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7 materials found

Licence: MIT License 

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, Scipy,...

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

Operations: Modelling and simulation, Visualisation

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

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: Computational biology, Systems biology, Simulation experiment

Operations: Visualisation, Modelling and simulation

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

Resource type: Documentation

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

Operations: Query and retrieval, Filtering

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

Resource type: Tutorial

Introduction to GitHub

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

Beginners introduction to Git and GitHub

Morning session (Sergio and Mark)

  • 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


Keywords: Git, GitHub, control version, Reproducibility

Resource type: Training materials

Open Science MOOC: Module 5, Open Research Software and Open Source

Software and technology underpin modern science. There is an increasing demand for more sophisticated open source software, matched by an increasing willingness for researchers to openly collaborate on new tools. These developments come with a specific ethical, legal and economic challenges that...

Keywords: open source

Introductory image processing on biological images using python.

This is an image processing practical for students with an interest in analysing biologically derived images. It is written in the language python and utilises jupyter notebook for annotation and visualisation of the code. The practical is beginner level, although some knowledge of python is...

Resource type: Jupyter notebook, PDF