Licence: MIT License or Creative Commons Attributio...
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: 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
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
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
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
Morning session (Sergio and Mark) https://tinyurl.com/git-intro-zoology:
- 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
__Afternoon...
Keywords: Git, GitHub, control version, Reproducibility
Resource type: Training materials
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
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