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Scientific topics: Software engineering 


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 https://tess.elixir-europe.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. 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://tess.elixir-europe.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 https://tess.elixir-europe.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. 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 https://tess.elixir-europe.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. 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 https://tess.elixir-europe.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. 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://tess.elixir-europe.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 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://tess.elixir-europe.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. 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://tess.elixir-europe.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. 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://tess.elixir-europe.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. Software engineering Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09