“Modern bioinformatics encompasses a broad and ever-changing range of activities involved with the management and analysis of data from molecular biology experiments. Despite the diversity of activities and applications, the basic methodology and core tools needed to tackle bioinformatics problems is common to many projects. Building Bioinformatics Solutions provides a comprehensive introduction to this methodology, explaining how to acquire and use the most popular development tools, how to apply them to build processing pipelines, and how to make the results available through visualisations and web-based services for deployment either locally or via the Internet. The main development tools covered in this book are the MySQL database management system, the Perl programming language, and the R language for statistical computing. These industry standard open source tools form the core of many bioinformatics projects, both in academia and industry. The methodologies introduced are platform independent, and all the examples that feature have been tested on Windows, Linux and Mac OS. This advanced textbook is suitable for graduate students and researchers in the life sciences who wish to automate analyses or create their own databases and web-based tools. No prior knowledge of software development is assumed. Having worked through the book, the reader should have the necessary core skills to develop computational solutions for their specific research programmes. The book will also help the reader overcome the inertia associated with penetrating this field, and provide them with the confidence and understanding required to go on to develop more advanced bioinformatics skills.”

The book that I am a co-author on, Building Bioinformatics Solutions is shortly going to be available on Amazon (UK) and Amazon (US) as well as other countries.

If you’re looking for an introduction to some of the tools used in the field of Bioinformatics (programming, databases, data analysis) or even just looking for a general introduction to Perl programming, MySQL or R why not check it out.

Still here and after more?!?! Why not head on over to bixsolutions.net - the companion site for the book, and take a peek at what’s on offer.

Now get off my lawn!

The default ls on OS X comes from BSD and compared to the GNU/Linux alternative is slightly lacking when it comes to comes to changing how things look - so what I like to do is replace it with the GNU ls available in MacPorts - this allows me to get a terminal setup like below:

To get this done is pretty simple, once you have MacPorts set up correctly (if you can type man port and get a manual page you’re ready), just run the following command:

sudo port install coreutils +with_default_names

This installs the ‘GNU File, Shell, and Text utilities’ which ls is part of - the extra option at the end +with_default_names makes it override (only override - not replace, this is totally removable) the default ls and other tools otherwise they will have a ‘g’ prefix - i.e. ls would be gls.

Next we add some extra configuration to our ~/.bash_profile file (i’ll include my MacPorts config in case you get stuck above)…

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# MacPorts
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
export MANPATH=/opt/local/share/man:$MANPATH
 
# Terminal colours (after installing GNU coreutils)
NM="\[\033[0;38m\]" #means no background and white lines
HI="\[\033[0;37m\]" #change this for letter colors
HII="\[\033[0;31m\]" #change this for letter colors
SI="\[\033[0;33m\]" #this is for the current directory
IN="\[\033[0m\]"
 
export PS1="$NM[ $HI\u $HII\h $SI\w$NM ] $IN"
 
if [ "$TERM" != "dumb" ]; then
    export LS_OPTIONS='--color=auto'
    eval `dircolors ~/.dir_colors`
fi
 
# Useful aliases
alias ls='ls $LS_OPTIONS -hF'
alias ll='ls $LS_OPTIONS -lhF'
alias l='ls $LS_OPTIONS -lAhF'
alias cd..="cd .."
alias c="clear"
alias e="exit"
alias ssh="ssh -X"
alias ..="cd .."

Then finally we need to create a file called .dir_colors in our home directory that allows us to configure the colours used by ls:

touch ~/.dir_colors

Then add the contents of the file here:

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# Configuration file for dircolors, a utility to help you set the
# LS_COLORS environment variable used by GNU ls with the --color option.
 
# The keywords COLOR, OPTIONS, and EIGHTBIT (honored by the
# slackware version of dircolors) are recognized but ignored.
 
# Below, there should be one TERM entry for each termtype that is colorizable
TERM linux
TERM linux-c
TERM mach-color
TERM console
TERM con132x25
TERM con132x30
TERM con132x43
TERM con132x60
TERM con80x25
TERM con80x28
TERM con80x30
TERM con80x43
TERM con80x50
TERM con80x60
TERM xterm
TERM xterm-color
TERM xterm-debian
TERM rxvt
TERM screen
TERM screen-w
TERM vt100
 
# Below are the color init strings for the basic file types. A color init
# string consists of one or more of the following numeric codes:
# Attribute codes:
# 00=none 01=bold 04=underscore 05=blink 07=reverse 08=concealed
# Text color codes:
# 30=black 31=red 32=green 33=yellow 34=blue 35=magenta 36=cyan 37=white
# Background color codes:
# 40=black 41=red 42=green 43=yellow 44=blue 45=magenta 46=cyan 47=white
NORMAL 00	# global default, although everything should be something.
FILE 00 	# normal file
DIR 01;36 	# directory
LINK 01;37 	# symbolic link.  (If you set this to 'target' instead of a
           	# numerical value, the color is as for the file pointed to.)
FIFO 40;33	# pipe
SOCK 01;35	# socket
DOOR 01;35	# door
BLK 40;33;01	# block device driver
CHR 40;33;01 	# character device driver
ORPHAN 40;31;01 # symlink to nonexistent file
 
# This is for files with execute permission:
EXEC 01;35
 
# List any file extensions like '.gz' or '.tar' that you would like ls
# to colorize below. Put the extension, a space, and the color init string.
# (and any comments you want to add after a '#')
 
# If you use DOS-style suffixes, you may want to uncomment the following:
#.cmd 01;32 # executables (bright green)
#.exe 01;32
#.com 01;32
#.btm 01;32
#.bat 01;32
 
.tar 01;31 # archives or compressed (bright red)
.tgz 01;31
.arj 01;31
.taz 01;31
.lzh 01;31
.zip 01;31
.z   01;31
.Z   01;31
.gz  01;31
.bz2 01;31
.deb 01;31
.rpm 01;31
.jar 01;31
.dmg 01;31
 
# image formats
.jpg 01;35
.png 01;35
.gif 01;35
.bmp 01;35
.ppm 01;35
.tga 01;35
.xbm 01;35
.xpm 01;35
.tif 01;35
.png 01;35
.mpg 01;35
.avi 01;35
.fli 01;35
.gl 01;35
.dl 01;35
 
# source code files
.pl 00;33
.PL 00;33
.pm 00;33
.tt 00;33
.yml 00;33
.sql 00;33
.html 00;33
.css 00;33
.js 00;33

Finally, all you need to do is close and re-open the Terminal. Now we should be sorted.

Well, basically this is going to be a place for me, Darren Oakley to dump my thoughts and little ideas that I have on a semi-regular basis… Expect posts on subjects such as Apple (god - not another mac blogger!), Perl programming, Bioinformatics (it’s what I do for a living), Unix geekiness, Xbox 360 and many things in between as I go about my daily life.

Anyway - enough of this boring first post nonsense! Will be back soon with more interesting things to say!