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Bioinformatics and Linux Course (210007) Summer 2009
News
MotivationToday, even fairly small labs can generate a substantial amount of biological sequence data. However, to make use of these data in further experimental analysis as well as gaining insight in biological problems, efficient and task specific computational tools are required. Even though some of these tools are available online, they are often limited in resources and requires much manual intervention. This is true even of many otherwise user-friendly commercial bioinformatics packages: they automate some analysis tasks well, but make the automation of other tasks substantially more complicated and demanding than necessary.The bioinformatic challenges in designing methods and specific tools can be well coped with in the Linux (Unix) operating system. In addition, specific tools and existing programs, can well be implemented and integrated by the scripting language Perl. Motivation, however, is more than just applying tools, but also to use and develop them to gain insight in molecular mechanisms. Finally, it can be a time saving factor, as expressed by Alan Bleasby (The Biochemist, Oct. 1997):
GoalThe aim of the course is to introduce basic concepts of bioinformatics, along with basic concepts of Linux and the Perl script language such that the student is able to construct the needed tools for automated analysis of biological sequences. The student should also aquire basic skills to navigate in a bioinformatics command line environment.
Intended audienceThe course is mainly intended to students with little or no skills in Linux and Perl. We can also recommend the course to researchers interested in improving their skills in handling large scale data.
Lectures and ExercisesEven though the lectures mainly will provide an overview of relevant topics (and go in detail with the hard ones), students will be expected to take actively part of the problems discussed in the lectures. Not all reading material will be addressed during the lectures, but will still be a necessity for the exercises. In the exercises the students will be faced with a number of practical bioinformatic problems they should solve. If the exercises are not completed within the available time, they are to be considered as home work. Note that exercises might be based on previous solved exercises.
ContentsThe main topics in the course:
Recommended skillsBasic knowledge to computers, basic courses in mathematics, statistics, molecular genetics, molecular biology or equivalent.
ExaminationTo pass the course, each student must carry out an individual mini-project, implementing a bioinformatics algorithm, and writing a report. See the details here. In addition the report will also contain a detailed description of a topic from one of the lectures. Also
Course typeCommon for both bachelor and Master of science.
Reading materialCourse will be based on the following books, but other material might also be handed out:
Practical informationHow to find the course @ LIFE:The course has LIFE number: 210007.Time and PlaceThe course takes place in the period August 10, 2009 to September 23rd, 2009. Lectures and exercises will be from August 10 to August 21, but no teaching on wednesday, which should used to read up for the following days.Location (lectures and exercises): room H60 in the library. The typical structure of a day is as follows, but we might deviate if appropriate:
Reports carried outReports are written in the period August 24th to September 23rd, 2009 and is due September 23rd, 2009, 2pm. See details here.Teachers
When will this course be available again?The plan is August-September 2010.
ScheduleThe schedule is preliminary and will updated as the course progresses. So changes are very likely to appear. Links to lecture slides remain empty until just before or after the lectures. You need a password to download the lecture slides.
Comments, questions, etc., email
webmaster@genome.ku.dk. |
| Last updated July 17th, 2009 by Jan Gorodkin |