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12 materials found

Authors: allegra.via Via  or Julie Sullivan 


InterMine user tutorial

InterMine integrates biological data sources, making it easy to query and analyse data. It is a downloadable platform that operators can install and integrate with their own systems.

InterMine is a generic model-based platform that is used to provide data to end users in many different life...

Keywords: Data querying, Data analysis, Data download, FAIR

Resource type: Tutorial

InterMine user manual

InterMine integrates biological data sources, making it easy to query and analyse data. It is a downloadable platform that operators can install and integrate with their own systems.

InterMine is a generic model-based platform that is used to provide data to end users in many different life...

Keywords: Data querying, data visualization, Data download, FAIR

Resource type: Documentation

InterMine operator manual

InterMine integrates biological data sources, making it easy to query and analyse data. It is a downloadable platform that operators can install and integrate with their own systems.

InterMine is a generic model-based platform that is used to provide data to end users in many different life...

Keywords: Data integration, Data analysis, Data publishing, FAIR

Resource type: Documentation

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

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

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

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

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

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

Linear Motifs and Phosphorylation Sites

This is a lecture on linear motifs and phophorylation sites (P-sites). Some materials from other lectures are reused.
The lecture is basically about computational approaches to encode, predict, analyse, and use functional motifs and P-sites.
Here you can find:

    A definition of linear motifs and...

Keywords: Bioinformatics

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

Introduction to Unix

Introductory lecture to the Unix/Linux command-line

    Description of the computer shell and the command-line interface

    Differences between graphical and command-line interfaces

    The most commond Unix/Linux commands are provided

 
 

Keywords: Bioinformatics, Programming, Unixlinux