FAIR software tools
CINECA webinar discussing the importance of the FAIR principles for software tools used in research
Scientific topics: Software engineering
Keywords: FAIR, software tools, Software
Resource type: Video
FAIR software tools
https://www.youtube.com/watch?v=VEvHBrJlE6M
http://tess.elixir-uk.org/materials/fair-software-tools
CINECA webinar discussing the importance of the FAIR principles for software tools used in research
Carlos Martinez Ortiz
Marta Lloret Llinares
Software engineering
FAIR, software tools, Software
Introduction to R
R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus...
Scientific topics: Software engineering
Keywords: R programming, Babraham Institute
Introduction to R
http://www.bioinformatics.babraham.ac.uk/training.html#rintro
http://tess.elixir-uk.org/materials/introduction-to-r
R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus on entering and manipulating data in R and producing simple graphs. A few functions for basic statistics will be briefly introduced, but statistical functions will not be covered in detail.
Laura Biggins
Simon Andrews
Software engineering
R programming, Babraham Institute
Learning Python
Python is an object-oriented programming language that is ideal for biological data analysis. The following tutorials and video lectures start with very basic language concepts and instructions and cover the usual researchers needs such as writing basic code, reading and processing data, plotting...
Scientific topics: Software engineering
Learning Python
https://bioinformatics.ibers.aber.ac.uk/training/tutorials/#Python
http://tess.elixir-uk.org/materials/learning-python
Python is an object-oriented programming language that is ideal for biological data analysis. The following tutorials and video lectures start with very basic language concepts and instructions and cover the usual researchers needs such as writing basic code, reading and processing data, plotting data and using databases and APIs. [*N.B.* Not all materials from this course are publicly-accessible.]
Software engineering
Python for Biologists: Programming for Scientific Computing
Python is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences.
Scientific topics: Software engineering
Keywords: Python for Biologists, John Innes Centre, JIC
Python for Biologists: Programming for Scientific Computing
http://training.scicomp.jic.ac.uk/docs/python_for_biologists_book/index.html
http://tess.elixir-uk.org/materials/python-for-biologists-programming-for-scientific-computing
Python is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences.
Tjelvar Olsson
Matthew Hartley
Software engineering
Python for Biologists, John Innes Centre, JIC
For beginners interested in using Python to solve problems in Biology.
Introduction to R: A software environment for statistical computing
R is a free software environment for statistical computing and graphics. It is widely used in scientific data analysis. R is a great tool for biologists, since it provides cutting edge statistical techniques, excellent graph and figure plotting capabilities and bioinformatics tools all in one...
Scientific topics: Software engineering, Statistics and probability
Keywords: John Innes Centre, JIC
Introduction to R: A software environment for statistical computing
http://training.scicomp.jic.ac.uk/docs/r_intro_course_book/index.html
http://tess.elixir-uk.org/materials/introduction-to-r-a-software-environment-for-statistical-computing
R is a free software environment for statistical computing and graphics. It is widely used in scientific data analysis. R is a great tool for biologists, since it provides cutting edge statistical techniques, excellent graph and figure plotting capabilities and bioinformatics tools all in one package.
The John Innes Centre
Software engineering
Statistics and probability
John Innes Centre, JIC
Any students, postdocs or RAs who have an interest in bioinformatics and who intend to carry out statistical analysis of their experimental data using R. This two day course is planned to be a very gentle introduction to the very basic concepts of R.
Introduction to Perl: Programming for bioinformatics
Perl is a powerful programming language that is heavily used in the bioinformatics community. This course will provide a full introduction to the basics of Perl, as well as how to carry out common bioinformatics tasks.
Scientific topics: Software engineering
Keywords: perl, John Innes Centre, JIC
Introduction to Perl: Programming for bioinformatics
http://training.scicomp.jic.ac.uk/docs/perl_intro_course_book/index.html
http://tess.elixir-uk.org/materials/introduction-to-perl
Perl is a powerful programming language that is heavily used in the bioinformatics community. This course will provide a full introduction to the basics of Perl, as well as how to carry out common bioinformatics tasks.
Govind Chandra
Software engineering
perl, John Innes Centre, JIC
Any students, postdocs or RAs who have an interest in programming and who intend to carry out computational analysis of their experimental data. Perl is often used for preparing input files for more specialized software such as R, and also to post-process the output from R and various other bioinformatics tools. It is a glue language allowing you to build pipelines of analyses of arbitrary complexity. This two day course is planned to be a gentle introduction to the basic concepts of Perl and will also introduce you to the BioPerl library of modules.
EMBL-ABR workshop on Open Source and Software Development Best Practice
This workshop will provide an interactive forum to discuss, review and gain an overview of Open Source and Software Development and will be based on content from the ELIXIR Software Development Best Practices group and aims to explore how to harmonise EMBL-ABR efforts in this area
Scientific topics: Software engineering
Keywords: bioinformatics
EMBL-ABR workshop on Open Source and Software Development Best Practice
https://www.embl-abr.org.au/bioinformatics-sw-workshop/
http://tess.elixir-uk.org/materials/embl-abr-workshop-on-open-source-and-software-development-best-practice
This workshop will provide an interactive forum to discuss, review and gain an overview of Open Source and Software Development and will be based on content from the ELIXIR Software Development Best Practices group and aims to explore how to harmonise EMBL-ABR efforts in this area
Vicky Schneider
Rafael C Jimenez
Jason Williams
Software engineering
bioinformatics
software developers, bioinformaticians
Introduction to Biopython
Biopython is the best-known Python library to process biological data. This training is aimed to empower you to use Biopython to make your research more efficient.
The first day of the training is to give an overview of Biopython. You are going to start with your first steps in Biopython on the...
Scientific topics: Software engineering
Introduction to Biopython
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/176-biopython
http://tess.elixir-uk.org/materials/introduction-to-biopython-8ccf2441-bd7d-46f2-84f8-c2b123844a23
Biopython is the best-known Python library to process biological data. This training is aimed to empower you to use Biopython to make your research more efficient.
The first day of the training is to give an overview of Biopython. You are going to start with your first steps in Biopython on the command line. Afterwards you will take a tour of the most important components: sequences, NCBI queries, BLAST, trees, and 3D structures. You will try each of these modules on practical examples. Please don't hesitate to ask questions about Python basics or particular data formats (e.g. XML or NGS data).
The second day of the training is to broaden your perspective: What other features does the library have? How can you use the documentation effectively? What is Biopython not capable of? What can I do to visualize my data? Are there alternatives? If you have your own data that you would like to work on with Biopython in more detail, there is room for that.
For us, the most important thing is to identify concrete Python modules and functions that help you to get your research done.
Participants are encouraged to submit a description of their research topic and/or the questions they would like to answer with Biopython. Additionally, participants can bring their own data that they would like to process in Python to the training.
Kristian Rother
Software engineering
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
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
Gentle hands-on introduction to Python programming
This course is organised over two full days. With the help of plenty hands-on exercises, you will get introduced into the different types of variables in python, the peculiarities of python and good programming habits. This course will provide you an ideal stepping stone for further developing...
Scientific topics: Software engineering
Gentle hands-on introduction to Python programming
https://www.bits.vib.be/training-list/111-bits/training/previous-trainings/92-python
http://tess.elixir-uk.org/materials/gentle-hands-on-introduction-to-python-programming
This course is organised over two full days. With the help of plenty hands-on exercises, you will get introduced into the different types of variables in python, the peculiarities of python and good programming habits. This course will provide you an ideal stepping stone for further developing programming skills in Python.
Tuur Muyldermans / Alexander Botzki
Software engineering
Life Science Researchers
PhD students
beginner bioinformaticians
post-docs
2016-04-22
2017-10-09
