Programming for Biologists Training Course

Course Code

progbio

Duration

28 hours (usually 4 days including breaks)

Requirements

Basic biological knowledge about protein, RNA and DNA sequences.

Overview

This is a practical course, which shows why programming is a powerful tool in the context of solving biological problems. During the course participants will be taught the Python programming language, a language widely considered both powerful as well as easy to use. This course might be considered as a demonstration how bioinformatics improves biologists lives.

The course is designed and aimed for people without computer science background who want to learn to program.

This course is suited for:

  • Researchers dealing with biological data.
  • Scientists who would like to learn how to automate everyday tasks and analyse data.
  • Managers who want to learn how programming improves workflows and conducting projects.

By the end of the course, participants will be able to write short programs, which will allow them to manipulate, analyse and deal with biological data and present results in a graphical format.

Course Outline

Introduction to the Python programming language

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

Working with protein and RNA/DNA sequences

  • Finding motives
  • Transcription and translation in silico
  • Handling sequence alignments

Parsing data in different biological formats

  • Parsing FASTA
  • Data format conversions

Running biological analyses

  • BLAST
  • Accessing biological web services

Dealing with biological 3D structures using Python

Python facilitates statistical analysis

Visualizing data

  • Creating bar and scatter plots
  • Calculating an 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 create an automated data processing pipeline

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