15. Sequence (DNA/RNA)
Comparative genomics & phylogeny
Protein sequence analysis &
Regulation of gene evolution
expression; transcription
factors & micro RNAs
Protein structure & function:
computational crystallography
Protein families,
motifs and domains
Chemical biology
Protein interactions & complexes: modelling and prediction
Pathway analysis
Data integration & literature mining
Image analysis Systems
modelling
25. 2 open‐bio.org
• The Open Bioinformatics Foundation is a non profit,
volunteer run organization focused on supporting
open source programming in bioinformatics.
• Its main activities are:
– Underwriting and supporting the BOSC conferences
– Organizing and supporting developer‐centric quot;hackathonquot;
events (Bio*)
42. BioMart is a simple and robust data integration system for large
scale data querying, providing researchers with fast and flexible
access to biological databases
http://www.biomart.org/
47. RESTful web services
GET, POST
HTML,XML,PNG
REST: REpresentational State Transfer
http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/uniprot/slpi_human
54. EBI web services (analysis tools)
run(params, data)
jobid
checkStatus (jobid)
status
getResults (jobid)
results available
poll (jobid, type)
result file
55. Perl client
use SOAP::Lite;
my $WSDL = 'http://www.ebi.ac.uk/Tools/webservices/wsdl/WSFasta.wsdl';
my $fasta_client = SOAP::Lite->service($WSDL);
my %params=();
$params{'program'}='fasta3';
$params{'database'}='uniprot';
$params{'email'}='your@email.com';
$params{‘async'}= 1;
$data={type=>quot;sequencequot;,
content=>quot;MRCSISLVLGLLALEVALARNLQEHVFNSVQSMCSDDSFSEDTECIquot;};
# $data={type=>quot;sequencequot;,
# content=>“uniprot:slpi_humanquot;};
my $jobid = $fasta_client >runFasta(
SOAP::Data->name('params')->type(map=>%params),
SOAP::Data->name( content => [$data]));
print $fasta_client->poll($jobid);
56. Perl client (cont.)
# set a loop for checking job submission status
# RUNNING, NOT_FOUND, ERROR, DONE
my $status = $fasta_client ->checkStatus($jobid);
while (status eq quot;RUNNINGquot;) {
sleep 10; $status = $fasta_client->checkStatus($jobid);
}
# when job is done, poll for the results
my $result = $fasta_client ->poll($jobid) if ($status eq quot;DONEquot;) ;
print $result;
64. What to standarize?
• CONTENT: Minimal/Core Information to be
reported ‐> MIBBI (http://www.mibbi.org)
• SEMANTIC: Terminology Used ‐>
Ontologies, OBI (http://obi‐ontology.org)
• SYNTAX: Data Model, Data Exchange ‐
>Fuge (http://fuge.sourceforge.net/) ISA‐
TAB, MAGE‐TAB, PRIDE
67. Biological question
Microarray
Experimental design
Microarray experiment
Image analysis
Expression quantification Pre‐processing
A
Normalization n
RT‐PCR a
l
Testing
Estimation Prediction
Clustering
y
s
Biological verification i
and interpretation s
68. r‐project.org
R is an open source implementation of the S Language
•
Many statistical and machine learning algorithms
•
Good visualization capabilities
•
Possible to write scripts that can be reused
•
Sophisticated package creation and distribution system
•
Supports many data technologies: XML, DBI, SOAP
•
Interacts with other languages: C; Perl; Python; Java
•
R is largely platform independent: Unix; Windows; OSX
•
R has an active user community
•
cran.r‐project.org
71. Bioconductor for Microarray Analysis
Quickly becoming the accepted approach
•
Open source
•
Flexible
•
(fairly) simple to use ‐ intuitive
•
Wide applications – many packages
•
85. Open Microscopy Environment
• OME is a multi‐site collaborative effort among academic
laboratories and a number of commercial entities that
produces open tools to support data management for
biological light microscopy.
• The original OME server is an application written in Perl
running under Apache. It is accessed using a Web User
Interface, via a Java API, or using a plugin for ImageJ.
• The server can support images in a wide range of file
formats. This model is also extendable allowing custom
data to be stored in the server.
• It supports multiple users and provides appropriate
security for private research and collaboration.
http://openmicroscopy.org
90. At $150,000, the Polonator is the cheapest
instrument on the market, says Harvard
University's George Church, whose lab
developed the technology in conjunction
with Dover Systems, Plus, the tool uses five‐
fold less reagents than other platforms, and
is the smallest instrument available.
http://www.polonator.org/
98. [Phil Bourne]
Growth of open access scientists
digital natives, always online, hybrids
catalysts for change
99.
100. • Making scientific research “re‐useful” — We help
people and organizations open and mark their research
and data for reuse.
• Enabling “one‐click” access to research materials —
We help streamline the materials‐transfer process so
researchers can easily replicate, verify and extend
research.
• Integrating fragmented information sources — We
help researchers find, analyze and use data from
disparate sources by marking and integrating the
information with a common, computer‐readable
language.