Section outline

  • General

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    First Steps with UNIX in Life Sciences

    Bern, 26 May 2015

    Overview

    This "First Steps with..." course is addressed to beginners wanting to become familiar with the UNIX environment and master the most common commands, which could be useful to run software dedicated to high-throughput data management.

    Note: This course is a prerequisite for most of the courses that will follow such as HPC, NGS, etc... We such highly encourage you to follow this course if you are willing to attend futur courses.

    Objectives

    At the end of the course, you will get familiar with the UNIX environment and use the most common UNIX commands.

    Requirements

    As it is a course for beginners, no background in UNIX or any programming language is required. However, you are encouraged to visit and follow the UNIX Fundamentals e-learning module we created. The level of the module is beyond the objectives of the course, but you can visit it anyway.

    Technical requirements: a laptop with at least 10 Go free on hard disk and 4 Go of RAM. As we plan to do exercises from a virtual machine, we will provide further information.

    Application

    The registration fees for academics are 50 CHF. Participants from non-academic institutions should contact us before application.

    The applications are now closed.

    Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

    Deadline for registration and free-of-charge cancellation is set to May 22. Cancellation after this date will not be reimbursed.

    You will be informed by email of your registration confirmation. Your application will be considered only if you fill in the "Comments" field indicating your background and your current project that could benefit from taking this course.

    Location

    This one-day course is held in at the University of Bern.

    • University of Bern, Hochschulstrasse 4
    • Seminar room Nr. 331 / 3. OG West

    Sessions runs from 9:00 to 17:00 approximately, with a lunch break.

    Additional information

    The course will be taught by Walid Gharib and Grégoire Rossier.

    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.

  • Schedule

    Morning session (9:00 - 12:30)

    What is UNIX and why should biologists use it?

    UNIX filesystem

    Coffee break

    UNIX Shell: User environment & process commands

    Working with directories and files

    Afternoon session (13:45 - 17:00 / 17:30)

    Working with file content

    Coffee break

    Practicals