Topic outline

  • General

    Learning Python for life sciences

    Biozentrum Basel, 1-3 December 2014

    Overview

    The course will cover the essentials of Python programming. It is aimed at biologists or bioinformaticians who would like to learn how to automatize data processing and analysis. Some libraries and methods for protein structure and genomics data analysis will be introduced as examples of use of the language.

    Please note that this is an introductory level course.

    Lecturers: Adam Mazur, Mikhail Pachkov, Juergen Haas, Gabriel Studer and Thierry Sengstag

    Objectives

    • Acquire the fundamental syntax and concepts of the language (lists, dictionaries, loops, conditions, functions, comprehensions, classes, exceptions)
    • Learn about key libraries (numpy, scipy, matplotlib, logging, sqlite, ...)
    • Be aware of best practices in Python coding
    • Work on practical examples of data from life-science (OpenStructure, BioPython, ...)

    Requirements

    No prior knowledge of the Python language is required, but some hands-on experience with work at the command line (Linux) and/or with basic scripting using languages such as R is required.

    Application

    The registration fees for academics are 150 CHF. This includes course content material and coffee breaks. Participants from non-academic institutions should contact us before application.

    THE COURSE IS NOW FULLY BOOKED. 

    The contact person for the course is Thierry Sengstag: thierry.sengstag@isb-sib.ch

    Location

    Biozentrum annex, Klingelbergstr 61 (opposite the main Biozentrum building)

    Additional information

    This course does not provide ECTS credits.

    You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

    • Topic of the day

      Getting ready for the course

      Software: Anaconda

      The course will use the Anaconda IPython environment, which comes with a number of scientific libraries for Python and the Spyder python editor. Anaconda is available for Windows, Mac and Linux.

      As much as possible, students should install Anaconda before the course (to save installation time).

      The URL to download Anaconda: https://store.continuum.io/cshop/anaconda/

      In case you were not successful with the installation of the program, please come to the lecture room 30 minutes earlier to let us fix your installation.

      Course schedule

      The time slots for the courses are as follows:

      • Mon, Dec 1: 10:00-17:30
      • Tue, Dec 2:  9:00-17:30
      • Wed, Dec 3:  9:00-16:00
      • All course files

        The ZIP file below contains all material presented during the course.

        IPython notebooks have been renamed in a consistent way to facilitate navigation.