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Linux and Perl for Bioscientists (8th Semester)

[ 4th Year ]
LECTURERS: Grigorios Amoutzias, Georgios Papadopoulos
CONTENT – Aim of the course

The aim of this course is to familiarize the students with the Linux operating system and introduce them to the basic principles of programming, with emphasis on PERL & TCL. The generation of a vast amount of data from the modern technologies in i) Genomics, ii) Functional Genomics, iii) Proteomics, iv) Molecular Simulations as well as bio-data from other sources makes imperative for the modern bioscientist the familiarization with basic programmatic tools, in order to be able to manipulate and analyze all these data.

The course is structured in 3 thematic units i) familiarization with the linux operating system ii) introduction to the TCL programming language, ii) introduction to the PERL programming language. Teaching will be in the form of 3-hour (per week) lectures/practicals in the Computer lab. Students may be absent in only one lecture/practical per thematic unit.

ANALYTICAL DESCRIPTION OF THE COURSE
       1st thematic unit
  • Introduction to Linux.
  • Introduction to the VI editor.
  • Shell scripts & program installation in Linux.

    2nd thematic unit
  • Introduction to TCL.
  • TCL & VMD.

    3rd
    thematic unit
  • Indroduction to PERL.
  • Variabes, control of programming flow, loops.
  • Lists, arrays, hashes.
  • Sub-routines.
  • Regular expressions.
ASSESSMENT

Assessment will be in the form of solving programming exercises (during the 3-hour course) at the end of each thematic unit (there will be no final exam).

TEACHING MATERIAL- READING SUGGESTIONS

Material will be handed in the form of Powerpoint presentations by the lecturers.

E-class: http://eclass.uth.gr/eclass/modules/document/index.php?course=SEYC189&openDir=/513fbfbef7va

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