Section outline

  • General

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    First Steps with UNIX in Life Sciences

    Geneva, 21 May 2015

    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.

    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.

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

    Application is 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 14. 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

    Auditorium C150 - CMU building, Rue Michel-Servet / Avenue de Champel.

    Additional information

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

    We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the session).

    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