Methoden der Bioinformatik – WS 2017/2018 [*]

Note

If you have a Windows Laptop (Windows < Windows 10) and want to run a linux system inside, the simplest way is to run a Virtual Machine using VirtualBox. You can check the following site for informations

Note

If you have a windows 10 laptop, this is even simpler: check this website

Schedule

Important notice : Lectures start c.t., practicals start s.t. !!

Date	Topic	Type	Location	Time
19.10	Introduction	Lecture 1 : intro to Bioinfo	BQ	10-12
20.10	Bash intro	Practicals	IPMB	10-11.30/11.30-13
26.10	Bash (cont.)	Practicals	IPMB	10-11/11-12
27.10	Bash	Practicals	IPMB	10-11.30/11.30-13
02.11	Awk	Lecture/Practical	IPMB	10-11/11-12
03.11	Variablen	Practicals	IPMB	10-11.30/11.30-13
09.11	Lists	Practicals	IPMB	10-11/11-12
10.11	Loops/Tests	Practicals	IPMB	10-11.30/11.30-13
16.11	Reading files	Practicals	IPMB	10-11/11-12
17.11	Conclusion	Practicals	IPMB	10-11.30/11.30-13

Practicals

• Part 1 : First steps using Bash
  • Why Linux ?
  • First steps
  • Working with files
  • Some statistics on transcript and genes
• Part 2 : Going further using bedtools and awk
  • Genomic coordinates
  • Which fraction of the human genome is covered by exons ?
• Part 3 : First steps in Python
  • Why Python ?
  • Open an interactive session
  • Variables and data structure
  • Variables and methods
  • Lists and tuples
  • Dictionnaries
• Part 4 : Loops and control structures
  • Why Python ?
  • For and while loops
  • Conditional structures

Links

• Programming for biologists
• Python for biologists

[*]	Strongly inspired by the lectures of Denis Puthier, TAGC Marseille. Merci !