A.A. 2013-2014

CORSO INTEGRATO DI INFORMATICA E

BIOINFORMATICAper il CLT in BIOLOGIA MOLECOLAREScuola di Scienze, Università di Padova

Docenti: Dr. Mauro Conti (Informatica) e Dr. Stefania Bortoluzzi (Bioinformatica)

SVOLGIMENTO DEL CORSO INTEGRATO E MODALITÀ D’ESAME

• II semestre del I anno• Impegno didattico di 5 crediti:

• 24 ore di lezione frontale• 32 ore di esercitazioni al computerCosì suddivise:

• Valutazione finale (Idoneità): in base all’esito delle esercitazioni e di una verifica scritta individuale.

Insegnamento Lezione Esercitazione

INFORMATICA 16 16

BIOINFORMATICA 8 16

WEB SITE DEDICATO AL CORSOhttp://compgen.bio.unipd.it/~stefania/Didattica/AA2013-2014/

ORGANIZZAZIONE DEL CORSO INTEGRATO

ORARIO E AULE ONLINE

TESTI e materiali CONSIGLIATIINFORMATICA•Colussi, File', Rossi, Informatica di base, Libreria progetto, 2003.•J. Glenn Brookshear (2006) Informatica: una panoramica generale. Pearson/Addison Wesley. (approfondimenti) •Python: http://www.python.it/doc/Howtothink/HowToThink_ITA.pdf

BIOINFORMATICA•Materiale lezioni•Risorse e tutorial online•Per approfondimento facoltativo: Fondamenti di Bioinformatica, Krane e Raymer, Pearson, 2007

“Researchers need to be obliged to document and manage their data with as much professionalism as they devote to their experiments.”

THE BIG DATA ERA

Nature journal Issue of 4 2008

Importance of data:• Retrieval• Integration• Analysis

An at least basic knowledge of bioinformatic methods in unavoidable also for experimental researchers

Bioinformaticsfrom basic methods for managing biosequences to systems biology models

NIH BIG DATA to Knowledge (BD2K)With advances in technologies, investigators are increasingly generating and using large, complex, and diverse datasets.

Consequently, the biomedical research enterprise is increasingly becoming data-intensive and data-driven.

However, the ability of researchers to locate, analyze, and use Big Data (and more generally all biomedical and behavioral data) is often limited for reasons related to access to relevant software and tools, expertise, and other factors.

D2K aims to develop the new approaches, standards, methods, tools, software, and competencies that will enhance the use of biomedical Big Data by supporting research, implementation, and training in data science and other relevant fields.

Importance of BioinformaticsDeep sequencing data analysis

DATABASES AND DATA RETRIEVALBiosequences and Gene-related info

WORKING WITH BIOSEQUENCESAlignments and similarity search

gene details

Ann

otat

ion

Trac

ks

officialsequence

comparisons

SNPs

NAVIGATING GENOMESBy Genome Browsers

EXAMPLES FROM MORE ADVANCED BIOINFORMATICS

Gene expression and RNA-seq data analysis

Opportunities and Challenges OPPORTUNITIES:

• estimate the odds of your future children being born with something like Down syndrome• secure paternity test• customized cancer-fighting drugs• personalized medicine

Opportunities and Challenges

“When your bank account or credit card is compromised, the situation is painful but recoverable. You can close the account, wipe the slate clean and start over. You cannot change or revoke your DNA once it’s leaked,” says Gene Tsudik – UCI – GenoDroid project.

OPPORTUNITIES:• estimate the odds of your future children being born with something like Down syndrome• secure paternity test• customized cancer-fighting drugs• personalized medicine

CHALLENGES:• do you have something more “private” than your DNA?• consumers fear losing insurance coverage if results are shared, companies don’t want to reveal proprietary information about customized treatments