runBioSimulations tutorial and help
runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA),...
Scientific topics: Simulation experiment, Computational biology, Systems biology
Operations: Modelling and simulation
Keywords: biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL
Resource type: Tutorial, Documentation
runBioSimulations tutorial and help
https://run.biosimulations.org/help
http://tess.elixir-uk.org/materials/runbiosimulations-tutorial-and-help
runBioSimulations is a web application for executing a broad range of modeling studies and visualizing their results. runBioSimulations uses BioSimulators to supports a broad range of modeling frameworks (e.g., logical, constraint-based, kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BNGL, SBML). runBioSimulations also provides a REST API for programmatic access to the same simulation capabilities.
The runBioSimulations tutorial and help describes how to use this web application and web service to execute simulations and visualize their results. This includes instructions on how to create COMBINE/OMEX archives of modeling projects.
Jonathan Karr
Ion Moraru
Bilal Shaikh
Gnaneswara Marupilla
Simulation experiment
Computational biology
Systems biology
biosimulators, COMBINE, OMEX, SED-ML, Modeling, dynamic simulations, SBML, BNGL
modelers
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
https://biosimulators.org/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.
Jonathan Karr
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
https://github.com/KarrLab/de_sim
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*.
Jonathan Karr
Arthur Goldberg
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
https://www.biosimulations.org/about/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.
Jonathan Karr
Bilal Shaikh
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
https://www.datanator.info/help
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.
Yosef Roth
Jonathan Karr
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
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
Introduction to GitHub
https://github.com/semacu/20190927_IntroductionGithub_HDRUK/blob/master/README.md
http://tess.elixir-uk.org/materials/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
Sergio Martínez Cuesta
Gabriella Rustici
GitHub, Reproducibility
Senior Managers
Beginners introduction to Git and GitHub
__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
Beginners introduction to Git and GitHub
https://github.com/semacu/20181003_Intro_git_GitHub/blob/master/README.md
http://tess.elixir-uk.org/materials/beginners-introduction-to-git-and-github
__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 session__ (Mark and Anne) https://tinyurl.com/git-course: markdown, pages and wikis; creating good README files; issue tracking; sofware licenses
Sergio Martínez Cuesta
Mark Fernandes
pajanne
Git, GitHub, control version, Reproducibility
Researchers
Helis Academy - FAIRify your data
FAIRify your data: FAIRification & Data modelling using linked data
Keywords: linked data, Wikidata, data management
Resource type: Slides
Helis Academy - FAIRify your data
https://zenodo.org/record/3238328#.XeYXKuhKiUk
http://tess.elixir-uk.org/materials/helis-academy-fairify-your-data
FAIRify your data: FAIRification & Data modelling using linked data
Andra Waagmeester
linked data, Wikidata, data management
bioinformaticians
software developers, bioinformaticians
Life Science Researchers
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...
Open Science MOOC: Module 5, Open Research Software and Open Source
https://doi.org/10.5281/zenodo.1325080
http://tess.elixir-uk.org/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 impact upon research workflows. This module will introduce the necessary tools required for transforming software into something that can be openly accessed and re-used by others.
open source
Data visualisation with R and ggplot2
This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R...
Keywords: R-programming
Resource type: course materials
Data visualisation with R and ggplot2
https://github.com/semacu/20180531_DataVisualisationRggplot2_Wolfson_Cambridge/
http://tess.elixir-uk.org/materials/data-visualisation-with-r-and-ggplot2
This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R standard functions and the library ggplot2. Everybody is welcome; if you would like to follow along with your laptop, please bring R and RStudio downloaded and installed before the session.
Sergio Martínez Cuesta
R-programming
PhD students
Researchers
Introduction to GitHub for chemists
Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following:
- Background and motivation
- What is Git? What is version control? What is GitHub?
- How can Git and GitHub be useful for you?
-...
Keywords: Git, GitHub
Resource type: course materials
Introduction to GitHub for chemists
https://github.com/semacu/20171024_GitHub_Chemistry_Cambridge/blob/master/README.md
http://tess.elixir-uk.org/materials/introduction-to-github-for-chemists
Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following:
- Background and motivation
- What is Git? What is version control? What is GitHub?
- How can Git and GitHub be useful for you?
- Practical session: working with Git and GitHub
Sergio Martínez Cuesta
Clair Castle
Git, GitHub
Researchers
PhD students
Staff
Make your academic life easy with ORCID: an introduction
Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure...
Keywords: ORCID
Resource type: Tutorial
Make your academic life easy with ORCID: an introduction
https://github.com/semacu/20180223_ORCID_Chemistry_Cambridge/blob/master/README.md
http://tess.elixir-uk.org/materials/make-your-academic-life-easy-with-orcid-an-introduction
Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure how best to use it? Bring your own device to this practical session and register for an ORCID id, explore its features and find out more
Sergio Martínez Cuesta
Clair Castle
ORCID
Researchers
PhD students
Staff
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.
https://github.com/dwaithe/model-training/
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.
Dominic Waithe
Anatole Chessel
Volker Baecker
Bioimage Analysts
Image Analysts
Computer Vision scientists
bioinformaticians
computational scientists
Biophysicists
Biologists
Microscopists
Python for Biologists
PhD students