KNOB Knoppix for Bio Itoshi NIKAIDO <itoshi@users.sourceforge.jp>
Linux
Grasp the KNOB! grasp 1, (grip). 2,, (understand). [ 2 ]
What s KNOB CD Linux Bioinformatics
KNOB
Why KNOB? Bioinformatics
What s KNOB KNOB = Knoppix for Bio
What s Knoppix CD Debian GNU/Linux
Knoppix for Bio BioRuby/BioPerl/BioJava, EMBOSS NTFS Database Kernel /home Boot Loader Mini Root Internet cloop file Bio databases cloop = 700MB = 2GB GenomeNet KEGG NCBI GenBank EMBL
KNOB have... C/C++, Perl, Ruby, Python, Fortrun, R, Lisp BioPerl, BioRuby, EMBOSS, NCBI-Tools (BLAST, epcr etc), boxshade, loki, Glimmer, ReadSeq, tree-puzzle, rasmol, pymol, Njplot, Bioconductor, SMA, ClustalW, FASTA2, FASTA3, G-language, fastlink, fastdnaml, Graphviz, gnuplot, HMMER...
Databases EMBOSS DDBJNEW, DDBJRELEASE, EMBL, REFSEQ, GenBANK, SpTrEMBL, PIR, REFSEQ Protein, SwissProt, SWall BioPerl/BioRuby KEGG, SwissProt, EMBL, GenBank, RefSeq
EMBOSS JAMBO (JApan emboss Users Group) EMBOSS 5 ops2_ ID clustalw
$ seqret SWISSPROT:ops2_* $ emma ops2.fasta $ prettyplot ops2.aln EMBOSS::GUI http://localhost/emboss/
Perl + BLAST + SOAP DNA Internet (SWISSPROT) (BLASTX)
BioRuby 1.1.1.1 URL 1.1.1.1
VMware/Virtual PC/ colinux䛑䜏 RealVNC/SSH SFS Server 䝑䝇䝌䝳䞀䜳䛑䜏 SFS client SFS Knoppix Kernel Boot Loader SFS deamon Internet/LAN SFS Client KNOB http://staff.aist.go.jp/ cloop file Mini Root
KNOB Kernel BioRuby/BioPerl/BioJava, EMBOSS NTFS Database /home Boot Loader Mini Root Internet cloop file Bio databases cloop = 700MB = 2GB GenomeNet KEGG NCBI GenBank EMBL
KNOB Kernel BioRuby/BioPerl/BioJava, EMBOSS /master /source Boot Loader Mini Root cloop file cloop = 700MB = 2GB
KNOB BioRuby/BioPerl/BioJava, EMBOSS Kernel Boot Loader Mini Root chroot HDD /master /source./configure; make; make install apt-get install cloop file Internet cloop = 700MB = 2GB apt server
KNOB Kernel Boot Loader BioRuby/BioPerl/BioJava, EMBOSS HDD /master /source Mini Root cloop file cloop = 700MB = 2GB
KNOB Kernel BioRuby/BioPerl/BioJava, EMBOSS Boot Loader CD image HDD /master /source Mini Root cloop file cloop = 700MB = 2GB
KNOPPIX Root Shell $ mkdir -p /mnt/sda1/source/v3.7 $ mkdir -p /mnt/sda1/master/ $ cp -a /KNOPPIX/* /mnt/sda1/source/v3.7 $ cp -p /cdrom/* /mnt/sda1/master $ chroot /mnt/sda1/source/v3.7 $ mount -t proc /proc proc $ apt-get install hoge $ wget http://hogeurl/hoge.tar.gz $ tar zxvf hoge.tar.gz; cd hoge; $./configure; make; make install; $ umount /proc $ mkisofs -R -L -V "KNOB 1.3.0" -hide-rr-moved -v /mnt/sda1/source/v3.7 create_compressed_fs - 65536 > /mnt/sda1/master/knoppix/knoppix $ cd /mnt/sda1/master $ mkisofs -v -R -J -no-emul-boot -boot-load-size 4 -boot-info-table -b boot/isolinux/ isolinux.bin -c boot/isolinux/boot.cat -hide-rr-moved -o /mnt/sda1/master/ knob1.3.0.iso /mnt/sda1/master
KNOB
! KNOB vs. hoge Mac OS X Xcode Windows Cygwin Linux
KNOB KNOB
Project KNOB http://knob.sourceforge.jp/ Download http://knob.sourceforge.jp/pub/ Mailing List Knob-friends ( ) Knob-friends@sourceforge.jp Knob-dev ( ) Knob-dev@sourceforge.jp Itoshi NIKAIDO http://itoshi.tv/
Grasp the KNOB! grasp 1, (grip). 2,, (understand). [ 2 ]