Authors: allegra.via Via or Sergio Martínez Cuesta
The aim for today is to learn the basics of GitHub so that you can use it for your own projects.
- Background
- What is version control? What is Git? What is GitHub?
- How can you use GitHub? How can it be useful for your work?
- Practical session: working with GitHub
Keywords: GitHub, Reproducibility
Resource type: Training materials
Morning session (Sergio and Mark) https://tinyurl.com/git-intro-zoology:
- Background and motivation
- What is version control? What is Git? What is GitHub?
- How can you use Git and GitHub? How can they be useful for you?
- Practical session: working with Git and GitHub
__Afternoon...
Keywords: Git, GitHub, control version, Reproducibility
Resource type: Training materials
An overview of Unix and R for bioinformatics
Keywords: Unix, R-programming
Resource type: Training materials
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data...
Keywords: Data analysis, Data carpentry, SoftwareCarpentry
Resource type: course materials
This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R...
Keywords: R-programming
Resource type: course materials
Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following:
- Background and motivation
- What is Git? What is version control? What is GitHub?
- How can Git and GitHub be useful for you? -...
Keywords: Git, GitHub
Resource type: course materials
Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure...
Keywords: ORCID
Resource type: Tutorial
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
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 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
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
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