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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 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. 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 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
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 http://tess.elixir-uk.org/materials/helis-academy-fairify-your-data FAIRify your data: FAIRification & Data modelling using linked data linked data, Wikidata, data management bioinformaticians software developers, bioinformaticians Life Science Researchers
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 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. 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 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 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 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 ORCID Researchers PhD students Staff
Viewing 3D Structures with Deep View

Many proteins have had their structures experimentally determined, and an examination of these structures can provide valuable insights into the function of these molecules. This course will show you how to use the free Deep View software to view and analyse both single and multiple protein...

Scientific topics: Protein structure analysis

Viewing 3D Structures with Deep View http://tess.elixir-uk.org/materials/viewing-3d-structures-with-deep-view Many proteins have had their structures experimentally determined, and an examination of these structures can provide valuable insights into the function of these molecules. This course will show you how to use the free Deep View software to view and analyse both single and multiple protein structures. It will also show you how to make impressive molecular graphics for your reports or posters. Protein structure analysis
Extracting biological information from gene lists

Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting...

Keywords: Functional analysis, Gene lists, Babraham Institute

Extracting biological information from gene lists http://tess.elixir-uk.org/materials/extracting-biological-information-from-gene-lists Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists. This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication. Functional analysis, Gene lists, Babraham Institute
Analysing bisulfite methylation sequencing data

This course builds on the core skills introduced in the Introduction to R, Introduction to Unix and Introduction to SeqMonk courses to provide a more in depth look at the analysis of bisulphite sequencing data. The course is a mix of theoretical lectures and hands on practicals which go through...

Scientific topics: DNA methylation

Analysing bisulfite methylation sequencing data http://tess.elixir-uk.org/materials/analysing-bisulfite-methylation-sequencing-data This course builds on the core skills introduced in the Introduction to R, Introduction to Unix and Introduction to SeqMonk courses to provide a more in depth look at the analysis of bisulphite sequencing data. The course is a mix of theoretical lectures and hands on practicals which go through the whole analysis pipeline, starting from raw sequence data and covering QC, visualisation, quantitation and differential methylation analysis. DNA methylation
Sample size estimation

Power analysis is a method to estimate the samples sizes needed to detect statistical effects with high probability. This course provides an introduction to the basic principles of power analysis and goes through the variables for power calculation. It also addresses the issues associated with...

Keywords: Power analysis, Sample size, Babraham Institute

Sample size estimation http://tess.elixir-uk.org/materials/sample-size-estimation Power analysis is a method to estimate the samples sizes needed to detect statistical effects with high probability. This course provides an introduction to the basic principles of power analysis and goes through the variables for power calculation. It also addresses the issues associated with technical and biological replicates. The program is intended for people who have no prior knowledge of power. Basic statistical knowledge is extremely useful but prior attendance on a statistics course is not compulsary. Power analysis, Sample size, Babraham Institute
Statistical Analysis using SPSS

Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package.

Scientific topics: Statistics and probability

Keywords: Babraham Institute

Statistical Analysis using SPSS http://tess.elixir-uk.org/materials/statistical-analysis-using-spss Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package. Statistics and probability Babraham Institute
Statistical Analysis using GraphPad Prism

GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data.

Keywords: GraphPad Prism, Babraham Institute

Statistical Analysis using GraphPad Prism http://tess.elixir-uk.org/materials/statistical-analysis-using-graphpad-prism GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data. GraphPad Prism, Babraham Institute
Scientific Figure Design

This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and...

Scientific topics: Data visualisation

Keywords: Figure design, Babraham Institute

Scientific Figure Design http://tess.elixir-uk.org/materials/scientific-figure-design This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures. The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools. Data visualisation Figure design, Babraham Institute
An Introduction to Unix

Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this. This course provides an introduction to the concepts of unix and provides a...

Keywords: Unix, Babraham Institute

An Introduction to Unix http://tess.elixir-uk.org/materials/an-introduction-to-unix Increasing amounts of bioinformatics work is done in a command line unix environment. Most large scale processing applications are written for unix and most large scale compute environments are also based on this. This course provides an introduction to the concepts of unix and provides a practical introduction to working in this environment. Internally we link this course to a more specific course illustrating the use of our internal cluster environment and this part of the course could be adapted for other sites with different compute infrastructure. Unix, Babraham Institute
An Introduction to ggplot

Ggplot is the most popular plotting extension to R and replicates many of the graph types found in the core plotting libraries. This course provides an introduction to the ggplot2 libraries and gives a practical guide for how to use these to create different types of graphs.

Keywords: ggPlot, Babraham Institute

An Introduction to ggplot http://tess.elixir-uk.org/materials/an-introduction-to-ggplot Ggplot is the most popular plotting extension to R and replicates many of the graph types found in the core plotting libraries. This course provides an introduction to the ggplot2 libraries and gives a practical guide for how to use these to create different types of graphs. ggPlot, Babraham Institute
Plotting complex figures with R

This course is a comprehensive guide to the use of the built in R plotting functionality to construct everything from customised simple plots to complex multi-layered figures. It follows on from the material in our introductory R course and participants are expected to have a basic understanding...

Keywords: Graph plotting, R Programming, Babraham Institute

Plotting complex figures with R http://tess.elixir-uk.org/materials/plotting-complex-figures-with-r This course is a comprehensive guide to the use of the built in R plotting functionality to construct everything from customised simple plots to complex multi-layered figures. It follows on from the material in our introductory R course and participants are expected to have a basic understanding of R - enough to load and do basic manipulation of datasets. Graph plotting, R Programming, Babraham Institute
Advanced R

This course follows on from the introductory course. It goes into more detail on practical guides to filtering and combining complex data sets. It also looks at other core R concepts such as looping with apply statements and using packages. Finally it looks at how to document your R analyses and...

Keywords: R programming, Babraham Institute

Advanced R http://tess.elixir-uk.org/materials/advanced-r This course follows on from the introductory course. It goes into more detail on practical guides to filtering and combining complex data sets. It also looks at other core R concepts such as looping with apply statements and using packages. Finally it looks at how to document your R analyses and generate complete analysis reports. R programming, Babraham Institute
Introduction to R

R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus...

Scientific topics: Software engineering

Keywords: R programming, Babraham Institute

Introduction to R http://tess.elixir-uk.org/materials/introduction-to-r R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus on entering and manipulating data in R and producing simple graphs. A few functions for basic statistics will be briefly introduced, but statistical functions will not be covered in detail. Software engineering R programming, Babraham Institute
Learning to Program with Perl

This course aims to introduce the basic features of the Perl language. At the end you should have everything you need to write moderately complicated programs, and enough pointers to other resources to get you started on bigger projects. The course tries to provide a grounding in the basic theory...

Keywords: perl, Babraham Institute

Learning to Program with Perl http://tess.elixir-uk.org/materials/learning-to-program-with-perl This course aims to introduce the basic features of the Perl language. At the end you should have everything you need to write moderately complicated programs, and enough pointers to other resources to get you started on bigger projects. The course tries to provide a grounding in the basic theory you'll need to write programs in any language as well as an appreciation for the right way to do things in Perl. perl, Babraham Institute
Analysing Mapped Sequence Data with SeqMonk

SeqMonk is a program which can analyse large data sets of mapped genomic positions. It is most commonly used to work with data coming from high-throughput sequencing pipelines. The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let...

Scientific topics: Sequence alignment

Keywords: Babraham Institute

Analysing Mapped Sequence Data with SeqMonk http://tess.elixir-uk.org/materials/analysing-mapped-sequence-data-with-seqmonk SeqMonk is a program which can analyse large data sets of mapped genomic positions. It is most commonly used to work with data coming from high-throughput sequencing pipelines. The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets. This course provides an introduction to the main features of SeqMonk and will run through the anlaysis of a couple of different datasets to show what sort of analysis options it provides. Sequence alignment Babraham Institute
Unix and Perl primers for biologists

The following tutorial aims to introduce the basic features of the Unix operating system and the Perl language suitable for biological analysis. At the end you should have everything you need to navigate through your folders, to manipulate your files and write useful scripts for your purposes.

Keywords: IBERS, Institute of Biological, Environmental and Rural Sciences

Unix and Perl primers for biologists http://tess.elixir-uk.org/materials/unix-and-perl-primers-for-biologists The following tutorial aims to introduce the basic features of the Unix operating system and the Perl language suitable for biological analysis. At the end you should have everything you need to navigate through your folders, to manipulate your files and write useful scripts for your purposes. IBERS, Institute of Biological, Environmental and Rural Sciences Biologists