel that it is not well designed for "Einsteiger" , there should be an "easy-mode", foolproof
                      just for the basics. On the first home computers the operating system was installed on ROM,
                      the programming language or compiler was just one executable.
                      Then came more features and options ... but also more compatibility problems, more errors,
                      more complicated and longer manuals. "More" is not necessarily an advantage.
                      I gave up German forums, English traffic is usually ~10 times more

                      Comment


                      • #12
                        Your issue is pretty off-topic here. You should get familiar with some basic linux stuff, as I wrote.

                        For all those people who find it more convenient to bother you with their question rather than to Google it for themselves.


                        I still don't get what you are trying to achieve ..

                        Comment


                        • #13
                          I can't be the only one with such problems ?!
                          IMO it's of basic importance for using bio-software.

                          I'm trying to get the whole process easier, including compiling,
                          compatibility ,
                          Last edited by gsgs; 12-10-2015, 05:29 AM.

                          Comment


                          • #14
                            Originally posted by gsgs View Post
                            thanks for the replies above. (I didn't get an email about that, as usual)
                            sklages,
                            I just feel that it is not well designed for "Einsteiger" , there should be an "easy-mode", foolproof
                            just for the basics. On the first home computers the operating system was installed on ROM,
                            the programming language or compiler was just one executable.
                            Then came more features and options ... but also more compatibility problems, more errors,
                            more complicated and longer manuals. "More" is not necessarily an advantage.
                            I gave up German forums, English traffic is usually ~10 times more
                            The "easy-mode" is called "Desktop Envionment". The power of linux/unix is not the "easy-mode" but the command line and the large number of tools. You are not urged to use the command line to use linux and some bioinformatics software. But you won't get far without command line...

                            my 2p ;-)

                            Comment


                            • #15
                              command line would be ok for me, I'm using it in DOS (windows-cmd)
                              I'm not sure whether that desktop environment is usually easier and should be recommended
                              for bio-software. But I'm a Linux,beginner, what do I know ...
                              In DOS however I found it superior in such tasks, where you handle and manipulate shared files and use multiple
                              software.

                              --------------edit-----------------

                              What's the Linux equivalent to Windows batch files?

                              someone replied:
                              > You need to learn to write bash scripts. These are the Linux equivalent of
                              > windows batch files. The syntax isn't too difficult to get your head around.
                              > I suggest googling as there are many great freely accessible tutorials.

                              another reply:
                              > Make sure you have installed wine , then do the following command in a terminal:
                              > wine cmd
                              > This will open up a Windows command prompt. Start your .bat from there.
                              [sounds good to me, searching wine ...https://en.wikipedia.org/wiki/Wine_(software) :
                              > aims to allow applications designed for Microsoft Windows to run on Unix-like
                              > operating systems.
                              > ... Wine does not have good support for MS-DOS, but starting with development
                              > version 1.3.12, Wine tries running MS-DOS programs in DOSBox if DOSBox is
                              > available on the system.[48] However, due to a bug, current versions of Wine
                              > incorrectly identify Windows 1.x and Windows 2.x programs as MS-DOS
                              > programs, attempting to run them in DOSBox (which does not work).[49]



                              another reply:
                              > You might want to learn python.
                              > It's easy to learn and more readable than some other scripting language... ;-)

                              [sound really complicated to me]

                              ----------------edit-----------
                              seems that "wine" is included in knoppix since version ~7.0.3
                              Last edited by gsgs; 12-10-2015, 06:03 AM.

                              Comment

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