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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 https://tess.elixir-europe.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
RRegrs package

This tutorial explains how to use a collection of R regression tools for estimating the optimal model via a fully validated procedure.

Keywords: Regression Models

RRegrs package https://tess.elixir-europe.org/materials/rregrs-package This tutorial explains how to use a collection of R regression tools for estimating the optimal model via a fully validated procedure. Regression Models PhD students post-docs
Graphical & Computational Modelling of Biological Pathways

Lecture by professor Tom Freeman. Filmed at The Roslin Institute, The University of Edinburgh, March 2015

Keywords: Graphical modelling, Computational modelling, Roslin Institute

Graphical & Computational Modelling of Biological Pathways https://tess.elixir-europe.org/materials/graphical-computational-modelling-of-biological-pathways Lecture by professor Tom Freeman. Filmed at The Roslin Institute, The University of Edinburgh, March 2015 Graphical modelling, Computational modelling, Roslin Institute
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://tess.elixir-europe.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
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://tess.elixir-europe.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
Exploratory analysis and downstream analysis

This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods...

Keywords: Statistical-model, Exploratory-analysis

Exploratory analysis and downstream analysis https://tess.elixir-europe.org/materials/exploratory-analysis-and-downstream-analysis This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods developed (e.g.) for microarray data. Statistical-model, Exploratory-analysis
Differential expression analysis

This lecture covers the process from count matrix to statistical analysis results (differential expression). More specifically, it covers experimental design, normalization, statistical modeling and parameter estimation, multiple hypothesis testing and a more detailed look at some of the most...

Keywords: Differential-expression, Statistical-model

Differential expression analysis https://tess.elixir-europe.org/materials/differential-expression-analysis This lecture covers the process from count matrix to statistical analysis results (differential expression). More specifically, it covers experimental design, normalization, statistical modeling and parameter estimation, multiple hypothesis testing and a more detailed look at some of the most common differential expression methods as well as a comparison between them. Differential-expression, Statistical-model
Introduction to Mixed Models

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Mixed models, Roslin Institute

Introduction to Mixed Models https://tess.elixir-europe.org/materials/introduction-to-mixed-models Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Mixed models, Roslin Institute
Introduction to Statistical Modelling

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Statistical modelling, Roslin Institute

Introduction to Statistical Modelling https://tess.elixir-europe.org/materials/introduction-to-statistical-modelling Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, December 2015. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Statistical modelling, Roslin Institute
Graphical & Computational Modelling of Biological Pathways

Lecture by professor Tom Freeman. Filmed at The Roslin Institute, The University of Edinburgh, March 2015

Keywords: Graphical modelling, Roslin Institute

Graphical & Computational Modelling of Biological Pathways https://tess.elixir-europe.org/materials/graphical-computational-modelling-of-biological-pathways-d0b38ce1-0e2e-4ba9-9e0c-39c6af558782 Lecture by professor Tom Freeman. Filmed at The Roslin Institute, The University of Edinburgh, March 2015 Graphical modelling, Roslin Institute
PSLS20 - Practical Statistics for the Life Sciences (2020)

Training material that covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences.

Keywords: Statistics, General Linear Models

Resource type: Documentation, Exercise, Handout, Scripts

PSLS20 - Practical Statistics for the Life Sciences (2020) https://tess.elixir-europe.org/materials/psls20-practical-statistics-for-the-life-sciences-2020 Training material that covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. Lieven Clement Jeroen Gilis Statistics, General Linear Models Academia/ Research Institution Industry Healthcare Non-Profit Organisation
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://tess.elixir-europe.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
Differential analysis of RNA-Seq data

Design, describe, explore and model

Keywords: Genomics, RNA-seq

Differential analysis of RNA-Seq data https://tess.elixir-europe.org/materials/differential-analysis-of-rna-seq-data Design, describe, explore and model Genomics, RNA-seq
Day 4 - RNA-Seq Analysis

Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation.

Keywords: Exploratory-analysis, Differential-expression, Statistical-model, Annotation

Day 4 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-4-rna-seq-analysis Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation. Exploratory-analysis, Differential-expression, Statistical-model, Annotation
Differential expression analysis on the Robinson, Delhomme et al. dataset.

A differential expression analysis conducted on the **[Robinson, Delhomme et al., dataset](https://microasp.upsc.se/ngs_trainers/Materials/blob/master/Datasets/Robinson-Delhomme-Populus-tremula-shows-no-evidence-of-sexual-dimorphism.md)**. The dataset has 17 samples and 2 important meta-data: the...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Differential-expression, R-programming, Statistical-model

Differential expression analysis on the Robinson, Delhomme et al. dataset. https://tess.elixir-europe.org/materials/differential-expression-analysis-on-the-robinson-delhomme-et-al-dataset A differential expression analysis conducted on the **[Robinson, Delhomme et al., dataset](https://microasp.upsc.se/ngs_trainers/Materials/blob/master/Datasets/Robinson-Delhomme-Populus-tremula-shows-no-evidence-of-sexual-dimorphism.md)**. The dataset has 17 samples and 2 important meta-data: the sample sex and year of collection. The goal is to test whether genes are involved in different processes based on the sex of the tree; _i.e._ is there a sexual dimorphism in _Populus tremula_ trees. It has indeed been hypothesized that male tree should be taller so as to spread their pollen further, whereas female would be more resistant to pests and diseases. The existing literature is contradictory, however it resulted from studies where plants were grown in controlled environment. In the present dataset, plant samples were collected in the wild, at a 2 years interval. The latter is a very important factor in the analysis as the 'year effect' is a strong confounding factor that hides the 'sex effect'. The present tutorial, hence, introduces a differential-expression analysis, but goes further by adressing confounding factors and how to _block_ them in an analysis. It is a good dataset to remind trainees that they should always be critical towards the conclusion they draw from their data. RNA-Seq RNA-Seq, Differential-expression, R-programming, Statistical-model
Material provided by Charlotte Soneson

This folder contains material provided by Charlotte Soneson. The following material is included:

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis

Material provided by Charlotte Soneson https://tess.elixir-europe.org/materials/material-provided-by-charlotte-soneson This folder contains material provided by Charlotte Soneson. The following material is included: RNA-Seq RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis
Day 3 - RNA-Seq Analysis

Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons.

Keywords: QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing

Day 3 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-3-rna-seq-analysis Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons. QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing
Statistics and RNA-Seq

This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

Statistics and RNA-Seq https://tess.elixir-europe.org/materials/statistics-and-rna-seq This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
RNA-seq module Frederik Coppens

Material concerning RNA-seq analysis, with an emphasis on the statistical aspects.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens-4a328fa8-0bef-471c-84e4-b0d89d216128 Material concerning RNA-seq analysis, with an emphasis on the statistical aspects. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Jaqpot Hackathon - Training materials

Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, attendees learned how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file. Jaqpot is a computational platform for in silico...

Keywords: nanoinformatics, toxicity prediction, e-tools, Modeling, data FAIRness

Jaqpot Hackathon - Training materials https://tess.elixir-europe.org/materials/jaqpot-hackathon-training-materials Under the subtitle “Take your research from the bench to the community by making your models available as a web service”, attendees learned how to use the Jaqpot suite and python to go from data to model, starting from a common CSV file. Jaqpot is a computational platform for in silico modelling of chemical compounds, that provides both access to its services both over a User Interface (GUI) and an Application Programming Interface (API). It is a cloud-ready application that uses the benefits of Java, R and Python, having incorporated functionality by various established and open-source machine learning and data analysis toolkits, while algorithms in any programming algorithm can be added to Jaqpot. Attached you find the following presentations: 1. Intro to NanoCommons by Martin Himly, PLUS 2. Electronic Lab Notebooks by Iseult Lynch, UoB 3. NanoCommons Knowledgebase by Dieter Maier, Biomax 4. Jaqpot Suite by Philip Doganis, NTUA Lee Walker, UKCEH Christine Balmer, UKCEH Irini Liampa, NTUA Pantelis Karatzas, NTUA Beatriz Alfaro Serrano, BNN Harry Sarimveis, NTUA nanoinformatics, toxicity prediction, e-tools, Modeling, data FAIRness
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://tess.elixir-europe.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
Introduction to Analysing Repeated Measures Data

Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute.

Keywords: Data analysis, Repeated measures, Roslin Institute

Introduction to Analysing Repeated Measures Data https://tess.elixir-europe.org/materials/introduction-to-analysing-repeated-measures-data Training session with Dr Helen Brown, Senior Statistician, at The Roslin Institute, March 2016. These training sessions were given to staff and research students at the Roslin Institute. The material is also used for the Animal Biosciences MSc course taught at the Institute. Data analysis, Repeated measures, Roslin Institute
Genome3D Structures

Introduction to examining and comparing Genome3D's 3D structural models

Genome3D Structures https://tess.elixir-europe.org/materials/genome3d-structures Introduction to examining and comparing Genome3D's 3D structural models 2017-10-05
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://tess.elixir-europe.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
FAIRification & Data modelling

Wikidata fairification

Keywords: FAIR, linked data, ontologies, metadata

Resource type: Slides

FAIRification & Data modelling https://tess.elixir-europe.org/materials/fairification-data-modelling Wikidata fairification FAIR, linked data, ontologies, metadata Life Science Researchers bioinformaticians
Introduction to linear models

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Introduction to linear models https://tess.elixir-europe.org/materials/introduction-to-linear-models Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Statistics and probability
Lecture slides for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exercises for the course RNA-seq data analysis with Chipster

This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Exercises for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/exercises-for-the-course-rna-seq-data-analysis-with-chipster This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
RNA-seq module Eija Korpelainen

All material concerning RNA-seq data analysis with Chipster

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Eija Korpelainen https://tess.elixir-europe.org/materials/rna-seq-module-eija-korpelainen All material concerning RNA-seq data analysis with Chipster FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
An Introduction to Mathematical Modelling

This course provides an introduction to the concepts of modelling biological systems. It is intended for biologists who have no experience in modelling but would like to know how it might apply to their area of research. The course provides a complete background to the history of modelling and...

An Introduction to Mathematical Modelling https://tess.elixir-europe.org/materials/an-introduction-to-mathematical-modelling This course provides an introduction to the concepts of modelling biological systems. It is intended for biologists who have no experience in modelling but would like to know how it might apply to their area of research. The course provides a complete background to the history of modelling and the different approaches through which a biological system can be approximated by mathematical methods. The course also provides a practical introduction to the [COPASI](http://copasi.org/) modelling environment.
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  • models

    Shweta Mahajan
Showing 1 event.

  • Integrated modeling and optimization

    13 - 17 December 2021

    Wageningen Campus, Netherlands

    Elixir node event
    Integrated modeling and optimization https://tess.elixir-europe.org/events/integrated-modeling-and-optimization Course date 13-17 December 2021, Wageningen Course coordinator Natal van Riel, Eindhoven University of Technology Lecturers Prof. Natal van Riel, Eindhoven University of Technology (course coordinator) Dr. Aalt-Jan van Dijk, Wageningen University & Research Prof. Jaap Molenaar, Wageningen University &… The post Integrated modeling and optimization appeared first on Dutch Techcentre for Life Sciences. 2021-12-13 09:00:00 UTC 2021-12-17 00:00:00 UTC Wageningen Campus, Netherlands, Wageningen Campus, Netherlands Wageningen Campus, Netherlands Wageningen Campus Netherlands [] [] [] workshops_and_courses [] []
Showing 7 content providers.

  • Genome 3D

    Genome3D provides consensus structural annotations and 3D models for sequences from model...

    8 training materials
    Genome 3D https://tess.elixir-europe.org/content_providers/genome-3d Genome3D provides consensus structural annotations and 3D models for sequences from model organisms, including human. These data are generated by several UK based resources in the Genome3D consortium: SCOP, CATH, SUPERFAMILY, Gene3D, FUGUE, THREADER, PHYRE. /system/content_providers/images/000/000/006/original/images?1469458224

  • FAIRDOM

    Research Infrastructure supporting life scientists in managing their data and models FAIRly....

    0 upcoming events (1 past event)
    FAIRDOM https://tess.elixir-europe.org/content_providers/fairdom Research Infrastructure supporting life scientists in managing their data and models FAIRly. Specifically designed for interdisciplinary research such as systems biology, systems medicine, and synthetic biology. /system/content_providers/images/000/000/100/original/Screen_Shot_2018-09-06_at_15.54.17.png?1536245244

  • Open Science MOOC

    Open Science MOOC is a mission-driven project to help make ‘Open’ the default setting for all...

    1 training material
    Open Science MOOC https://tess.elixir-europe.org/content_providers/open-science-mooc Open Science MOOC is a mission-driven project to help make ‘Open’ the default setting for all global research. We want to help create a welcoming and supporting community, with good tools, teachers, and role-models, and built upon a solid values-based foundation of freedom and equitable access to research. /system/content_providers/images/000/000/101/original/31343113?1536821365

  • eNanoMapper

    eNanoMapper developed a computational infrastructure for toxicological data management of...

    10 training materials
    eNanoMapper https://tess.elixir-europe.org/content_providers/enanomapper eNanoMapper developed a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs) based on open standards, ontologies and an interoperable design to enable a more effective, integrated approach to European research in nanotechnology. eNanoMapper supports the collaborative safety assessment for ENMs by creating a modular, extensible infrastructure for transparent data sharing, data analysis, and the creation of computational toxicology models for ENMs. eNanoMapper was funded by the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 604134. /system/content_providers/images/000/000/092/original/logo.png?1528313779

  • Biomedical Sciences Research Center "Alexander Fleming"

    The Biomedical Sciences Research Center "Alexander Fleming" is a non-profit research organisation...

    1 training material
    Biomedical Sciences Research Center "Alexander Fleming" https://tess.elixir-europe.org/content_providers/biomedical-sciences-research-center-alexander-fleming The Biomedical Sciences Research Center "Alexander Fleming" is a non-profit research organisation based in Vari, Athens, Greece. Since the beginning of its operations in 1998, the Center develops basic as well as translational and applied research programs at the cutting edge of modern biomedical sciences. Currently, the Center hosts 14 research groups distributed in 4 Institutes (Immunology, Molecular Oncology, Molecular Biology and Genetics, Cellular & Developmental Biology). Over the short period since its establishment, BSRC "Alexander Fleming" has gained extensive visibility in the European science arena. Fleming researchers have established transgenic animal models for rheumatoid arthritis, inflammatory bowel disease and multiple sclerosis and these models have served as a basis for multiple collaborations with the international biopharmaceutical industry in the evaluation of novel therapeutic compounds, or as tools for collaborative R&D. The Center is equipped with state-of-the-art Core Units which include: an Expression Profiling Facility, a Flow Cytometry Facility, a Protein Chemistry Lab, a Transgenics and gene targeting Unit, and a BioIT Unit, all of which serve internal collaborations, as well as external partners in academia and industry. The Center also runs an Innovation and Enterprise Unit that facilitates the protection and exploitation of the Center’s research and technologies. Fleming operates its own Animal House, which can house up to 15,000 mice, and has its own complete mouse histopathology unit. Fleming’s Animal house (certified with ISO 9001) provides husbandry of animals and services to the biomedical research community since 2001. It covers an area of approximately 600 m2 within the Center and is equipped with highly automated systems that provide the best possible conditions for mouse reproduction and maintenance. Its main activity is the reproduction and maintenance of mice stocks either of inbred strains or genetically engineered mice, such as transgenic and knockout mouse lines, as well as chemically induced mutants developed by Fleming researchers. The Animal House has a capacity to house more than 18,000 mice and is currently the largest Mouse Unit in Greece in terms of number and variety of mice. The Facility became a full member of EMMA in 2009. Main areas of research: Functional genomics and proteomics; Molecular and cellular immunology; Animal models of human disease; Transcriptional and post-transcriptional mechanisms of gene regulation; DNA repair; Stem Cell differentiation; Epigenetics; Learning and memory; ECM biology. Fields of excellence: Molecular mechanisms of disease (inflammation, cancer, metabolic syndrome, CNS disorders). /system/content_providers/images/000/000/051/original/logo.png?1469458221

  • EMBL-ABR

    EMBL Australia Bioinformatics Resource (EMBL-ABR) is a distributed national research...

    9 training materials
    0 upcoming events (193 past events)
    EMBL-ABR https://tess.elixir-europe.org/content_providers/embl-abr EMBL Australia Bioinformatics Resource (EMBL-ABR) is a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. EMBL-ABR aims to: 1. increase Australia’s capacity to collect, integrate, analyse, exploit, share and archive the large heterogeneous data sets now part of modern life sciences research 2. contribute to the development of and provide training in data, tools and platforms to enable Australia’s life science researchers to undertake research in the age of big data 3. showcase Australian research and datasets at an international level 4. enable engagement in international programs that create, deploy and develop best practice approaches to data management, software tools and methods, computational platforms and bioinformatics services. EMBL-ABR is structured as a hub/nodes model, with the Hub located at Melbourne Bioinformatics (formerly VLSCI), University of Melbourne. EMBL-ABR is also currently exploring engagement with the European infrastructure for biological information, ELIXIR, and other relevant international efforts. One of EMBL-ABR Key areas is TRAINING, and as such we are involved in diverse projects relevant for bioinformatics training in Australia, with a current focus on Open Science and Bioinformatics. /system/content_providers/images/000/000/072/original/embl-australia-logo-colour-FIN-e1462860151765.jpg?1488905402

  • INB: Spanish National Bioinformatics Institute

    The Spanish National Bioinformatics Institute (‘Instituto Nacional de Bioinformática’ in Spanish,...

    0 upcoming events (13 past events)
    INB: Spanish National Bioinformatics Institute https://tess.elixir-europe.org/content_providers/inb-spanish-national-bioinformatics-institute The Spanish National Bioinformatics Institute (‘Instituto Nacional de Bioinformática’ in Spanish, or short INB), founded in 2003 following the decentralized model of nodes of the Swiss Institute of Bioinformatics (SIB), is the bioinformatics technology platform of the Carlos III Health Institute (‘Instituto de Salud Carlos III‘ or ISCIII) since January 2018. The INB has increased the participant nodes to 19 research groups distributed across 13 institutions in Spain. The two main overarching objectives are maintaining and increasing the alignment of the INB with ELIXIR (European Life Science Infrastructure for Biological Information) looking for deeper synergies, while increasing the translational capacity of the INB towards the Spanish National Health System (SNS). The INB serves in the coordination, integration and development of Spanish bioinformatics resources in projects in the areas of genomics, proteomics and translational medicine. It has contributed to the creation of a consistent computational infrastructure in the area of bioinformatics, participated in national and international genome projects, and trained bioinformatics users and developers. The INB is in a strategic position as an interface between developments at the national and international level by research centers, initiatives such as the Global Alliance for Genomics and Health (GA4GH), and organizations such as ELIXIR, and bioinformatic groups directly related to clinical practice. **Spain is member of ELIXIR since 2015, with the INB as the Spanish national node**. Within ELIXIR, the INB is responsible for the bioinformatics infrastructure offered by Spain, and therefore, should guarantee its alignment to the strategic areas put forward by ELIXIR. /system/content_providers/images/000/000/110/original/logoINB.png?1550073283
Showing 12 workflows.

  • Homology Modelling with SWISS-MODEL

    This is the workflow of homology modelling with the SWISS-MODEL expert system

    SWISS-MODEL is a web-based integrated service dedicated to protein structure homology modelling. It guides the user in building protein homology models at [different levels of...

  • Protein Structure Modelling

    This is the a workflow of protein modelling.

  • DMPonline standard - Implementation strategy

    DMPonline standard - Implementation strategy

  • Structural bioinformatics workflow

    A workflow with suggested common stages taken in structural bioinformatics

  • ELIXIR Structural Bioinformatics 3: Predicting the effect of mutation on protein function

    This workflow builds on the previous training workflows in this series on building protein models and identifying functional domains or ligand binding sites - and introduces methods to predict how mutations can impact on protein function.

    It is designed to lead you through the process of...

  • ELIXIR Structural Bioinformatics 1: Getting a structure for a protein of interest

    This training workflow is designed to lead you through the process of finding experimentally-determined structures for a protein you are interested in - or predicting structure information if one is not available.

    It will then help guide you through visualising that structure as a prerequisite...

  • EBI metagenomics pipeline 2.0

    EBI metagenomics pipeline 2.0

  • Metagenomics

  • Training course in Transcriptomics

    Workflow for Transcirptomics course for CABANA learning

  • ELIXIR Structural Bioinformatics 2: Exploring protein domains and functional sites

    This training workflow introduces how to search (using query protein sequences or structures) for protein domains, conservation and protein family information, surface and topological interfaces, and possible ligand binding sites.

    It is designed to lead you through the process of finding...

  • Fork of ELIXIR Structural Bioinformatics 2: Exploring protein domains and functional sites

    This training workflow introduces how to search (using query protein sequences or structures) for protein domains, conservation and protein family information, surface and topological interfaces, and possible ligand binding sites.

    It is designed to lead you through the process of finding...

  • EMBER: A practical guide to Bioinformatics

    This practical introduces a range of Web-based databases and tools, allowing their relative strengths and weaknesses to be compared. The practical comprises several modules, each broken down into simple steps.