Duration: 5 days lecture & practical workshop
Scientific Organizers: Allegra Via (Uni. La Sapienza, Rome) & Vicky Schneider (TGAC)
When: 7-11 October 2013
Venue:
Chris Lamb Training Suite,
The Genome Analysis Centre (TGAC)
Norwich Research Park
Norwich, NR4 7UH, UK
The Genome Analysis Centre (TGAC)
Norwich Research Park
Norwich, NR4 7UH, UK
Registration: £150 (includes tea/coffee, lunch and one course dinner), limited spaces available.
REGISTER HERE Deadline 10 July 2013
Aims: Python is an object-oriented programming
language that is ideal for biological data analysis. The course will
start with very basic language concepts and instructions and will cover
all the main language aspects, including variables, types, modules,
functions, exceptions, control of flux, input, output, and classes. All
the examples and practical sessions will focus on solving particular
biological problems. In particular, examples and practical sessions will
cover:
- working with DNA and protein sequences
- data retrieval from files and their manipulation
- running applications, such as BLAST, locally and from a script
- finding motifs in sequences
- parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc.
Biopython will be also introduced and applied to some of the mentioned examples.
The course is meant to be highly interactive and the students will continuously put theory into practice while learning.
By the end of the course, the students will have a good understanding
of Python basics and will have acquired the skills to manage any type
of bioinformatics record and to run applications from scripts.
Unix/linux basic skills will be provided at the beginning of the course.
Course Pre-requisites
Basic familiarity with bioinformatics data resources such as
Uniprot/Swiss-Prot, Blast, ENSEMBL, PDB, etc. The course is directed to
biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data.
Target Audience
End-users of bioinformatics databases and tools that aim at
developing hands-on capabilities for biological data analysis, ie
writing their own or adapting somebody else's Python scripts in an
autonomous way.
Instructors:
Allegra Via
graduated in Theoretical Physics at Sapienza University of Rome and
obtained her PhD in Cellular and Molecular Biology in 2002. Since 1998
she works in Computational Biology and regularly teaches Bioinformatics
and Python Programming Language to bioinformaticians and biologists. She
was Postdoctoral Fellow at the University of Rome 'Tor Vergata' where
she has been Adjunct Professor in 2005-2010. Since the academic year
2010-2011 she teaches at Sapienza University of Rome. She also gives
invited lectures in other universities and in training courses (e.g.
GTPB). Currently she works as researcher in the Biocomputing Group of
Sapienza University of Rome headed by Anna Tramontano. Her main research
interests include protein structural bioinformatics and protein
function prediction and analysis. Besides her research activity, she
wrote two book chapters related to Internet for Cell and Molecular
Biologists.
Affiliation: Sapienza Università di Roma, Roma, IT
Affiliation: Sapienza Università di Roma, Roma, IT
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