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31 materials found

Target audience: Intermediate  or computational scientists 


BioExcel Building Blocks (BioBB) Training Material

BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR.

Keywords: molecular dynamics, Docking, Modeling, life sciences

Resource type: Jupyter notebook

BioExcel Building Blocks (BioBB) Training Material http://tess.elixir-uk.org/materials/bioexcel-building-blocks-biobb-training-material BioExcel Building Blocks (BioBB) is a software library for interoperable biomolecular simulation workflows, built within the BioExcel CoE project, and developed following best practices on software development aligned with ELIXIR. Josep Lluís Gelpí Stian Soiland-Reyes molecular dynamics, Docking, Modeling, life sciences PhD students computational scientists Computational biologists
FAIR principles applied to bioinformatics

Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure...

Keywords: FAIR, Reproducible Science, Open science, Data analysis, Data processing

Resource type: Training materials

FAIR principles applied to bioinformatics http://tess.elixir-uk.org/materials/fair-principles-applied-to-bioinformatics Content of the training material: - Introduction to reproducibility - encapsulate a work environment (docker) - design and execute workflows (snakemake) - IFB infrastructure (Slurm cluster) - managing software versions (git) - managing software environments (conda) - ensure the traceability of analysis using Notebooks. The training material is in french Hélène Chiapello FAIR, Reproducible Science, Open science, Data analysis, Data processing bioinformaticians software developers, bioinformaticians computational scientists Researchers
DE-Sim examples, tutorials, and documentation

*DE-Sim* is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as [NumPy](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html),...

Scientific topics: Computational biology, Mathematics, Computer science, Simulation experiment

Operations: Visualisation, Modelling and simulation

Keywords: data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science

Resource type: examples, Tutorial, Jupyter notebook, API reference

DE-Sim examples, tutorials, and documentation http://tess.elixir-uk.org/materials/de-sim-examples-tutorials-and-documentation *DE-Sim* is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as [NumPy](https://numpy.org/), [Scipy](https://scipy.org/scipylib/index.html), [pandas](https://pandas.pydata.org/), and [SQLAlchemy](https://www.sqlalchemy.org/) to build and simulate complex computational models. Similar to [Simula](http://www.simula67.info/), *DE-Sim* models are implemented by defining logical process objects which read the values of a set of shared variables and schedule events to modify their values at discrete instants in time. This website provides examples, tutorials, and documentation for *DE-Sim*. Computational biology Mathematics Computer science Simulation experiment data-driven modeling, Computational modelling, discrete-event simulation, DES, object-oriented programming, Python, data visualization, Data Science computational scientists Computational biologists bioinformaticians software engineers programmers
Introductory image processing on biological images using python.

A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.

Resource type: Jupyter notebook, PDF

Introductory image processing on biological images using python. http://tess.elixir-uk.org/materials/introductory-image-processing-on-biological-images-using-python A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples. Anatole Chessel Volker Baecker Bioimage Analysts Image Analysts Computer Vision scientists bioinformaticians computational scientists Biophysicists Biologists Microscopists Python for Biologists PhD students
Variables

Variables from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/04-variables.md.

Keywords: Make

Variables http://tess.elixir-uk.org/materials/variables-649c1684-c3a3-4b70-ac79-e770a635fd2c Variables from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/04-variables.md. Make Intermediate
HTML

HTML from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/webdata/03-html.md.

Keywords: Webdata

HTML http://tess.elixir-uk.org/materials/html HTML from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/webdata/03-html.md. Webdata Intermediate
Filename Expansion

Filename Expansion from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/05-expansion.md.

Keywords: Shell

Filename Expansion http://tess.elixir-uk.org/materials/filename-expansion Filename Expansion from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/05-expansion.md. Shell Intermediate
Job Control

Job Control from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/04-job.md.

Keywords: Shell

Job Control http://tess.elixir-uk.org/materials/job-control Job Control from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/04-job.md. Shell Intermediate
Instructor's Guide

Instructor's Guide from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/guide.md.

Keywords: Shell

Instructor's Guide http://tess.elixir-uk.org/materials/instructor-s-guide Instructor's Guide from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/guide.md. Shell Intermediate
Summing Up

Summing Up from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/08-summing-up.md.

Keywords: Regex

Summing Up http://tess.elixir-uk.org/materials/summing-up Summing Up from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/08-summing-up.md. Regex Intermediate
More tools

More tools from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/06-more-tools.md.

Keywords: Regex

More tools http://tess.elixir-uk.org/materials/more-tools More tools from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/06-more-tools.md. Regex Intermediate
Operators

Operators from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/03-operators.md.

Keywords: Regex

Operators http://tess.elixir-uk.org/materials/operators Operators from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/03-operators.md. Regex Intermediate
One last Wrinkle

One last Wrinkle from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/07-one-last-wrinkle.md.

Keywords: Regex

One last Wrinkle http://tess.elixir-uk.org/materials/one-last-wrinkle One last Wrinkle from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/07-one-last-wrinkle.md. Regex Intermediate
More Patterns

More Patterns from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/05-more-patterns.md.

Keywords: Regex

More Patterns http://tess.elixir-uk.org/materials/more-patterns More Patterns from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/05-more-patterns.md. Regex Intermediate
Simple Patterns

Simple Patterns from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/02-simple-patterns.md.

Keywords: Regex

Simple Patterns http://tess.elixir-uk.org/materials/simple-patterns Simple Patterns from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/02-simple-patterns.md. Regex Intermediate
Introduction to Regular Expressions

Introduction to Regular Expressions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/01-intro-regex.md.

Keywords: Regex

Introduction to Regular Expressions http://tess.elixir-uk.org/materials/introduction-to-regular-expressions Introduction to Regular Expressions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/01-intro-regex.md. Regex Intermediate
Under the Hood

Under the Hood from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/04-under-the-hood.md.

Keywords: Regex

Under the Hood http://tess.elixir-uk.org/materials/under-the-hood Under the Hood from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/regex/04-under-the-hood.md. Regex Intermediate
Variables

Variables from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/03-var.md.

Keywords: Shell

Variables http://tess.elixir-uk.org/materials/variables Variables from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/03-var.md. Shell Intermediate
Basic Tasks

Basic Tasks from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/01-basics.md.

Keywords: Make

Basic Tasks http://tess.elixir-uk.org/materials/basic-tasks Basic Tasks from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/01-basics.md. Make Intermediate
Further reading

Further reading from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/05-futher-reading.md.

Keywords: Make

Further reading http://tess.elixir-uk.org/materials/further-reading Further reading from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/05-futher-reading.md. Make Intermediate
Automatic variables and wildcards

Automatic variables and wildcards from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/02-automatic-variables.md.

Keywords: Make

Automatic variables and wildcards http://tess.elixir-uk.org/materials/automatic-variables-and-wildcards Automatic variables and wildcards from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/02-automatic-variables.md. Make Intermediate
Introduction

Introduction from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/00-intro.md.

Keywords: Make

Introduction http://tess.elixir-uk.org/materials/introduction Introduction from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/00-intro.md. Make Intermediate
Make Reference

Make Reference from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/reference.md.

Keywords: Make

Make Reference http://tess.elixir-uk.org/materials/make-reference Make Reference from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/reference.md. Make Intermediate
Patterns

Patterns from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/03-patterns.md.

Keywords: Make

Patterns http://tess.elixir-uk.org/materials/patterns Patterns from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/make/03-patterns.md. Make Intermediate
Introducing Distributed Version Control, and Introducing Yourself to Git

Introducing Distributed Version Control, and Introducing Yourself to Git from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/git/00-intro.md.

Keywords: Git

Introducing Distributed Version Control, and Introducing Yourself to Git http://tess.elixir-uk.org/materials/introducing-distributed-version-control-and-introducing-yourself-to-git Introducing Distributed Version Control, and Introducing Yourself to Git from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/git/00-intro.md. Git Intermediate
Conversational Git

Conversational Git from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/git/01-conversational-git.md.

Keywords: Git

Conversational Git http://tess.elixir-uk.org/materials/conversational-git Conversational Git from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/git/01-conversational-git.md. Git Intermediate
Basic Relational Structure of Git Repositories

Basic Relational Structure of Git Repositories from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/git/02-relational-structure.md.

Keywords: Git

Basic Relational Structure of Git Repositories http://tess.elixir-uk.org/materials/basic-relational-structure-of-git-repositories Basic Relational Structure of Git Repositories from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/git/02-relational-structure.md. Git Intermediate
A comparison of Make and doit

A comparison of Make and doit from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/doit/make-vs-doit.md.

Keywords: Doit

A comparison of Make and doit http://tess.elixir-uk.org/materials/a-comparison-of-make-and-doit A comparison of Make and doit from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/doit/make-vs-doit.md. Doit Intermediate
Permissions

Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/01-perm.md.

Keywords: Shell

Permissions http://tess.elixir-uk.org/materials/permissions Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/01-perm.md. Shell Intermediate
Working Remotely

Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/02-ssh.md.

Keywords: Shell

Working Remotely http://tess.elixir-uk.org/materials/working-remotely Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/02-ssh.md. Shell Intermediate