Learning structural bioinformatics and evolution with a snake puzzle
We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding.
Scientific topics: Protein structure analysis, Molecular biology, Evolutionary biology, Bioinformatics
Resource type: course materials
Learning structural bioinformatics and evolution with a snake puzzle
https://peerj.com/articles/cs-100/
https://tess.elixir-europe.org/materials/learning-structural-bioinformatics-and-evolution-with-a-snake-puzzle
We propose here a working unit for teaching basic concepts of structural bioinformatics and evolution through the example of a wooden snake puzzle, strikingly similar to toy models widely used in the literature of protein folding.
Gonzalo S. Nido
Ludovica Bachschmid-Romano
Ugo Bastolla
Alberto Pascual-García
Protein structure analysis
Molecular biology
Evolutionary biology
Bioinformatics
Master students
Undergraduate students
Galaxy Proteomics workshop Prague 2018
Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic
Scientific topics: Proteomics
Keywords: Galaxy, training, proteomics, eLearning, EeLP
Resource type: course materials, Training materials, Slides
Galaxy Proteomics workshop Prague 2018
https://elixir.mf.uni-lj.si/course/view.php?id=41
https://tess.elixir-europe.org/materials/galaxy-proteomics-workshop-prague-2018
Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic
Andrea Argentini
Frederik Coppens
Pavel Dvorak
Matthias Fahrner
Melanie Foell
Björn Grüning
Martin Hubalek
Hana Pergl Sustkova
Marek Vrbacky
Andrea Argentini
Frederik Coppens
Pavel Dvorak
Matthias Fahrner
Melanie Foell
Björn Grüning
Martin Hubalek
Hana Pergl Sustkova
Marek Vrbacky
Proteomics
Galaxy, training, proteomics, eLearning, EeLP
life scientists
Researchers
PhD Students
How to get the most out of your microarray experiment. A Webinar
Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017
Scientific topics: Microarray experiment
Keywords: life sciences, microarrays, eLearning, EeLP
Resource type: course materials, Training materials, Slides
How to get the most out of your microarray experiment. A Webinar
https://elixir.mf.uni-lj.si/course/view.php?id=16
https://tess.elixir-europe.org/materials/how-to-get-the-most-out-of-your-microarray-experiment-a-webinar
Materials from the ELIXIR webinar "How to get the most out of your microarray experiment", Feb 14, 2017
Eva Freyhult
Jessica Lindvall
Mihaela Martis
Eva Freyhult
Jessica Lindvall
Mihaela Martis
Microarray experiment
life sciences, microarrays, eLearning, EeLP
Researchers
ELIXIR eLearning definitions
Materials from the asynchronous learning course "ELIXIR eLearning definitions"
Keywords: eLearning, training, EeLP
Resource type: course materials, Training materials, Documentation
ELIXIR eLearning definitions
https://elixir.mf.uni-lj.si/course/view.php?id=10
https://tess.elixir-europe.org/materials/elixir-elearning-definitions
Materials from the asynchronous learning course "ELIXIR eLearning definitions"
Brane Leskosek
Jure Dimec
Eija Korpelainen
Teresa Attwood
Sarah Morgan
Nicola Mulder
Celia van Gelder
Patricia Palagi
Brane Leskosek
Jure Dimec
Eija Korpelainen
Teresa Attwood
Sarah Morgan
Nicola Mulder
Celia van Gelder
Patricia Palagi
eLearning, training, EeLP
Researchers
teachers
Trainers
RNA-seq data analysis using Chipster
Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017
Scientific topics: Transcriptomics, Genomics
Keywords: transcriptomics, RNA-Seq, eLearning, EeLP
Resource type: course materials, Training materials, Slides, Video
RNA-seq data analysis using Chipster
https://elixir.mf.uni-lj.si/course/view.php?id=9
https://tess.elixir-europe.org/materials/rna-seq-data-analysis-using-chipster
Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017
Eija Korpelainen
Maria Lehtivaara
Eija Korpelainen
Maria Lehtivaara
Transcriptomics
Genomics
transcriptomics, RNA-Seq, eLearning, EeLP
Researchers
ELIXIR TtR course: Basic genomics using advanced analysis tools
Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
Scientific topics: Genomics
Keywords: Galaxy, training, Genomics, eLearning, EeLP
Resource type: course materials, Training materials, Slides
ELIXIR TtR course: Basic genomics using advanced analysis tools
https://elixir.mf.uni-lj.si/course/view.php?id=42
https://tess.elixir-europe.org/materials/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools
Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
Christophe Antoniewski
Olivier Inizan
Christophe Antoniewski
Olivier Inizan
Genomics
Galaxy, training, Genomics, eLearning, EeLP
life scientists
beginner bioinformaticians
Postgraduate students
Hands-on workshop in Marine Metagenomics
Materials from the ELIXIR workshop “Hands-on workshop in Marine Metagenomics”, Nov 26-30 2018 at the Arctic University of Norway, Tromso, Norway
Scientific topics: Marine biology, Metagenomics, Genomics
Keywords: Marine Metagenomics, eLearning, EeLP
Resource type: course materials, Training materials, Slides
Hands-on workshop in Marine Metagenomics
https://elixir.mf.uni-lj.si/course/view.php?id=43
https://tess.elixir-europe.org/materials/hands-on-workshop-in-marine-metagenomics
Materials from the ELIXIR workshop “Hands-on workshop in Marine Metagenomics”, Nov 26-30 2018 at the Arctic University of Norway, Tromso, Norway
Erik Hjerde
Nils Peder Willassen
Espen Aberg
Espen Mikal Robertsen
Erik Hjerde
Nils Peder Willassen
Espen Aberg
Espen Mikal Robertsen
Marine biology
Metagenomics
Genomics
Marine Metagenomics, eLearning, EeLP
Researchers
Master students
PhD students
Implementation of Data Management Plans & Data Stewardship in practice
Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece.
Scientific topics: Data submission, annotation and curation, Data management
Keywords: data management, data stewardship, eLearning, EeLP
Resource type: course materials, Training materials, Slides
Implementation of Data Management Plans & Data Stewardship in practice
https://elixir.mf.uni-lj.si/course/view.php?id=40
https://tess.elixir-europe.org/materials/implementation-of-data-management-plans-data-stewardship-in-practice
Materials from the ELIXIR workshop “Implementation of Data Management Plans & Data Stewardship in practice”, Sept 11, 2018 at ECCB2018, Athens, Greece.
Celia van Gelder
Mateusz Kuzak
Roland Krause
Marko Vidak
Celia van Gelder
Roland Krause
Mateusz Kuzak
Brane Leskosek
Marko Vidak
Robert Pergl
Marek Suchanek
Jan Slifka
Vojtech Knaisl
Data submission, annotation and curation
Data management
data management, data stewardship, eLearning, EeLP
bioinformaticians
data stewards
Single cell RNA-seq data analysis with R
This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and...
Scientific topics: RNA-Seq
Keywords: RNA-Seq, Single Cell technologies, scRNA-seq
Resource type: course materials
Single cell RNA-seq data analysis with R
https://www.csc.fi/en/web/training/-/single-cell-rnaseq-r-2018
https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-with-r
This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular tools and R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime analysis.
Heli Pessa
Bishwa Ghimire
Eija Korpelainen
RNA-Seq
RNA-Seq, Single Cell technologies, scRNA-seq
bioinformaticians
Biologists
Single cell RNA-seq data analysis with Chipster
This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...
Scientific topics: RNA-Seq
Keywords: RNA-Seq, Single Cell technologies, scRNA-seq
Resource type: course materials, Video
Single cell RNA-seq data analysis with Chipster
https://chipster.csc.fi/manual/courses.html#single-cell
https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430
This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Eija Korpelainen
Maria Lehtivaara
Eija Korpelainen
RNA-Seq
RNA-Seq, Single Cell technologies, scRNA-seq
Biologists
bioinformaticians
Data Carpentry in R
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data...
Keywords: Data analysis, Data carpentry, SoftwareCarpentry
Resource type: course materials
Data Carpentry in R
https://tavareshugo.github.io/2018-06-28-cambridge/
https://tess.elixir-europe.org/materials/data-carpentry-in-r
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data cleaning with OpenRefine, and learn how to use the statistical program R. If time allows we will also talk about Interacting with databases from R. Participants will be encouraged to help one another and to apply what they have learned to their own research problems
Sandra Cortijo
Hugo Tavares
Sergio Martínez Cuesta
Data analysis, Data carpentry, SoftwareCarpentry
Anyone
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/
https://tess.elixir-europe.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 R
This course provides a short beginners introduction to the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to input, explore, plot and output data in R. Everybody is welcome, if you would like to follow along...
Keywords: R-programming
Resource type: course materials
Introduction to R
https://github.com/semacu/20180315_IntroductionToR_Wolfson_Cambridge/blob/master/README.Rmd
https://tess.elixir-europe.org/materials/introduction-to-r-327a9c78-9b0c-4133-adfc-180c02c93023
This course provides a short beginners introduction to the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to input, explore, plot and output data in R. 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
https://tess.elixir-europe.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
Community analysis of amplicon sequencing data (16S rRNA)
This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...
Resource type: course materials, Video
Community analysis of amplicon sequencing data (16S rRNA)
https://chipster.csc.fi/manual/courses.html#16S
https://tess.elixir-europe.org/materials/community-analysis-of-amplicon-sequencing-data-16s-rrna
This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Eija Korpelainen
Maria Lehtivaara
Jarno Tuimala
Anu Mikkonen
Virus detection using small RNA-seq
This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....
Scientific topics: RNA-Seq
Resource type: course materials, Video
Virus detection using small RNA-seq
https://chipster.csc.fi/manual/courses.html#virusdetect
https://tess.elixir-europe.org/materials/virus-detection-using-small-rna-seq
This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Eija Korpelainen
Eija Korpelainen
RNA-Seq
RNA-seq data analysis
This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...
Scientific topics: RNA-Seq
Resource type: course materials, Video
RNA-seq data analysis
https://chipster.csc.fi/manual/courses.html#rna
https://tess.elixir-europe.org/materials/rna-seq-data-analysis-with-chipster
This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Eija Korpelainen
Maria Lehtivaara
Eija Korpelainen
RNA-Seq
Metagenomics data analysis
This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of...
Scientific topics: Metagenomics
Resource type: Video, course materials
Metagenomics data analysis
https://www.csc.fi/web/training/-/metagenomics
https://tess.elixir-europe.org/materials/metagenomics-data-analysis
This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced. The course material includes slides, exercises and lecture videos.
The workshop is organized in collaboration with the ELIXIR EXCELERATE project and PRACE, and it is part of the PRACE Advanced Training Centre activity.
Eija Korpelainen
Nils Peder Willassen
Espen Mikal Robertsen
Erik Hjerde
Rob Finn
Anu Mikkonen
Jenni Hultman
Petri Auvinen
Kimmo Mattila
Maria Lehtivaara
Jarno Tuimala
Eija Korpelainen
Metagenomics
Advanced in silico drug design
Advanced in silico drug design workshop - Olomouc, 2018
Scientific topics: Drug discovery
Resource type: course materials
Advanced in silico drug design
http://fch.upol.cz/en/teaching/advanced-in-silico-drug-design-add/
https://tess.elixir-europe.org/materials/advanced-in-silico-drug-design
Advanced in silico drug design workshop - Olomouc, 2018
Karel Berka
Pavel Polishchuk
Jindřich Fanfrlík
Martin Lepšík
Drug discovery
PhD students
postdocs