Python programming primer
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
Python programming primer
https://www.mygoblet.org/training-portal/materials/python-programming-primer
http://tess.elixir-uk.org/materials/python-programming-primer
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 :-).
Inheritance (base and derived classes), polymorphism.
Write your own script to convert BED files to GFF.
Command-line option processing, file I/O, error handling.
András Aszódi
Software engineering
Python biologists
2016-04-21
2017-10-09
Introduction to Biopython
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
Introduction to Biopython
https://www.mygoblet.org/training-portal/materials/introduction-biopython
http://tess.elixir-uk.org/materials/introduction-to-biopython
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.
allegra.via Via
Bioinformatics, Biopython, Programming, Python, Python biologists
Biologists
Biologists, Genomicists, Computer Scientists
bioinformaticians
2013-11-04
2017-10-09
Python @ TGAC - Python for Life Scientists: Managing biological data with Python
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
Python @ TGAC - Python for Life Scientists: Managing biological data with Python
https://www.mygoblet.org/training-portal/materials/python-tgac-python-life-scientists-managing-biological-data-python
http://tess.elixir-uk.org/materials/python-tgac-python-for-life-scientists-managing-biological-data-with-python
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, output, and classes. All the examples and practical sessions will focus on solving particular biological problems. In particular, examples and practical sessions will cover:
Working with DNA and protein sequences
Data retrieval from files and their manipulation
Running applications, such as BLAST, locally and from a script
Finding motifs in sequences
Parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc.
Biopython will be also introduced and applied to some of the mentioned examples.
The course is meant to be highly interactive and the students will continuously put theory into practice while learning.
By the end of the course, the students will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics record and to run applications from scripts.
Unix/Linux basic skills will be provided at the beginning of the course.
Paul Yorke
Biopython, Python, Python biologists
PhD
post-docs
2015-07-14
2017-10-09
Using R with Python
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
Using R with Python
https://www.mygoblet.org/training-portal/materials/using-r-python
http://tess.elixir-uk.org/materials/using-r-with-python
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 are also provided.
allegra.via Via
Programming, Python, Python biologists
Biologists
Biologists, Genomicists, Computer Scientists
beginner bioinformaticians
bioinformaticians
2013-11-04
2017-10-09
Searching data using Python
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
Searching data using Python
https://www.mygoblet.org/training-portal/materials/searching-data-using-python
http://tess.elixir-uk.org/materials/searching-data-using-python
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 how to use sets to find unique records in two datasets and remove redundancy.
allegra.via Via
Programming, Python, Python biologists
Biologists
Biologists, Genomicists, Computer Scientists
beginner bioinformaticians
2013-11-04
2017-10-09
Pattern Matching
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
Pattern Matching
https://www.mygoblet.org/training-portal/materials/pattern-matching
http://tess.elixir-uk.org/materials/pattern-matching
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 sequences and in regular text, such as PubMed abstracts. Exercises and suggested solutions are presented in a separate file.
allegra.via Via
Pattern matching, Programming, Python, Python biologists
Biologists
Biologists, Genomicists, Computer Scientists
beginner bioinformaticians
2013-11-04
2017-10-09
Writing functions in Python programming
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
Writing functions in Python programming
https://www.mygoblet.org/training-portal/materials/writing-functions-python-programming
http://tess.elixir-uk.org/materials/writing-functions-in-python-programming
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.
allegra.via Via
Bioinformatics
Programming, Python, Python biologists
Biologists
Biologists, Genomicists, Computer Scientists
beginner bioinformaticians
2013-11-04
2017-10-09
Python Programs
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
Python Programs
https://www.mygoblet.org/training-portal/materials/python-programs
http://tess.elixir-uk.org/materials/python-programs
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.
allegra.via Via
Programming, Python, Python biologists
Biologists
Biologists, Genomicists, Computer Scientists
beginner bioinformaticians
2013-11-04
2017-10-09
Parsing data records using Python programming
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
Parsing data records using Python programming
https://www.mygoblet.org/training-portal/materials/parsing-data-records-using-python-programming
http://tess.elixir-uk.org/materials/parsing-data-records-using-python-programming
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 text of exercises is provided in a separate file.
allegra.via Via
Bioinformatics, Programming, Python, Python biologists, Record parsing
Biologists
beginner bioinformaticians
bioinformaticians
programmers
2013-07-05
2017-10-09