Presentation at the Bioinformatics Open Days, Universidade de Lisboa in April 10, 2015 http://bod2015.ciencias.ulisboa.pt

1. Master in Bioinformatics
and Computational
Biology
Francisco Couto
April 10, 2014
Bioinformatics Open Days, Universidade de Lisboa

2. Why?
• An Explosion Of Bioinformatics Careers
– in Science of June 13, 2014 DOI
http://dx.doi.org/10.1126/science.opms.r1400143
• Global Bioinformatics Market Will reach USD
12,542.4 million in 2020
– in Finances, December 31, 2014
http://www.finances.com/analyses-and-opinions/analysis-opinions/49771-global-bioinformatics-market-will-reach-usd-12542-4-million-
2020.htm

3. How?
• Experts agree that
– the most successful bioinformaticists (and the ones
who land the jobs) are those who have a multitude of
skills
• At Roche,
– “we offer continuous training in various areas and
encourage our staff to attend conferences, publish, or
pursue higher degrees”
In An Explosion Of Bioinformatics Careers in Science of June 13, 2014

4. What?
• BBC offers advanced formation in
– Bioinformatics
– and Computational Biology
• As a complement to 1st cycles
• Multidisciplinary formation
• With application to
– Academic Research
– Biotechnology, Pharmaceutical, Health, …

5. For students
• With 1st Cycle in
– Biology, Biochemistry, Pharmacy, Medicine,
Veterinary, Agronomy, Health Sciences and other
related
– Informatics, Information technologies, Statistics,
Mathematics and other related

6. Access
• 20 students per yer
• Academic degree (1st cycle)
– in related areas
• Tuiton 1200 euros per year

7. Selection criteria
• Academic degree
– 40% (Grade)
• Academic, scientific, technical curriculum
– 35%
• Professional experience in related areas
– 25%

8. Number of Students
0
10
20
30
40
50
60
2003/04 2004/05 2005/06 2006/07 2007/08 2008/09 2009/10 2010/11 2011/12 2012/13 2013/14 2014/15

9. Coordenation
• Departaments involved in coordination
– Informatics (current coordinator)
– Animal Biology
– Vegetal Biology
• Other involved departments
– Statistics
– Chemistry and biochemistry
– Mathematics

10. Curricular Plan
• Profiles (18 ECTS mandatory)
– 12+30 ECTS optional
• 60 ECTS in dissertation course unit
– Bioinformatics and Computational Biology
– Free to choose: instititution, topic, and advisors
Profile Informatics Statistics Biology Biology/
BioChemistry
Biology 6 ECTS 6 ECTS 6 ECTS
Informatics 6 ECTS 6 ECTS 6 ECTS
Math and Physics 6 ECTS 6 ECTS 6 ECTS

11. Course units
Fundamentos de Programação
Introdução às Bases de Dados
Apredizagem Automática em Ciencias
Programação por Objectos
Vida artificial
Visualização de Dados Científicos
Bioestatística para a Bioinformática
Fundamentos de Bioestatistica
Análise de Dados Multivariados
Genética Molecular
Biologia Molecular
Genética Populacional
Dinâmica Populacional
Métodos Computacionais em Evolução e Ecologia
Filogenética
Biologia Computacional e Genómica
Evolução Experimental
Deteção Remota e Sistemas de Informação Geográfica
Introdução aos Modelos Biomatemáticos
Modelos e Métodos Computacionais em Biologia
Data Warehousing e Data Mining
Integração e processamento Analitico de informação
Ontologias Aplicadas às Ciencias
Sistemas Interactivos em Ciências
Inteligência Artificial em Ciências
Complementos de programação
Bioinformática
Aplicações na Web
Métodos Estatisticos em Bionformatica
Regulação de Sistemas Bioquimicos
Regulação Bioquimica
Simulação Bioquimica
Evolução Molecular
Computação na Medição de Fenómenos Biológicos
Epidemiologia e Doenças Transmissiveis
Biologia Computacional na Prática Biomédica
Perspectivas em Biologia Computacional
Investigação em Bioinformática
Aplicações Avançadas em Biologia
Análise Computacional da Morfologia e Dinamica de Material
Biológico

12. Thesis at
repositorio.ul.pt
ProGenViZ: a novel interactive tool for prokaryotic genome visualization
and comparison, BFR Gonçalves - 2014
Identifying interactions between chemical entities in text, AFM Lamúrias -
2014
Analysis of RNA-seq data from the interaction of Coffea spp.-
Colletotrichum kahawae, JRV Fino - 2014
Genome-wide profiling of RNA polymerase II and associated co-
transcriptional processes using advanced NET-seq data, TPC Gomes - 2014
NGSOnto: proposta de uma ontologia para descrever o processo de
sequenciação de alto desempenho, MS Silva - 2014
Automatic recognition of vocalizations in the lusitanian toadfish
(Halobatrachus didactylus): acoustic rhythms and interactions, MAG
Vieira - 2013
Metagenomic analysis of Mariana Trench sediment samples, VML
Carvalho - 2013
TreeHop: a method to improve orthology detection, BMMF Gomes - 2013
Studies on the influence of a TO I RNA editing on protein evolution, DAM
Ribeiro - 2012
Coupling metabolic footprinting and flux balance analysis to predict how
single gene knockouts perturb microbial metabolism, GS Correia - 2012
Comparative analysis of 454 pyrosequencing data from coffee
transcriptomes, DAP Santos - 2011
In silico analysis of miRNA promoters, FMM Martins – 2011
Quantitative analysis of Bicyclus anynana's eyespot wing pattern images,
PS Lopes - 2011
Machine learning algorithms to predict blood-brain barrier permeability
of drug molecules, IFS Martins - 2011
Microsatellite characterization and marker development from massive
sequencing data of the blenny Salaria pavo, SJD Cardoso - 2011
Supervised and unsupervised spermatozoa detection, classification and
tracking in imaging data, PÂP Silva – 2011
Crescimento de raízes no solo baseado em modelos de enxame, TN Matos
- 2011
Multisource epidemic data collector, JMQM Zamite - 2010
Estudo computacional das interacções proteína-proteína, SMCM Santos –
2010
Protein identification in FTMS: a new scoring system and data analysis
platform development, JPSCB Canhita - 2009

13. Applications 2015/16
• 1st Phase
– In May/June 2015
– http://www.fc.ul.pt/pt/pagina/5461/candidaturas

14. DOCTORAL DEGREE IN
INFORMATICS

15. Why?
• Period of freedman to pursue your own dream
• After the PhD degree
– Make a startup in IT
• Easier to get investment capital
– Join the Research Dept. of IT company
• Google Genomics
• Philips Healthcare
• Siemens Healthcare
– Continue as a postdoctoral researcher

16. How?
• Select a topic
– Incremental
• The same thing but better
– Disruptive
• A new way to solve a problem
• Select the research lab
• Select the advisor
• Apply for PhD grants
• Apply for PhD programme

17. What?
• PhD in Informatics at FCUL:
– a curricular component,
– the qualification exam,
– active participation in doctoral seminaries
– and final examination of the PhD thesis.
• Specializations
– Bioinformatics
– Computer Science
– Informatics Engineering
http://www.ciencias.ulisboa.pt/en/cursos/doutoramento/informatica

18. First thesis in Bioinformatics
• ReBIL: Relating Biological Information through
Literature, May-2006, Dept. of Informatics
http://repositorio.ul.pt/handle/10455/3127

19. LASIGE

20. Why?
• Scholarships
– for pre-doctoral
studies
• Working in
Bioinformatics
– since 2003
• Strong collaborations
with IT industry
• Top positions in
international
competitions

21. How?
• Work in Information and Knowledge
Management problems:
– Data and text mining
– Machine Learning
– Information Retrieval
– Ontology Matching
– Semantic Similarity
– Semantic web
– Linked data
– Health Data Security and Privacy
– Cloud Computing and Storage

22. What?
• Equipa da ULisboa premiada na SemEval 2015
http://www.ulisboa.pt/equipa-ulisboa-premiada-semeval-2015/
• Equipa da ULisboa vence “Ontology Alignment
Evaluation Initiative” 2014
http://www.ulisboa.pt/equipa-da-ulisboa-vence-ontology-alignment-evaluation-initiative-2014/
• KnowledgeCoins: os novos bitcoins de I&D?
http://labs.sapo.pt/portfolio/knowledgecoins-os-novos-bitcoins-de-id/
• BiobankCloud was presented by Jim Dowling, in a
keynote lecture, at SeqAhead:
– Next Generation Sequencing: a look into the future,
on March 16th 2015, in Bratislava.

23. Who?

24. ICBO 2015
International Conference on Biomedical Ontology
Lisbon, 27-30 July
http://icbo2015.fc.ul.pt/