A.A. 2014-2015

CORSO INTEGRATO DI INFORMATICA E

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

Docenti: Proff. Roberto di Pietro (Informatica)

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 computer

Così 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/AA2014-2015/

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 Bioinformatics

Deep sequencing data analysis

DATABASES AND DATA RETRIEVALBiosequences and Gene-related info

WORKING WITH BIOSEQUENCESAlignments and similarity search

gene details

An

nota

tion

Tra

cks

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 a genetic disease• 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

BioMol- Informatica e Bioinformatica - Modulo di Informatica

Roberto Di Pietro

Contatto: dipietro@math.unipd.itRicevimento: Per eventuali ricevimenti contattatemi via email; indicativamente mercoledì pomeriggio, in studio, 18.30 – fine

Il modulo si propone di fornire un’introduzione* su:- architettura degli elaboratori;- circuiti logici; - rappresentazione dell'informazione; - sistemi operativi;- reti di calcolatori;- Data Base, sicurezza --- cenni- programmazione (python).

Il modulo di Informatica si suddivide in lezioni di teoria (16 ore) e lezioni pratiche in lab. (16 ore).

*il programma di dettaglio verrà discusso durante la prima lezione e messo on-line.