Hospital Universitari Vall d’Hebron
Institut de Recerca - VHIR
Institut d’Investigació Sanitària de l’Instituto de Salud C...
We are drowning in information and
starved for knowledge
John Naisbitt
Who on efficient work is bent,
must choose the fitt...
1. What is Bioinformatics?
● The explosive growth of data
● The growth of GenBank
● Bioinformatics definition
● Bioinforma...
What is Bioinformatics?
413/05/2014
THE EXPLOSIVE GROWTH OF DATA
Hace ... Antes Ahora
Nucleótidos 26 años
(1982)
680338 pb
(GenBank)
> Miles de
millones
Prote...
THE GROWTH OF GENBANK
(1982-2000)
613/05/2014
GENOMES ONLINE DATABASE
713/05/2014
BIOINFORMATICS
• Born on the lookout for
– the development of new technologies and
– its application in the generation of ...
BIOINFORMATICS AND INTERDISCIPLINARITY
Mathematics
Statistics
Computer
Science
Informatics
Biology
Molecular
biology
Medic...
THE SCOPES OF BIOINFORMATICS
• Information organization
– Databanks and databases
– Algorithms and exploitation tools
• An...
INFORMATION ORGANIZATION
1113/05/2014
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
1213/05/2014
SYSTEMS BIOLOGY MODELING
1313/05/2014
INTEGRATIVE BIOINFORMATICS
1413/05/2014
IN SUMMARY…
Data Knowledge
Bioinformatics tools
and resources
1513/05/2014
What is a bioinformatician?
Environment, training, activities… of the bioinformaticians
1613/05/2014
WHAT DOES A BIOINFORMATICIAN KNOW?
17
• He/She must have “solid understanding” of
– Some biological discipline
• Biochemis...
WHAT DOES A BIOINFORMATICIAN DO?
18
• Information management
– Implementation and exploitation of local or online
database...
Where and how is
bioinformatics done?
1913/05/2014
WHERE IS BIOINFORMATICS DONE?
20
• Specialized centers
– EBI, NCBI, EMBL…
– INB, Plataforma Bioinformàtica de la UAB…
• Bi...
HOW IS BIOINFORMATICS DONE?
21
• Usually, though not necessarily, it has
“universal” purpose, to access a maximum
number o...
TO KNOW MORE
22
• There are a lot of free courses and training
activities:
– EBI’s 2scan
– NCBI’s tutorials
– Local traini...
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Introduction to Bioinformatics (UEB-UAT Bioinformatics Course - Session 1.1 - VHIR, Barcelona)

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Course: Bioinformatics for Biomedical Research (2014).
Session: 1.1- Introduction to Bioinformatics.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.

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Introduction to Bioinformatics (UEB-UAT Bioinformatics Course - Session 1.1 - VHIR, Barcelona)

  1. 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. 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. 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. 4. What is Bioinformatics? 413/05/2014
  5. 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. 6. THE GROWTH OF GENBANK (1982-2000) 613/05/2014
  7. 7. GENOMES ONLINE DATABASE 713/05/2014
  8. 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. 9. BIOINFORMATICS AND INTERDISCIPLINARITY Mathematics Statistics Computer Science Informatics Biology Molecular biology Medicine Chemistry Physics Bioinformatics 913/05/2014
  10. 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. 11. INFORMATION ORGANIZATION 1113/05/2014
  12. 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. 13. SYSTEMS BIOLOGY MODELING 1313/05/2014
  14. 14. INTEGRATIVE BIOINFORMATICS 1413/05/2014
  15. 15. IN SUMMARY… Data Knowledge Bioinformatics tools and resources 1513/05/2014
  16. 16. What is a bioinformatician? Environment, training, activities… of the bioinformaticians 1613/05/2014
  17. 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. 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. 19. Where and how is bioinformatics done? 1913/05/2014
  20. 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. 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. 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

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