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Target audience: Intermediate  or Computational biologists 

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
BioSimulators tutorial and help

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms,...

Scientific topics: Simulation experiment, Computational biology, Systems biology

Operations: Modelling and simulation

Keywords: Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL

Resource type: Tutorial, Documentation

BioSimulators tutorial and help http://tess.elixir-uk.org/materials/biosimulators-help BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (supported modeling frameworks, simulation algorithms, and modeling formats) needed for specific modeling projects. The BioSimulators help describes how to use this registry: - How to find a containerized simulation tools that are capable of executing a modeling study. - How to use containerized simulation tools to execute modeling studies. - How to containerize a simulation tool and submit it to the BioSimulators registry. Ion Moraru Bilal Shaikh Simulation experiment Computational biology Systems biology Modeling, biomodel, dynamic simulations, COMBINE, OMEX, SED-ML, SBML, BNGL modelers Computational biologists software developers, bioinformaticians
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
BioSimulations tutorial and help

BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and...

Scientific topics: Simulation experiment, Systems biology, Computational biology

Operations: Modelling and simulation, Visualisation

Keywords: SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE

Resource type: Documentation

BioSimulations tutorial and help http://tess.elixir-uk.org/materials/biosimulations-help BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface. Simulation experiment Systems biology Computational biology SystemsBiology, ComputationalBiology, Computational modelling, Modeling, Biomodelling, Model, Kinetic modeling, SED-ML, COMBINE Life Science Researchers Computational biologists modelers
Datanator tutorial

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA...

Scientific topics: Omics, Bioinformatics, Systems biology, Cell biology, Molecular biology

Operations: Filtering, Query and retrieval

Keywords: genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis

Resource type: Tutorial

Datanator tutorial http://tess.elixir-uk.org/materials/datanator-tutorial Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms. This tutorial provides a brief introduction to the Datanator database and web application. The tutorial illustrates how to search the Datanator database and obtain and refine clouds of data about specific metabolites, RNA, proteins, and reactions of interest. Omics Bioinformatics Systems biology Cell biology Molecular biology genomics, Proteomics, transcriptomics, Metabolomics, reaction kinetics, Kinetic modeling, meta analysis mololecular cell biologists systems biologists bioinformaticians Computational biologists modelers
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