[Debian-med-packaging] debian science biology live usb? or biolinux

[ibrahim acikbas]

Hello Mr Tille,
I am moleculer geneticist.
I am not familiar unix and linux OSs or any complilation and programing.
Unfortuanetly our institution do not have a bioinformatic facility.
I used to be some DOS commands. I have installed ms-winXP+bsd on same harddisk in pentium4 machine a few years ago but I used rarely and I could not be use effectively.
 
I need unix/linux OS for several genetic programs work on as well as emboss tool. I can not dedicate a separate PC for this now. I am planning to set up a live usb and use it on a ms-win xp pro sp3 pc machine:
gigabyte G31M-SL2 mainboard,
Pentium dual core E5200 3.38Ghz (32bit),
3GB RAM,
Nvidia GeForce 9500GT video-card with own 1GB memory.
one samsung 120GB harddisk with two partition.
(usb mouse/keyboard, usb laser printer samsung ML1610, Hans-G 19" squre LCD monitor with vga connection, 1280x1024 on winxp)
 
Some linux based bio-genetic programs Biolinux 5 (32bit), Debian scientific Biolgy blend, DNAlinux, Bioslax, Scientific linux, bioknoppix...are based on debian and/or ubuntu. This linux program may be more easeir for non familiar end users as me. However I were found desktopBSD in net. I hope the programs Phase, Haplotyper etc work on desktopbsd, but don't have any ideas in linux.
 
I think to try some live unix/bsd versions (because I want to write my data, input, output, sample... files on the same usb) but generally not recommended to me, they rather suggest ubuntu is an easier starting, I think  because of my unfamiliarity. After I was read about desktopbsd, I am be sure of myself. Please excuse me about that I asked a bsd question to a debian expert.
 
In biolinux and debian science bio I think all biosoftwares is installed as well as os and etc, ready to use.
However If I chose bsd way, the easy part is only desktopbsd,   I think I will do everything myself and not easy for me:  software downloads and installing these to bsd, may be organizing some make files.
 
What your suggesion to mine condition?
 
Where and how can I download any stable debian science bio live usb (blend) image? 
 
Can I download, prepare and install the image on usbstick in a ms-winxp machine? I have not any linux pc.
 
Should I format the usb stick to UFS/FFS/EXT/etc by program as Partition Manager in ms-winxp before isntall the image?
  
Can I make partitions in live usb? should I do?
If yes when partiotions should be make? before or after install the image?
 
How do I install /use my boiscientific programs don't already installed in debian, like phase, unphased, haploview, famhap, tomcat ?
 
Can live usb see my winxp partitions (C: and D: FAT/NTFS)? and make file transfer? may be from a swap area?
 
Phase: http://stephenslab.uchicago.edu/software.html
Unphased: http://www.mrc-bsu.cam.ac.uk/personal/frank/software/unphased/
Haploblock: http://www.cs.technion.ac.il/people/dang/
Haploview: http://www.broad.mit.edu/personal/jcbarret/haploview/
Tomcat: http://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html
SNPhap: http://www-gene.cimr.cam.ac.uk/clayton/software/
Famhap: http://www.uni-bonn.de/~umt70e/becker.html
 
Thanks for your interest.
sincerely
Dr Ibrahim Acikbas
Pamukkale University
Dept Medical Biology and Genetics
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