I found this book really helpful during my MSc assignments, group project and thesis project. It gives a nice informative introduction for each tool then works through towards developing advanced bioinformatics applications.

This book presents a well-written and complete overview of bioinformatics software development using Perl, R and MySQL.

The book is divided into 5 chapters. The first chapter begins with an interesting introduction on various bioinformatics resources and applications. This is followed by useful and descriptive chapters on MySQL, Perl, R and web programming.

A highlight of the book is it’s well-structured layout. For each chapter, there is easy introduction followed by concise explanations to developing advanced bioinformatics applications and well commented examples of code plus accompanying online resources on it’s website.

As this book is titled “Building Bioinformatics Solutions: with Perl, R and MySQL”, and it does cover its ground very well, plus there is no assumtion of prior knowledge on software development – hence, it is also suitable for those with minimal programming experience.

In conclusion, this book is a very valuable resource for software development in bioinformatics, both for those that are already working in this domain and for those desiring to do so. It is also appropriate as a general introduction into the area of bioinformatics for interested and literate non-specialists.

Bibliographic information from GoogleBooks

Title	Building bioinformatics solutions with Perl, R and MySQL Oxford biology
Authors	Conrad Bessant, Ian Shadforth, Darren Oakley
Publisher	Oxford University Press, 2009
ISBN	0199230234, 9780199230235
Length	241 pages
Subjects	Bioinformatics Business & Economics / Statistics Computers / Bioinformatics Computers / General Computers / Programming Languages / General Mathematics / Probability & Statistics / General Open source software Science / Applied Sciences

EUtilities is a very useful resource to retrieve data from NCBI database.

This script retrieves a brief summary and the genbank file for genes that are relevant to a search word.

There is also an option to limit you number of results returns (very handy).

Bio::DB::EUtilities is required to execute the search.

This method is much faster than using Bio::DB::Query::GenBank module.

If you require more information than the summary output, you can always get it from the genbank file.
The summary does not provide information such as references and sequences.

Chapter 10 of ‘Beginning Perl for Bioinformatics’ is a good and simple reference for retrieving data from from files in genbank format. This resource is freely available here.

Note that you can query for proteins as well. (uncomment line 15)

Installing new modules: this can be easily done using cpan.
Here is the documentation for cpan.
Or, here is documentation for installing modules manually.

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#!/usr/bin/perl -w
 
use Bio::DB::EUtilities; 
use strict;
 
#specify search term 
my $search_term = 'breast cancer';			
 
 
#maximum number of results to retrieve
my $retmax = 10;
 
#first search for a list of genbank ids that match your search term
my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
#                           -db => 'protein',
                         -db => 'nucleotide',
                         -term => $search_term,
                         -retmax => $retmax);
 
#list of Genbank IDs
my @ids = $factory->get_ids;
 
#loop through the list of IDs
foreach my $id (@ids){
 
	# get a summary and print details
		$factory->reset_parameters(-eutil => 'esummary',-db => 'nucleotide',-id => $id); 
		my $ds = $factory->next_DocSum; 
 
		# print flattened mode from summary above 
		while (my $item = $ds->next_Item('flattened'))  { 
			# checks id itens has contents
			printf("%-20s:%s\n",$item->get_name,$item->get_content) if $item->get_content; 
		} 
 
 
	# download the full genbank file 
		$factory = Bio::DB::EUtilities->new(-eutil => 'efetch', 
								-db => 'nucleotide', 
								-id => $id, 
								-rettype => 'gbwithparts'); 								
		$factory->get_Response(-file => "$id.gb"); 
 
}

This script retrieves the full articles (or the abstract if the full article are not available) that a relevant to a search term from the PubmedCentral (pmc) database.

The results are sorted in reverse chronological order.

There is also an option to limit you number of results returns (very handy).

The output is in xml format.

An example for a perl module to tranform XML files : XML:Simple

LWP::Simple is required to execute the search.

Installing new modules: this can be easily done using cpan.
Here is the documentation for cpan.
Or, here is documentation for installing modules manually.

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#!/usr/bin/perl -w
 
use strict;
use LWP::Simple;
 
 
#search term to find
my $search_term = 'breast cancer';
 
#maximum number of results to retrieve
my $retmax = 10;
 
my $utils = 'http://www.ncbi.nlm.nih.gov/entrez/eutils';
my $db_name = 'pmc';
 
# Submit the search and retrieve the XML based results
my $esearch_result = get( $utils . '/esearch.fcgi?db=' . $db_name . '&retmax='.$retmax.'&term=' . $search_term );
 
# paper IDs
my @ids = ($esearch_result =~ m|.*<Id>(.*)</Id>.*|g);
 
#loop through all the ids
# get individual papers (if not, then abstacts)
foreach my $id (@ids) {
 
	#get all details for each paper - full text if available	
	my $efetch = $utils . '/efetch.fcgi?db=' . $db_name . '&id=' . $id;   
 
	#prints out to a xml file (file name generated from database name and current paper ID)
	open(OUTFILE, ">$db_name$id.xml");
	print OUTFILE get($efetch);
	close OUTFILE;
}

But, it cannot be denied that amidst all this complexity, it is only simplicity that everyone finds interesting.

Anyway, back to TIde, an open source, platform independent tool to investigate ordinary differential equation models; a systematic approach could not only accelerate the drug research, but also save valuable of the time and money (resources that could be used elsewhere).

Good open source software  are the best things that have happened to the programming world.

Resources:

• Article from BMC Bioinformatics Journal
• TIde’s website

This object-oriented data mining system that lets one build complex queries from the underlying databases, and it’s web interface aids non-programmers (biologists) query for data with lesser effort; plus once one has defined what he wants to download using Biomart, he can simply generate an XML file.

I have to accept that the tools isn’t flawless, but hey, it’s open source, we can clean it up ourself. Plus, it should not be overlooked that Biomart has just being around for 6 years and there is still so much work being put into it – most of the mojor issues will be dealt with in their next major release, which they are now re-writing in Java.

I am quiet excited to start some real work on Biomart…