Topic outline

  • General

    First Steps with UNIX in Life Sciences

    21 January 2016, Lausanne

    Trainers: Diana Marek, Grégoire Rossier
    Venue: University of Lausanne, Genopode building
    ECTS: 0.25 (given a passed exam)
    Fee: 50 CHF for academics. Others, please contact us
    Application deadline:
    15 January 2016
    Application status: Closed

    Overview

    With a constant evolution of technologies, laboratory biologists are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis.

    Although several resources developed for such tasks have a web interface (most of the time, the first choice of biologists), many operations can be more efficiently handled with command-line programs and utilities.

    Audience

    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.

    Learning objectives

    At the end of the course you should:

    • be able to execute most basic UNIX commands
    • be able to build complex and combined commands using various parameters
    • be sufficiently skilled for further courses requiring basics of UNIX, like HPC or NGS courses

    Prerequisites

    Knowledge / competencies:

    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.

    Technical:

    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. This includes course content material and coffee breaks.Participants from non-academic institutions should contact us before application.

    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 January 15. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions.

    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

    University of Lausanne, Genopode building, classroom 2020 (Metro M1 line, Sorge station)

    Additional information

    The course will be taught by Diana Marek and Grégoire Rossier, with the assistance of Ivan Topolsky for the practicals.

    Coordination: Training & Outreach group.

    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

      Optional exam