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31 materials found

Resource type: Scripts  or Slideshow 

IBIP19 - Integrative Biological Interpretation using Proteomics (2019)

Training Material aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments.

Keywords: Proteomics

Resource type: Documentation, Exercise, Handout, Scripts

IBIP19 - Integrative Biological Interpretation using Proteomics (2019) http://tess.elixir-uk.org/materials/ibip19-integrative-biological-interpretation-using-proteomics-2019 Training Material aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments. David Bouyssié Veit Schwämmle Marc Vaudel Proteomics Academia/ Research Institution Industry Non-Profit Organisation Healthcare
CPANG19 - Computational PANGenomics (2019)

Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.

Keywords: Genomics

Resource type: Documentation, Exercise, Handout, Scripts

CPANG19 - Computational PANGenomics (2019) http://tess.elixir-uk.org/materials/cpang19-computational-pangenomics-2019 Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types. Erik Garrison Mikko Rautiainen Genomics Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ADER19F - Analysis of Differential Expression with RNAseq (First course in 2019)

Training material for an introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq.

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ADER19F - Analysis of Differential Expression with RNAseq (First course in 2019) http://tess.elixir-uk.org/materials/ader19f-analysis-of-differential-expression-with-rnaseq-first-course-in-2019 Training material for an introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq. Daniel Sobral Daniel Faria Daniel Neves RNA-Seq, Genomics, RNA Academia/ Research Institution Industry Non-Profit Organisation Healthcare
PGDH19 - Population Genetics Demographic History: model-based approaches (2019)

Training material for a hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH19 - Population Genetics Demographic History: model-based approaches (2019) http://tess.elixir-uk.org/materials/pgdh19-population-genetics-demographic-history-model-based-approaches-2019 Training material for a hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodriguez Vitor Sousa Armando Arredondo Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
PDA19 - Proteomics Data Analysis (2019)

Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis.

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

PDA19 - Proteomics Data Analysis (2019) http://tess.elixir-uk.org/materials/pda19-proteomics-data-analysis-2019 Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis. Lennart Martens Harald Barsnes Lieven Clement Proteomics, Biological databases, Mass spectrometry data Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ELB19F - Entry level Bioinformatics (First course in 2019)

Training material for an entry-level course in bioinformatics with a soft introduction to NGS data analysis.

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ELB19F - Entry level Bioinformatics (First course in 2019) http://tess.elixir-uk.org/materials/elb19f-entry-level-bioinformatics-first-course-in-2019 Training material for an entry-level course in bioinformatics with a soft introduction to NGS data analysis. David Philip Judge Daniel Sobral Pedro Fernandes Bioinformatics, Sequencing Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ELBS18 - Entry level Bioinformatics (Second course in 2018)

Training material for an entry-level course in bioinformatics with a soft introduction to NGS data analysis

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ELBS18 - Entry level Bioinformatics (Second course in 2018) http://tess.elixir-uk.org/materials/elbs18-entry-level-bioinformatics-second-course-in-2018 Training material for an entry-level course in bioinformatics with a soft introduction to NGS data analysis David Philip Judge Daniel Sobral Pedro Fernandes Bioinformatics, Sequencing Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018)

Training material for introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq.

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018) http://tess.elixir-uk.org/materials/ader18s-analysis-of-differential-expression-with-rnaseq-second-course-in-2018 Training material for introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq. Daniel Sobral Daniel Faria Daniel Neves RNA-Seq, Genomics, RNA Academia/ Research Institution Industry Non-Profit Organisation Healthcare
CPANG18 - Computational PANGenomics (2018)

Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types.

Keywords: Genomics

Resource type: Documentation, Exercise, Handout, Scripts

CPANG18 - Computational PANGenomics (2018) http://tess.elixir-uk.org/materials/cpang18-computational-pangenomics-2018 Training Material aimed in the exploration of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types. Erik Garrison Mikko Rautiainen Jordan Eizenga Genomics Academia/ Research Institution Industry Non-Profit Organisation
PDA18 - Proteomics Data Analysis (2018)

Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis.

Keywords: Proteomics, Biological databases, Mass spectrometry data

Resource type: Documentation, Exercise, Handout, Scripts

PDA18 - Proteomics Data Analysis (2018) http://tess.elixir-uk.org/materials/pda18-proteomics-data-analysis-2018 Training material that covers the concepts and methods of Mass spectrometry-based proteomic experiments, covering peptide and protein identification, quantification, and differential analysis. Lennart Martens Harald Barsnes Lieven Clement Proteomics, Biological databases, Mass spectrometry data Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018)

Training material for an introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq.

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018) http://tess.elixir-uk.org/materials/ader18f-analysis-of-differential-expression-with-rnaseq-first-course-in-2018 Training material for an introductory course that covers practical aspects of the analysis of differential gene expression by RNAseq. Daniel Sobral Daniel Faria Daniel Neves RNA-Seq, Genomics, RNA Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ELB18F - Entry level Bioinformatics (First course in 2018)

Training material for entry level course in bioinformatics with a soft introduction to NGS data analysis.

Keywords: Bioinformatics, Sequencing

Resource type: Documentation, Exercise, Handout, Scripts

ELB18F - Entry level Bioinformatics (First course in 2018) http://tess.elixir-uk.org/materials/elb18f-entry-level-bioinformatics-first-course-in-2018 Training material for entry level course in bioinformatics with a soft introduction to NGS data analysis. David Philip Judge Daniel Sobral Pedro Fernandes Bioinformatics, Sequencing Academia/ Research Institution Industry Non-Profit Organisation Healthcare
PPB18 - Programming in Python for Biologists (2018)

Training Material that covers the basic concepts of Python, such as calculation, organization of data, reading and writing files, program logic and writing larger programs. All the examples and exercises focus on solving biological problems.

Operations: Data handling, Data retrieval

Keywords: Bioinformatics, Biology, Biological databases

Resource type: Documentation, Exercise, Handout, Scripts

PPB18 - Programming in Python for Biologists (2018) http://tess.elixir-uk.org/materials/ppb18-programming-in-python-for-biologists-2018 Training Material that covers the basic concepts of Python, such as calculation, organization of data, reading and writing files, program logic and writing larger programs. All the examples and exercises focus on solving biological problems. Allegra Via Vincenza Colonna David Philip Judge Bioinformatics, Biology, Biological databases Academia/ Research Institution Industry Non-Profit Organisation Healthcare
3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018)

Training Material focused in 3C-Data Analysis and 3D Chromatin Folding

Keywords: Hi-C

Resource type: Documentation, Exercise, Handout, Scripts

3DAROC18 - 3C-based data analysis and 3D reconstruction of chromatin folding (2018) http://tess.elixir-uk.org/materials/3daroc18-3c-based-data-analysis-and-3d-reconstruction-of-chromatin-folding-2018 Training Material focused in 3C-Data Analysis and 3D Chromatin Folding Marc A. Martí-Renom François Serra David Castillo Hi-C Academia/ Research Institution Industry Non-Profit Organisation Healthcare
ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018)

Training Material centred in Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data.

Keywords: Statistics and probability

Resource type: Documentation, Exercise, Handout, Scripts

ABSTAT18 - Advanced Biostatistics for Bioinformatics Tool Users using R (2018) http://tess.elixir-uk.org/materials/abstat18-advanced-biostatistics-for-bioinformatics-tool-users-using-r-2018 Training Material centred in Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Lisete Sousa Carina Silva Statistics and probability Academia/ Research Institution Industry Non-Profit Organisation Healthcare
PGDH18 - Population Genetics and Demographic History: model-based approaches (2018)

Training material for hands-on course with a practical approach in the analysis of genetic and genomic data.

Keywords: Population Genomics, Phylogenetics

Resource type: Documentation, Exercise, Handout, Scripts

PGDH18 - Population Genetics and Demographic History: model-based approaches (2018) http://tess.elixir-uk.org/materials/pgdh18-population-genetics-and-demographic-history-model-based-approaches-2018 Training material for hands-on course with a practical approach in the analysis of genetic and genomic data. Mark Beaumont Lounès Chikhi Willy Rodríguez Armando Arredondo Soto Vitor Sousa Population Genomics, Phylogenetics Academia/ Research Institution Industry Non-Profit Organisation
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) http://tess.elixir-uk.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
High Performance Computing (HPC) in Life Sciences

High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used...

Scientific topics: Biology, Bioinformatics, Computer science

Keywords: High performance computing, high-performance computing

Resource type: Tutorial, Slideshow, e-learning

High Performance Computing (HPC) in Life Sciences http://tess.elixir-uk.org/materials/high-performance-computing-hpc-in-life-sciences High-throughput sequencing data analysis requires new technical competencies and HPC is one of them. SIB has developed an e-learning module in HPC, as part of the ELIXIR-EXCELERATE project. e-learning has the potential to reach a wider audience, in any location and any time, and can be used either as the electronic component of a blended training format or as a self-running learning product. Biology Bioinformatics Computer science High performance computing, high-performance computing PhD students All postgraduates Life Science Researchers
MATHEMATICS BOOT CAMP: Introduction to Complex Systems Tools

This repository contains didactic material used in an introductory course of mathematics at the Center for Complex Systems and Brain Sciences in Florida Atlantic University by Viktor K. Jirsa.

Scientific topics: Computational biology, Mathematics

Keywords: ComputationalBiology, Neuroscience, complex systems, Mathematics

Resource type: Notes, Scripts

MATHEMATICS BOOT CAMP: Introduction to Complex Systems Tools http://tess.elixir-uk.org/materials/mathematics-boot-camp-introduction-to-complex-systems-tools This repository contains didactic material used in an introductory course of mathematics at the Center for Complex Systems and Brain Sciences in Florida Atlantic University by Viktor K. Jirsa. Felix Almonte Collins Assisi Frederick Carver Gautam Vallabha Jaime Morris Ajay Pillai Armin Fuchs Computational biology Mathematics ComputationalBiology, Neuroscience, complex systems, Mathematics Undergraduate students
Epigenome Browser

Ting Wang (http://wang.wustl.edu/) addresses many of the challenges of navigating the complexity of genomic data and showcases the WashU Epigenome Browser that he is developing. The browser aims to give investigators maximum flexibility to explore and navigate the available genomic data in...

Keywords: Genome, Molecular

Resource type: Slideshow, Video

Epigenome Browser http://tess.elixir-uk.org/materials/epigenome-browser Ting Wang (http://wang.wustl.edu/) addresses many of the challenges of navigating the complexity of genomic data and showcases the WashU Epigenome Browser that he is developing. The browser aims to give investigators maximum flexibility to explore and navigate the available genomic data in multiple tracks, upload their own data as well as explore long-range interactions. He also highlights the need for the genome browsers to act as community resources and bioinformatics engines with the ability to analyse the mined data. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Dr. Ting Wang Genome, Molecular 2017-01-31
BiVi theme: Anatomy, Physiology and Atlases 2015

Richard Baldock and Bernard de Bono introduce session on bio-visualisation in Anatomy, Physiology and Atlases at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases

Resource type: Slideshow

BiVi theme: Anatomy, Physiology and Atlases 2015 http://tess.elixir-uk.org/materials/bivi-theme-anatomy-physiology-and-atlases-2015 Richard Baldock and Bernard de Bono introduce session on bio-visualisation in Anatomy, Physiology and Atlases at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Prof. Richard Baldock Anatomy Physiology and Atlases 2017-02-03
BiVi theme: Genomes

Andy Yates introduces the Genomes session at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Keywords: Genome

Resource type: Slideshow

BiVi theme: Genomes http://tess.elixir-uk.org/materials/bivi-theme-genomes Andy Yates introduces the Genomes session at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Mr. Andy Yates Genome 2017-02-03
BiVi theme: Molecular - Structural molecular graphics

Prof Michael Sternberg introduces the Molecular bio-visualsation session at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Keywords: Molecular

Resource type: Slideshow

BiVi theme: Molecular - Structural molecular graphics http://tess.elixir-uk.org/materials/bivi-theme-molecular-structural-molecular-graphics Prof Michael Sternberg introduces the Molecular bio-visualsation session at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Prof. Michael J E Sternberg Molecular 2017-02-03
Zegami: Image visualisation, annotation and searching

Stephen Taylor describes and demonstrates Zegami at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome

Resource type: Slideshow

Zegami: Image visualisation, annotation and searching http://tess.elixir-uk.org/materials/zegami-image-visualisation-annotation-and-searching Stephen Taylor describes and demonstrates Zegami at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Stephen Taylor Anatomy Physiology and Atlases, Cells and Organisms, Genome 2017-02-03
Intermine 2.0

Yo Yehudi describes Intermine, an open source data warehouse and analysis system at 2nd BiVi in 2015 Created at: 2nd BiVi Annual Meeting.

Keywords: Databases

Resource type: Slideshow

Intermine 2.0 http://tess.elixir-uk.org/materials/intermine-2-0 Yo Yehudi describes Intermine, an open source data warehouse and analysis system at 2nd BiVi in 2015 Created at: 2nd BiVi Annual Meeting. Ms. Yo Yehudi Databases 2017-02-03
Aequatus-vis

Anil Thanki describes the Aequatus-vis JavaScript plugin to visualise homologous genes through alignment and phylogeny information at 2nd BiVi in 2015. aequatus-vis preserves teh interactive functionality of Aequatus, an open-source web based tool to visualise homologous genes with phylogenetic...

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Slideshow

Aequatus-vis http://tess.elixir-uk.org/materials/aequatus-vis Anil Thanki describes the Aequatus-vis JavaScript plugin to visualise homologous genes through alignment and phylogeny information at 2nd BiVi in 2015. aequatus-vis preserves teh interactive functionality of Aequatus, an open-source web based tool to visualise homologous genes with phylogenetic tree . Created at: 2nd BiVi Annual Meeting. Anil S. Thanki Phylogenetics Genome, Phylogenetics 2017-02-03
MARender: A Simple JavaScript Library for Biomedical Visualisation

Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015.  Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Information visualisation

Resource type: Slideshow

MARender: A Simple JavaScript Library for Biomedical Visualisation http://tess.elixir-uk.org/materials/marender-a-simple-javascript-library-for-biomedical-visualisation Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015.  Created at: 2nd BiVi Annual Meeting. Mr. William Edward Hill Anatomy Physiology and Atlases, Information visualisation 2017-02-03
Joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles

Roland Schwarz's keynote about the joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Slideshow

Joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles http://tess.elixir-uk.org/materials/joint-visualisation-and-analysis-of-large-sequence-data-with-alvis-and-sequence-bundles Roland Schwarz's keynote about the joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Dr. Roland Schwarz Phylogenetics Genome, Phylogenetics 2017-02-03
Interacting with large biomolecules using haptic feedback

Dr Stephen Laycock describes using InteractinHaptiMOL to interact with large biomolecules using haptic feedback at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Keywords: Molecular

Resource type: Slideshow

Interacting with large biomolecules using haptic feedback http://tess.elixir-uk.org/materials/interacting-with-large-biomolecules-using-haptic-feedback Dr Stephen Laycock describes using InteractinHaptiMOL to interact with large biomolecules using haptic feedback at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Dr. Stephen David Laycock Molecular 2017-02-03
Reactome

Kostas Sidiropoulos disceusses the visualsation of biomolecular pathways and Reactome, a free, open-source, curated and peer-reviewed knowledge-base of biomolecular pathways at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Scientific topics: Pathway or network

Keywords: Pathway, Databases

Resource type: Slideshow

Reactome http://tess.elixir-uk.org/materials/reactome Kostas Sidiropoulos disceusses the visualsation of biomolecular pathways and Reactome, a free, open-source, curated and peer-reviewed knowledge-base of biomolecular pathways at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Dr. Konstantinos Sidiropoulos Pathway or network Pathway, Databases 2017-02-03