Bioinformatics using Python for Biomedical Researchers

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   IMPORTANT DATES for this Course
   Deadline for applications: July 4th 2016
   Latest notification of acceptance: July 6th 2016
   Course date: July 11th - July 15th 2016

Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants.


Allegra Via is a physicist and scientific researcher at the Institute of Biomembranes and Bioenergetics (IBBE) of the National Research Council (CNR, Bari, IT). In 2003, she got her PhD at the University of Rome "Tor Vergata", where she also worked six years as postdoc. In 2009 she moved to the Sapienza University as researcher, and, since January 2016, she works full time as the ELIXIR Italy Training Coordinator. She is involved in the design, organisation and delivery of bioinformatics training courses, in Train the Trainer activities, and collaborates with other ELIXIR's nodes on many training-related initiatives. She has a long track record of academic teaching (Macromolecular Structures, Python programming, Bioinformatics, Biochemistry, Protein interactions). Her main research interests include protein structural bioinformatics, protein function prediction and analysis, and protein interactions. She is a member of the Global Organisation of Bioinformatics Learning, Education and Training (GOBLET) and a Software/Data Carpentry instructor. She has created the first Python course in GTPB in 2010 and has been an instructor in all the editions of GTPB ever since. In 2014, she co-authored "Managing your biological data with Python", a book that budded from her experience as a training designer and as an instructor.

Affiliation: IBBE, CNR, Bari, IT

Vincenza Colonna is a group leader at the Institue of Genetics and Biophysics of the Italian National Research Council in Napoli, Italy. She works in human genomics and her main research interests are natural selection and consanguineous populations. She graduated from University of Napoli Federico II (Italy) and did postdoctoral work at University of Ferrara (Italy) and at the Wellcome Trust Sanger Institute (UK). She was lecturer in Genetics and Bioinformatics at the University of Ferrara (Italy). She is also leading the ObiLab project (http://www.igb.cnr.it/popgenlab/research) on training in bioinformatics. She is an instructor for ELIXIR-ITA and Software/Data Carpentry. She is also involved as collaborator and instructor in the ELIXIR-EXCELERATE Train the Trainer activities.

Affiliation: Institute of Genetics and Biophysics, CNR, Napoli, IT

Course Description

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will introduce the participants to all the basic concepts of Python such as calculating, organizing data, reading and writing files, program logic and writing larger programs. All the examples and practical sessions will focus on solving biological problems. In particular the 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 sequence
  • parsing common file formats (Uniprot, GenBank, PDB, BLAST) with Biopython
  • ways to find and correct program errors
The course will be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the participants will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics database record and to run applications from scripts. Basic Unix/Linux skills will be provided at the beginning of the course.

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.

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.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  May 15th 2016