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Course Outline

Introduction to the Python programming language

  • Why Python?
  • Using Python to handle biological data
  • Working with the iPython shell
  • Your first program
  • Writing Python scripts
  • Importing modules

Working with protein and RNA/DNA sequences

  • Identifying motifs
  • In silico transcription and translation
  • Handling sequence alignments

Parsing data in various biological formats

  • Parsing FASTA
  • Converting data formats

Conducting biological analyses

  • BLAST
  • Accessing biological web services

Handling biological 3D structures with Python

Python for statistical analysis

Data visualization

  • Creating bar and scatter plots
  • Calculating the Area Under Curve (AUC)

Working with .xls and .csv files

  • Importing data from and exporting to MS Excel / OpenOffice Calc
  • Writing .xls and .csv files

Using Python to build an automated data processing pipeline

Requirements

Basic biological knowledge of protein, RNA, and DNA sequences.

 28 Hours

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