This document provides an introduction to bioinformatics. It defines bioinformatics as the interdisciplinary field that develops methods for storing, organizing, and analyzing vast amounts of biological data generated by new technologies. It discusses the explosive growth of genomic and protein data. It also describes the roles and skills of bioinformaticians, including knowledge of biology, computer science, and quantitative disciplines. Finally, it outlines where bioinformatics is typically conducted, such as specialized centers and universities, and how it is usually done through online and open source solutions.

1. 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

2. We are drowning in information and
starved for knowledge
John Naisbitt
Who on efficient work is bent,
must choose the fittest instrument.
Goethe (Fausto)

3. 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
313/05/2014

4. What is Bioinformatics?
413/05/2014

5. 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
513/05/2014

6. THE GROWTH OF GENBANK
(1982-2000)
613/05/2014

7. GENOMES ONLINE DATABASE
713/05/2014

8. 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.
813/05/2014

9. BIOINFORMATICS AND INTERDISCIPLINARITY
Mathematics
Statistics
Computer
Science
Informatics
Biology
Molecular
biology
Medicine
Chemistry
Physics
Bioinformatics
913/05/2014

10. 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
1013/05/2014

11. INFORMATION ORGANIZATION
1113/05/2014

12. 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
1213/05/2014

13. SYSTEMS BIOLOGY MODELING
1313/05/2014

14. INTEGRATIVE BIOINFORMATICS
1413/05/2014

15. IN SUMMARY…
Data Knowledge
Bioinformatics tools
and resources
1513/05/2014

16. What is a bioinformatician?
Environment, training, activities… of the bioinformaticians
1613/05/2014

17. 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

18. 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

19. Where and how is
bioinformatics done?
1913/05/2014

20. 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

21. 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

22. 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