BPBR15

Bioinformatics using Python for Biomedical Researchers

Downloadable poster in PDF

   IMPORTANT DATES for this Course
   Deadline for applications: July 10th 2015 <---- NEW!
   Latest notification of acceptance: July 10th 2015
   Course date: July 20th - July 24th 2015

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

Instructors:

Allegra Via is a physicist and scientific researcher in the Biocomputing Unit of Sapienza Università (Roma, IT) where she also teaches Macromolecular Structure, Python programming, Bioinformatics and Biochemistry. Her main research interests include protein structural bioinformatics, protein function prediction and analysis, and protein interactions, though recently she started projects on DNA methylation and protein-¬≠RNA interactions. On top of her research activities, she is strongly involved in the design and delivery of bioinformatics training courses on Python programming for life scientists. She is the Training Coordinator for ELIXIR Italy, the ELIXIR.ITA local technical coordinator for Sapienza Università, and a member of the Global Organisation for Bioinformatics Learning, Education and Training, GOBLET. She has created the first Python course in GTPB in 2010 and has been an instructor in all the editions od BPB 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: Sapienza Università, Roma, IT

Kaja Milanowska graduated bioinformatics at Adam Mickiewicz University in Poznań. During her PhD research in Bioinformatics Laboratory, she worked mainly on the development of new biological databases, analysis of RNA maturation and degradation pathways and on pathways of DNA repair. She is an expert in the field of programming web applications in Django (she already has coached in two Django Girls meetings). She is interested in further education in the field of computer science (mainly web design, web applications, databases and Python programming). Currently she works at the Department of Gene Expression, Adam Mickiewicz University in Poznan dealing with the data from Next Generation Sequencing. From July Kaja is starting to work in two new projects at the Department of Molecular and Systems Biology, Polish Academy of Sciences in Warsawa. In addition to her scientific research activity, Kaja also cooperates with non-profit organizations such as PyLadies Poland or Geek Girls Carrots. She is actively working in the popularization of programming, mainly among women. At the latest Geek Girls Carrots meeting, in May 2015, she gave 2 presentations. Kaja was a co-founder of PyLadies Poland and has been a sopporter of that community in Poland, co-organizing meetings, teaching, mentoring or delivering seminars. PyLadies is a worldwide organisation that aims at making the Python community more diverse, especially by making it more friendly and welcoming for women. In her spare time, she keen on practising highly energetc sports - her passion is running (half-marathons, marathons, orienteering), alongside with hiking in the mountains and mountain-biking.

Affiliation: Polish Academy of Sciences, Department of Molecular and Systems Biology, Poznań, PL

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 25th 2015