Bioinformatikk plattform i integrert systembiologi

Workshops og kurs

NOTUR2012: Scripting course for beginners

June 11. 2012

Python/Cython tutorial.


Python: The first two hours will concern basic Python usage. Python is a highly flexible interpreted programming language with a large set of modules targeted towards scientific programming.
Cython: Cython has recently gained popularity as a tool for conveniently performing numerical computations in the Python environment, as well as mixing efficient calls to natively compiled libraries with Python code. We discuss Cython's features for fast NumPy array access in detail through examples and benchmarks. Using Cython to call natively compiled scientific libraries as well as using Cython in parallel computations is also given consideration. We conclude with a note on possible directions for future Cython development. (This session is not yet in the online registration form. Just put a comment in the dietary restrictions that you would like to attend to this session instead of the Schrödinger session.)

Lecturer(s): Dr. Jonas Juselius, UiT., M.Sc. Dag Sverre Seljebotn, UiO.
Registration before June 5.


Mer info:



Working with Pathogen Genomes

20-26 November 2011

Wellcome Trust Genome Campus, Hinxton, UK

Deadline for applications: 15 July 2011


In conjunction with the Wellcome Trust Advanced courses Matthew Holden and other member of the Pathogen Genomics group are running a "Working with Pathogen Genomes" workshop at Hinxton between the 20th and 25th of November 2011.


This five-day workshop aims to give molecular microbiologists a working knowledge of genomic analysis, which will cover the handling and processing of DNA sequence and transcriptomic data produced by ‘second generation’ sequencers. The workshop will take the form of a series of modules covering most aspects of sequence analysis and exploitation. Modules will be introduced with a short talk, followed by 'hands on' worked examples using bacterial and small eukaryotic pathogens.


The workshop begins with training in the use of genome analysis software (Artemis and ACT) developed at the Wellcome Trust Sanger Institute for genome exploration and comparative genomics. It then goes onto cover the mapping of Illumina sequence data and calling and recording SNPs and other sequence variation data. The course also features a module that aims to teach the basics of using genome/gene sequences to plot phylogenetic relationships between microbes, as well as an introduction to Perl programming for basic processing and mining of data.


Please see for more information and how to sign up for the workshop.









NorStruct, in collaboration with SYSBIO, BioStruct and the PhD school in Molecular and Structural Biology, will arrange “Workshop in bioinformatics. Introduction to sequence and structure analysis” at The University of Tromsø, 21-22 June, 2011.

The workshop is aimed students and researchers with basic background in bioinformatics. The workshop will consist of lectures which will be open to all, and a practical session for a limited number of people. Topics will include sequence alignments, pattern search, protein structure and folding, structure prediction, disorder prediction and homology modelling.

Lectures will be held by Associate Professor Uwe H. Sauer, Computational Life Science Cluster, CLiC, Umeå Centre for Molecular Research, Department of Chemistry, Umeå University.

There is no participation fee for the workshop, but registration for participation is required, both for the open and practical sessions. Participants to the practical part of the workshop will be selected based on their background and need for the hands-on experience. Applications should be sent before June 10, and should include a brief outline about your background and why you want to participate. Other participants can register until June 16.
Applications and registration can be sent to Ronny Helland (

For more information see





SYSBIO SEMINAR 6. mai 2011


"High resolution genotyping of MRSA reveals patterns of geographical micro-evolution and intercontinental transmission"


Current methods for differentiating isolates of predominant lineages of pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides a high-resolution view of the epidemiology and microevolution of a dominant strain of methicillin-resistant Staphylococcus aureus (MRSA). This approach reveals the global geographic structure within the lineage, its intercontinental transmission through four decades, and the potential to trace person-to-person transmission within a hospital environment. The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology.


Matthew Holden

Pathogen Genomics, The Wellcome Trust Sanger Institute


Friday May, 6th 2011 at
AUD 5, MH building,  10:15- 11:00

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Last updated: 03.05.2012 08:32