Keywords: Shell or Python biologists
The purpose of this training is to teach general programming concepts using Python as an instruction tool.
Topics:
Introduction to Python: basic principles.
Python data structures: strings, tuples, lists, dictionaries, sets.
Object-oriented programming: how to model coffee machines in Python...
Scientific topics: Software engineering
Keywords: Python biologists
This is a module from the "Python for Biologists" course. The module presents an introduction to Biopython. It shows how to deal with sequences and sequence records, how to download records from NCBI databases, how to run Blast and how to parse XML Blast outputs.
Keywords: Bioinformatics, Biopython, Programming, Python, Python biologists
Filename Expansion from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/05-expansion.md.
Keywords: Shell
Keywords: Shell
Instructor's Guide from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/guide.md.
Keywords: Shell
Keywords: Shell
Creating Things from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/02-create.md.
Keywords: Shell
Shell Scripts from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/05-script.md.
Keywords: Shell
Pipes and Filters from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/03-pipefilter.md.
Keywords: Shell
Introducing the Shell from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/00-intro.md.
Keywords: Shell
Finding Things from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/06-find.md.
Keywords: Shell
Files and Directories from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/01-filedir.md.
Keywords: Shell
Keywords: Shell
Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/02-ssh.md.
Keywords: Shell
Python is an object-oriented programming language that is ideal for biological data analysis. The course will start with very basic language concepts and instructions and will cover all the main language aspects, including variables, types, modules, functions, exceptions, control of flux, input,...
Keywords: Biopython, Python, Python biologists
This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...
Keywords: Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and...
Keywords: Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological...
Keywords: Pattern matching, Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file.
Scientific topics: Bioinformatics
Keywords: Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions.
Keywords: Programming, Python, Python biologists
This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list data structure. The...
Keywords: Bioinformatics, Programming, Python, Python biologists, Record parsing