Hospital Universitari Vall d’Hebron Institut de Recerca - VHIR

Institut d’Investigació Sanitària de l’Instituto de Salud Carlos III (ISCIII)

Bioinformàtica per la Recerca Biomèdica http://ueb.vhir.org/2014BRB

Alex Sánchez

alex.sanchez@vhir.org 13/05/2014

INTRODUCTION TO BIOINFORMATICS

We are drowning in information and starved for knowledge

John Naisbitt Who on efficient work is bent, must choose the fittest instrument.

Goethe (Fausto)

1. What is Bioinformatics? ● The explosive growth of data ● The growth of GenBank ● Bioinformatics definition ● Bioinformatics and interdisciplinarity ● The scope of bioinformatics

2. What is a bioinformatician?

● What does a bioinformatician know? ● What does a bioinformatician do?

3. Where and how is bioinformatics done? ● Where is bioinformatics done? ● How is bioinformatics done? ● To know more…

PRESENTATION OUTLINE

3 13/05/2014

What is Bioinformatics?

4 13/05/2014

THE EXPLOSIVE GROWTH OF DATA

Hace ... Antes Ahora

Nucleótidos 26 años (1982)

680338 pb (GenBank)

> Miles de millones

Proteínas 26 años 1500 300.000

DNA continuo 16 años 73 kb > 270 Mbases

SNPs 16 años centenares 11 millones

Genomas 11 años 0

organismos

1282

Organismos

(mediados 2010)

Expresión 10 años Limitado pocos genes

Miles de estudios con miles de genes

5 13/05/2014

THE GROWTH OF GENBANK

(1982-2000)

6 13/05/2014

GENOMES ONLINE DATABASE

7 13/05/2014

BIOINFORMATICS

• Born on the lookout for – the development of new technologies and – its application in the generation of huge

amounts of data.

• It is the interdisciplinary scientific field that develops methods for storing, retrieving, organizing and analyzing biological data.

8 13/05/2014

BIOINFORMATICS AND INTERDISCIPLINARITY

Mathematics Statistics

Computer Science Informatics

Biology Molecular biology

Medicine

Chemistry

Physics

Bioinformatics

9 13/05/2014

THE SCOPES OF BIOINFORMATICS

• Information organization – Databanks and databases – Algorithms and exploitation tools

• Analysis and interpretation of experimental results – Genome analysis and sequencing – Comparative genomics – Gene expression and transcription – Proteomics, protein-protein interaction

• Systems biology modeling

10 13/05/2014

INFORMATION ORGANIZATION

11 13/05/2014

ANALYSIS AND INTERPRETATION

A G G G T T A T G C G C G

A G A G T T C T G C T C G

12 13/05/2014

SYSTEMS BIOLOGY MODELING

13 13/05/2014

INTEGRATIVE BIOINFORMATICS

14 13/05/2014

IN SUMMARY…

Data Knowledge Bioinformatics tools

and resources

15 13/05/2014

What is a bioinformatician?

Environment, training, activities… of the bioinformaticians

16 13/05/2014

WHAT DOES A BIOINFORMATICIAN KNOW?

17

• He/She must have “solid understanding” of

– Some biological discipline • Biochemistry, Genetics,…

– Software development environments • OS [Linux], Scripting languages [Perl, Java, R],

Databases [SQL], Web development [PHP, ASP, Ajax…]

– Some quantitative discipline

• Mathematics, Statistics, Physics

At least two of the previous three!!

13/05/2014

WHAT DOES A BIOINFORMATICIAN DO?

18

• Information management – Implementation and exploitation of local or online

databases. – Installation and maintenance of web servers

• Software development – Creation of local or web-based applications

• Data analysis and exploitation – High Throughput and Next Gen Seq. data

…

13/05/2014

Where and how is bioinformatics done?

19 13/05/2014

WHERE IS BIOINFORMATICS DONE?

20

• Specialized centers – EBI, NCBI, EMBL… – INB, Plataforma Bioinformàtica de la UAB…

• Bioinformatics services in research centers – UEB, UBB, BU…

• Universities • Biotech companies • Pharmaceutical labs …

13/05/2014

HOW IS BIOINFORMATICS DONE?

21

• Usually, though not necessarily, it has “universal” purpose, to access a maximum number of users: – Often looking for online solutions – Often based on projects (more or less) open

source and freely distributed *

* It is not generalized at all – For instance, Ingenuity Pathways Analysis is not free

but is quite good.

13/05/2014

TO KNOW MORE

22

• There are a lot of free courses and training activities: – EBI’s 2scan – NCBI’s tutorials – Local training courses

• Introducción a la Bioinformática (Alex Sánchez, UEB/UB) • Invitació a la Bioinformàtica (Plataforma BioinfoUAB)

• A great variety of rerefence books: • List of books on bioinformatics

• Scientific Societies and Publications: – Bioinformatics, Briefings in Bioinformatics – International Society for Computational Biology

13/05/2014