 | Scripting 2005 |
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| Scripting 2005 |
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AboutIt's a sad fact of life that most scientific software packages are incompatible — if we wish to perform a number of calculations on a set of data, the output of one program never quite matches the input of the next, and although in many cases tools exist for translating one data format into another, often the translation looses information about the data. And although we often want to combine calculations in various tools, without manually inspecting the intermediate results, building a pipeline of calculations is often not immediately possible. In this course we will see how we can use a "scripting language" such as Python, Perl, Ruby, etc., to translate data formats for use with different tools, how to wrap the tools so that they can be called and controlled from scripts for easy pipelining of calculations, and how we can use databases for keeping track of data. PrerequisitesSome familiarity with programming, in particular the Python programming language, and some familiarity with basic text processing in Python (writing simple parsers and translating between simple text formats). ScheduleCheck the weekly schedule for information about each lecture. Lectures take place:
First lecture is on Tuesday, April 5. LiteratureThe main literature will be a set of lecture notes, with supplementary reading from Deitel's Python—how to program, the book you used in Jakob's Programming in Bioinformatics. ProjectsEach student must participate in the series of mandatory projects. Currently two projects are planned. The last project will be graded on the 13-scale and will be the final grade. LecturerIf you have any comments or questions related to the course, do not hesitate to contact me: Office: 090.110 |