Thursday, April 8, 2010

About Dual Boot

Optimizing Your Single Hard Drive Installation
There is a different setup for a single drive.
You can check any detected drive by using:
&] sudo fdisk -l
or
&] sudo blkid
or
&] ls -l /dev/disk/by-uuid

You can mount any FAT{16,32} by doing:
$] $myusb=/media/SHAR ; sudo mkdir $myusb
$] sudo mount -t vfat -o defaults,user,exec,uid=1000,gid=100,umask=000 /dev/sda8 $myusb

You can check the disks using the following command line:
&] sudo /sbin/fdisk -lu /dev/{h,s}d{a,b}



Optimizing Your Fedora
There are different ways.
You may check your Hard Drive with the following command:
&] sudo /sbin/fdisk -lu /dev/{h,s}d{a,b}

1st backup your files:
&] su
&] cp /etc/sudoers /etc/sudoers.orig
&] cp /etc/group /etc/group.orig

2nd become a sudoer:
  •  enable group wheel in /etc/sudoers
  •  add your username in wheel in /etc/group

3rd optimize yum:
&] sudo yum -y install yum-plugin-fastestmirror
&] sudo rpm -ivh http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm
&] sudo rpm -ivh http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-stable.noarch.rpm

4th optimize Network
&] sudo cp /etc/sysconfig/network-scripts/ifcfg-eth0 /etc/sysconfig/network-scripts/ifcfg-eth0.orig
&] sudo nano /etc/sysconfig/network-scripts/ifcfg-eth0

5th optimize mp3 players
&] sudo yum -y install xmms xmms-mp3 xmms-faad2 xmms-pulse xmms-skins
&] sudo yum -y install audacious audacious-plugins-freeworld*
&] sudo yum -y install banshee rhythmbox gstreamer-plugins-ugly gstreamer-plugins-bad gstreamer-ffmpeg
&] sudo yum -y install amarok xine-lib-extras-freeworld

6th optimize Media players
&] sudo yum -y install mplayer mplayer-gui gecko-mediaplayer mencoder
&] sudo yum -y install xine xine-lib-extras xine-lib-extras-freeworld
&] sudo wget  http://www.mplayerhq.hu/MPlayer/releases/codecs/all-20100303.tar.bz2
&] sudo mkdir -p /usr/lib/codecs
&] sudo tar -jxvf all-2010303.tar.bz2 --strip-components 1 -C /usr/lib/codecs/
&] sudo yum -y install vlc
&] sudo rpm -ivh http://rpm.livna.org/livna-release.rpm
&] sudo rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-livna
&] sudo yum -y install libdvdcss
&] wget http://uk.real.com/download2/realplayer/11/linux/rpm/RealPlayer11GOLD.rpm
&] sudo rpm -i RealPlayer11GOLD.rpm

7th optimize your fonts
&] sudo wget http://www.mjmwired.net/resources/files/msttcore-fonts-2.0-3.noarch.rpm
&] sudo rpm -ivh msttcore-fonts-2.0-3.noarch.rpm

8th optimize Adobe
&] sudo rpm -ivh http://linuxdownload.adobe.com/adobe-release/adobe-release-i386-1.0-1.noarch.rpm
&] sudo rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-adobe-linux
&] sudo yum -y install flash-plugin AdobeReader_enu

9th optimize GNU Java
&] sudo yum -y install java-1.6.0-openjdk java-1.6.0-openjdk-plugin

10th optimize Sun Java @ (rpm or bin) http://java.sun.com/javase/downloads/index.jsp
&] sudo sh jdk-6u19-linux-i586-rpm.bin
&] sudo /usr/sbin/alternatives --install /usr/bin/java java /usr/java/default/bin/java 20000
&] sudo /usr/sbin/alternatives --install /usr/lib/mozilla/plugins/libjavaplugin.so libjavaplugin.so /usr/java/default/lib/i386/libnpjp2.so 20000
&] sudo /usr/sbin/alternatives --config java
&] sudo /usr/sbin/alternatives --config libjavaplugin.so

11th optimize Samba
&] sudo cp /etc/samba/smb.conf /etc/samba/smb.conf.orig
&] sudo nano /etc/samba/smb.conf
&] sudo smbpasswd -a $username
&] sudo /etc/init.d/smb.conf start
&] /sbin/chkconfig --list smb
&] sudo /sbin/chkconfig --list smb
&] /sbin/chkconfig --level 35 smb on
&] sudo /sbin/chkconfig --list smb
&] sudo /etc/init.d/smb.conf restart
&] system-config-firewall
&] sudo system-config-firewall-tui
&] system-config-selinux

12th optimize Network configuration
&] sudo system-config-network
you can change localhost to any name
you can change .localdomain to any account (i.e. DynDNS.com)

17th optmize with Wine:
&] yum list|grep ^wine|awk '{print $1}'|xargs sudo yum -y install


Optimizing Your Kubuntu
There are different ways to do it, The Kunutnu installation is minimal.

1rst your software manager:
&] sudo apt-get -y install synatic

2nd edit your grub.cfg for a propet time out at login
&] grep time /boot/grub.cfg

3rd allow mount of ntfs:
&] apt-cache search ntfs|grep ntfs|awk '{print $1}' | grep -v dev | xargs sudo apt-get -y install

4th allow medibuntu:
&] sudo wget --output-document=/etc/apt/sources.list.d/medibuntu.list http://www.medibuntu.org/sources.list.d/$(lsb_release -cs).list && sudo apt-get --quiet update && sudo apt-get --yes --quiet --allow-unauthenticated install medibuntu-keyring && sudo apt-get --quiet update
&] sudo apt-get --yes install app-install-data-medibuntu apport-hooks-medibuntu
&] wget -c http://packages.medibuntu.org/pool/free/libd/libdvdcss/libdvdcss2_1.2.9-2medibuntu4_i386.deb
&] sudo dpkg -i libdvdcss2_1.2.9-2medibuntu4_i386.deb
&]  sudo apt-get -y install libdvdcss2 w32codecs alsa-firmware app-install-data-medibuntu hot-babe rmconverter realplayer non-free-codecs mplayer mplayer-gui mplayer-doc mencoder libavcodec-extra-52 libavdevice-extra-52 libavfilter-extra-0 libavformat-extra-52 libavutil-extra-49 libdvdcss2 libpostproc-extra-51 libswscale-extra-0

5th optimize with AdobeReader:
&] apt-cache search acroread|grep acroread|awk '{print $1}' |xargs sudo apt-get -y install

6th optimize using snort:
  • after installing snort,  answer the configuration prompt
  • Address range for the local network (router followed by /16 as 192.168.0.0/16)
7th optimize using debian-med port to ubuntu med-*

8th optimize using R:
&] apt-cache search r | awk '{print $1}' | grep ^r- | grep -v dbg | sudo xargs apt-get -y install

19th optimize with Wine (windows emulator) using apt-get

Friday, April 2, 2010

About MBF

Microsoft Biology Initiative

It is another intent to break into open source and free software in the scientific community but the community does not like it, you can follow their site.

Microsoft Biology Foundation Training

You can follow the installation requisites in their site.

Download and install the MBF.
Download and install the ShoRuntime.
Download and install the source code.

Microsoft Research Sho Library

Please refer to their site.
Please refer to the documentation.
Please refer to the API Reference.
Please refer to the Package Reference.
Please refer to the External API Guide.

Microsoft Biology Tools

Download and install the NodeXL.
Download and install the Sequence Assembler.
Download and install the BL!P (MS Silverlight PivotViewer needed).

Microsoft Research Biology Extension for Excel

Please refer to their site.

Microsoft Computational Biology Tools

Download and install the PhyloD, Epitope Prediction, HLA Completion & Assignement, Create Epitope and False Discovery Rate for 2x2 contingency tables.

Microsoft Biological Computation Tools

Download and install the Synthesizing Biological Theories: site, manual and package.

Microsoft Researcher Tools

Download and install the GenePattern Add-in for Word.
Download and install the Ontology Add-in for Word: site and Codeplex.
Download and install the Chemistry Add-in for Word: site, font DLL and Codeplex.
Download and install the Infer.NET machine learning library: site, package, follow the UserGuide, try the first tutorial, all the tutorials and examples, the API and the references.
Download and install the SIGMA Large Scale Machine Learning Toolkit: package.
Download and install the 3D Molecule Viewer.
Download and install the QUT.Bio: site.
Download and install the RNA Comparative Analysis Software Tool.
Download and install the Athena Modular CAD/CAM Software for Synthenic Biology.
Download and install the Project Trident from Codeplex.
Download and install the WinBioinfTools.

HTMLCode

HTMLCode Content