FAIR data - Module 4 (share and publish data)
Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données
Scientific topics: Data management, Biology, Bioinformatics
Keywords: data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse
Resource type: Slides
FAIR data - Module 4 (share and publish data)
https://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module4.html
http://tess.elixir-uk.org/materials/fair-data-module-4-share-and-publish-data
Partager et diffuser les données. Le cadre juridique, les entrepôts et les licences sur les données
Frédéric de Lamotte
Paulette Lieby
Lionel Maurel
Hélène Chiapello
Thomas Denecker
Jean-François Dufayard
Gautier Sarah
Julien Seiler
Data management
Biology
Bioinformatics
data sharing, Data publishing, legal framework, data warehouse, licensing, data reuse
Biologists
bioinformaticians
Biomedical researchers
FAIR data - Module 3 (Metadata)
Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données
Scientific topics: Data management, Biology, Bioinformatics
Operations: Data handling
Keywords: metadata, data annotation, life science standards, data sharing
Resource type: Slides
FAIR data - Module 3 (Metadata)
https://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module3.html
http://tess.elixir-uk.org/materials/fair-data-module-3-metadata
Les Métadonnées : les standards du domaine des données omiques en biologie et séances pratiques d’annotations de jeux de données
Frédéric de Lamotte
Hélène Chiapello
Thomas Denecker
Jean-François Dufayard
Gautier Sarah
Paulette Lieby
Data management
Biology
Bioinformatics
metadata, data annotation, life science standards, data sharing
Biologists
bioinformaticians
Biomedical researchers
FAIR data - Module 2 (data life cycle)
La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données
Scientific topics: Bioinformatics, Biology, Data management
Operations: Data handling
Keywords: Data preserving, Data storage
Resource type: Slides
FAIR data - Module 2 (data life cycle)
https://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module2.html
http://tess.elixir-uk.org/materials/fair-data-module-2
La vie des données pendant le projet : Principe et outils pour organiser, nommer, versionner, stocker, archiver, mes données
Frédéric de Lamotte
Julien Seiler
Bioinformatics
Biology
Data management
Data preserving, Data storage
Biologists
bioinformaticians
Biomedical researchers
FAIR data - Module 1 (research data)
Research data and their centrality in the research process.
This material is mostly in French.
Keywords: metadata, Data Life Cycle, Reproducibility, Data management plan
Resource type: Slides
FAIR data - Module 1 (research data)
https://ifb-elixirfr.github.io/IFB-FAIR-data-training/modules/module1.html
http://tess.elixir-uk.org/materials/fair-data-module-1
Research data and their centrality in the research process.
This material is mostly in French.
Frédéric de Lamotte
Gautier Sarah
Hélène Chiapello
Jean-François Dufayard
Julien Seiler
Lionel Maurel
Paulette Lieby
Thomas Denecker
metadata, Data Life Cycle, Reproducibility, Data management plan
Biologists
bioinformaticians
Biomedical researchers
Plant Phenotyping Data managment Webinar (MIAPPE)
The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org), has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking...
Scientific topics: Data submission, annotation, and curation, Data quality management, Phenomics, Plant biology
Operations: Standardisation and normalisation
Resource type: Video, Slides
Plant Phenotyping Data managment Webinar (MIAPPE)
https://youtu.be/4FOQPAWl6_M
http://tess.elixir-uk.org/materials/plant-phenotyping-data-managment-webinar-miappe
The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org), has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking between phenotype and genotype datasets, relevant section of MIAPPE are beginning to be used for genotyping standards. This Webinar will give an overview of the current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity inherent to research and breeding data sets. Data management approaches at some of the major research organizations will be given as examples.
The recording is available [here](https://youtu.be/4FOQPAWl6_M) and the slides are [here](https://drive.google.com/file/d/1FORlCX662T9dxiG4uzQwVXDXnq-sP0FP/view?usp=sharing)
Cyril Pommier
Cyril Pommier
Anne-Françoise Adam-Blondon
Célia Michotey
Data submission, annotation, and curation
Data quality management
Phenomics
Plant biology
Researchers
Biologists, Genomicists, Computer Scientists
Biologists
software developers, bioinformaticians
SPARQLing Biology: a beginners course
Course given at BioSB 2019 for biologists about SPARQL.
Scientific topics: Biology
Operations: Query and retrieval
Keywords: Sparql queries, Sparql syntax
Resource type: Tutorial
SPARQLing Biology: a beginners course
https://bigcat-um.github.io/SPARQLTutorialBioSB2019/
http://tess.elixir-uk.org/materials/sparqling-biology-a-beginners-course
Course given at BioSB 2019 for biologists about SPARQL.
Denise Slenter
Biology
Sparql queries, Sparql syntax
Biologists
Chemists
Plant Phenotyping Data managment (MIAPPE)
This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners...
Scientific topics: Data management, Plant biology, Phenomics
Operations: Formatting, Annotation
Keywords: Plant Phenotyping, Data-format, data sharing
Resource type: Training materials
Plant Phenotyping Data managment (MIAPPE)
https://github.com/MIAPPE/training/tree/master/Paris-Feb-2020
http://tess.elixir-uk.org/materials/plant-phenotyping-data-managment-miappe
This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners will know how to use standards and ontologies, how to describe their measurment protocole and practices how to fill a template with their data and how to apply the standards concept in some data managment tools.
Cyril Pommier
Daniel Faria
Evangelia Papoutsoglou
Célia Michotey
Elizabeth Arnaud
Anne-Françoise Adam-Blondon
Data management
Plant biology
Phenomics
Plant Phenotyping, Data-format, data sharing
Biologists
geneticists
plant researchers
software engineers
database managers
A Tidy Transcriptomics introduction to RNA-Seq analyses
This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.
Scientific topics: RNA-Seq
Keywords: Differential Expression, Gene Expression, RNA-seq, Transcriptomics
Resource type: Tutorial
A Tidy Transcriptomics introduction to RNA-Seq analyses
https://stemangiola.github.io/bioc_2020_tidytranscriptomics/
http://tess.elixir-uk.org/materials/a-tidy-transcriptomics-introduction-to-rna-seq-analyses
This workshop will present how to perform analysis of RNA sequencing data following the tidy data paradigm, using the tidybulk, tidyHeatmap and tidyverse packages.
Maria Doyle
Stefano Mangiola
RNA-Seq
Differential Expression, Gene Expression, RNA-seq, Transcriptomics
Biologists
Initiation to R programming and descriptive statistics
On-line course support for the initiation to R programming and descriptive statistics given to PhD students at Institut Pasteur (Paris, France).
Keywords: R-programming, Descriptive statistics, Statistics, Bioinformatics
Initiation to R programming and descriptive statistics
https://hub-courses.pages.pasteur.fr/R_pasteur_phd/index.html
http://tess.elixir-uk.org/materials/initiation-to-r-programming-and-descriptive-statistics
On-line course support for the initiation to R programming and descriptive statistics given to PhD students at Institut Pasteur (Paris, France).
Institut Pasteur, Bioinformatics and Biostatistics Hub
Blaise Li
Étienne Kornobis
Sébastien Mella
Vincent Guillemot
R-programming, Descriptive statistics, Statistics, Bioinformatics
PhD students
Post-Doctoral Fellows
Biologists
OpenRiskNet: Ontology Walkthrough and Workshop
Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.
Scientific topics: Ontology and terminology, Toxicology
Resource type: Tutorial
OpenRiskNet: Ontology Walkthrough and Workshop
https://openrisknet.github.io/workshop/OntologyWorkshop/
http://tess.elixir-uk.org/materials/openrisknet-ontology-walkthrough-and-workshop
Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.
Egon Willighagen
Ontology and terminology
Toxicology
Biologists
bioinformaticians
Chemists
BLAST and multiple sequence alignment (MSA) programs
Background
The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...
Keywords: Blast, E learning, Multiple sequence alignment
Resource type: e-learning
BLAST and multiple sequence alignment (MSA) programs
https://www.mygoblet.org/training-portal/materials/blast-and-multiple-sequence-alignment-msa-programs
http://tess.elixir-uk.org/materials/blast-and-multiple-sequence-alignment-msa-programs-0b2b34d0-a157-49d4-a065-3dcad67ff99d
Background
The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of new data is very useful to the research field through the development of bioinformatics tools and databases that deal with large amount of sequences. Among them, BLAST (Basic Local Alignment Search Tool) and MSA () programs are very efficient for protein or nucleotide sequence similarity search.
The present course introduces the main biological databases, alignment tool BLAST and Multiple sequence alignments (MSA) programs, and interpretation of results.
Goal
The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships.
Target audience
Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology.
AuthorsViral-zone, Swiss-Prot group at the SIB Swiss Institute of Bioinformatics
Patricia Palagi
Blast, E learning, Multiple sequence alignment
Bench biologists
Biologists
Laboratory technicians
Researchers
Veterinarians
2014-04-28
Phylogenetics of animal viral pathogens
Background
The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...
Keywords: Animal pathogens, E learning, Phylogenetics
Resource type: e-learning
Phylogenetics of animal viral pathogens
https://www.mygoblet.org/training-portal/materials/phylogenetics-animal-viral-pathogens
http://tess.elixir-uk.org/materials/phylogenetics-of-animal-viral-pathogens-428432a3-67ca-4284-8962-fefc2ade75db
Background
The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases.
The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study.
Goal
The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships.
Target audience
Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology.
AuthorsViral-Zone, Swiss-Prot Group at SIB Swiss Institute of Bioinformatics
Patricia Palagi
Animal pathogens, E learning, Phylogenetics
Bench biologists
Biologists
Laboratory technicians
Researchers
Veterinarians
2014-04-28
Single cell RNA-seq data analysis using Chipster
This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3...
Keywords: scRNA-seq
Resource type: Slides, Training materials
Single cell RNA-seq data analysis using Chipster
https://www.csc.fi/web/training/-/single-cell-chipster-2019
http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-using-chipster
This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3 tools embedded in the user-friendly Chipster software.
Eija Korpelainen
Maria Lehtivaara
scRNA-seq
Biologists
bioinformaticians
Mascot training course
The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises.
Scientific topics: Proteomics
Keywords: Protein identification, Protein Mass Spectrometry
Resource type: Slides, Video, Training materials
Mascot training course
http://www.matrixscience.com/training_webcast.html
http://tess.elixir-uk.org/materials/mascot-training-course
The Mascot training course covers every aspect of protein identification and characterisation using Matrix Science products: Mascot Server, Mascot Distiller and Mascot Daemon. The webcast is on-demand, self-paced and free, and includes hands-on exercises.
Matrix Science Ltd
Proteomics
Protein identification, Protein Mass Spectrometry
Biologists
bioinformaticians
Biochemists
mass spectrometry
Single cell RNA-seq data analysis with R
This international hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is kindly sponsored by the ELIXIR EXCELERATE...
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/web/training/-/scrnaseq
http://tess.elixir-uk.org/materials/single-cell-rna-seq-data-analysis-with-r-26ec3ec0-8f43-47db-9788-7f8f63eb447b
This international hands-on course covers several aspects of single cell RNA-seq data analysis, ranging from clustering and differential gene expression analysis to trajectories, cell type identification and spatial transcriptomics. The course is kindly sponsored by the ELIXIR EXCELERATE project.
Note: You can find all the course material including the R code and data files in the course [GitHub](https://github.com/NBISweden/excelerate-scRNAseq) repository, and the lecture videos are available as a [YouTube playlist](https://www.youtube.com/playlist?list=PLjiXAZO27elC_xnk7gVNM85I2IQl5BEJN).
Eija Korpelainen @eija, ekorpelainen@gmail.com
RNA-Seq
RNA-Seq, Single Cell technologies, scRNA-seq
bioinformaticians
Biologists
Groovy Cheminformatics with the Chemistry Development Kit
Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language.
Scientific topics: Chemistry, Cheminformatics
Resource type: Book
Groovy Cheminformatics with the Chemistry Development Kit
https://egonw.github.io/cdkbook/
http://tess.elixir-uk.org/materials/groovy-cheminformatics-with-the-chemistry-development-kit
Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language.
Egon Willighagen
Chemistry
Cheminformatics
PhD candidates
Master students
Chemists
Biologists
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
http://tess.elixir-uk.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
http://tess.elixir-uk.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
How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene
Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping.
Scientific topics: Genomics, Genetic variation
Keywords: ELIXIR RIR, BridgeDb
Resource type: Tutorial
How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene
https://bigcat-um.github.io/BridgeDbVariantDatabase/Local_BridgeDb_IMS_installation.html
http://tess.elixir-uk.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene
Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping.
Friederike Ehrhart
Jonathan Mélius
Egon Willighagen
Genomics
Genetic variation
ELIXIR RIR, BridgeDb
Biologists
#metawinterschool contribution by BiGCaT
Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.
Scientific topics: Metabolomics
Keywords: Metabolomics, Identifiers, ELIXIR RIR, BridgeDb
Resource type: Tutorial
#metawinterschool contribution by BiGCaT
https://egonw.github.io/metawinterschool-bigcat/
http://tess.elixir-uk.org/materials/metawinterschool-contribution-by-bigcat
Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.
Egon Willighagen
Metabolomics
Metabolomics, Identifiers, ELIXIR RIR, BridgeDb
Biologists
BridgeDbR Tutorial
Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites.
Keywords: ELIXIR RIR, BridgeDb
Resource type: Tutorial, Vignette
BridgeDbR Tutorial
https://bioconductor.org/packages/release/bioc/vignettes/BridgeDbR/inst/doc/tutorial.html
http://tess.elixir-uk.org/materials/bridgedbr-tutorial
Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites.
Egon Willighagen
ELIXIR RIR, BridgeDb
Biologists
Chemists
Biocuration: An Introduction
Claire O'Donovan, leader of the Protein Function Content team at EMBL-EBI, gives an introduction into biocuration and talks about what it is like to work as a biocurator and the skill sets you need.
This webinar was recorded on 2 March 2016 and is best viewed using Google Chrome and in...
Biocuration: An Introduction
https://www.mygoblet.org/training-portal/materials/biocuration-introduction
http://tess.elixir-uk.org/materials/biocuration-an-introduction-bdbaa48f-b505-4b5d-affb-83328bc2fac1
Claire O'Donovan, leader of the Protein Function Content team at EMBL-EBI, gives an introduction into biocuration and talks about what it is like to work as a biocurator and the skill sets you need.
This webinar was recorded on 2 March 2016 and is best viewed using Google Chrome and in full-screen mode.
Nicole Vasilevsky
Biocuration
Biologists
biocurators
life scientists
2018-05-11
Introductory image processing on biological images using python.
A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.
Resource type: Jupyter notebook, PDF
Introductory image processing on biological images using python.
https://github.com/dwaithe/model-training/
http://tess.elixir-uk.org/materials/introductory-image-processing-on-biological-images-using-python
A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.
Dominic Waithe
Anatole Chessel
Volker Baecker
Bioimage Analysts
Image Analysts
Computer Vision scientists
bioinformaticians
computational scientists
Biophysicists
Biologists
Microscopists
Python for Biologists
PhD students
Text-mining exercises
Hands-on exercises using a variety of text-mining tools and databases based on text mining, to interpret the results from microbiome studies.
Scientific topics: Data mining, Natural language processing, Metagenomics, Microbial ecology
Text-mining exercises
http://jensenlab.org/training/textmining/
http://tess.elixir-uk.org/materials/text-mining-exercises
Hands-on exercises using a variety of text-mining tools and databases based on text mining, to interpret the results from microbiome studies.
Evangelos Pafilis
Lars Juhl Jensen
Manimozhiyan Arumugam
Data mining
Natural language processing
Metagenomics
Microbial ecology
Bioinformaticians
Biologists
STRING exercises
Hands-on exercises using the STRING, STITCH, and DISEASES databases through their respective web interfaces.
Scientific topics: Protein interactions, Molecular interactions, pathways and networks, Bioinformatics
STRING exercises
http://jensenlab.org/training/string/
http://tess.elixir-uk.org/materials/string-exercises
Hands-on exercises using the STRING, STITCH, and DISEASES databases through their respective web interfaces.
Lars Juhl Jensen
Protein interactions
Molecular interactions, pathways and networks
Bioinformatics
Bioinformaticians
Biologists
Cytoscape stringApp exercises
Hands-on exercises using the stringApp for Cytoscape to retrieve molecular networks from the STRING and STITCH databases.
Scientific topics: Data visualisation, Proteomics, Protein interactions, Molecular interactions, pathways and networks, Bioinformatics
Cytoscape stringApp exercises
http://jensenlab.org/training/stringapp/
http://tess.elixir-uk.org/materials/cytoscape-stringapp-exercises
Hands-on exercises using the stringApp for Cytoscape to retrieve molecular networks from the STRING and STITCH databases.
Lars Juhl Jensen
Nadezhda T. Doncheva
Helen V. Cook
John "Scooter" Morris
Data visualisation
Proteomics
Protein interactions
Molecular interactions, pathways and networks
Bioinformatics
Bioinformaticians
Biologists
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
https://bioinformatics.ibers.aber.ac.uk/training/tutorials/#Unix_Perl
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.
Keith Bradnam
Ian Korf
IBERS, Institute of Biological, Environmental and Rural Sciences
Biologists
NGS overview
This course covers:
Sequencing technologies
Applications
Categories of analysis
Sample preparation
Potential services in NGS
Appendix
Scientific topics: Sequencing, High-throughput sequencing
Keywords: bioinformatics, Australia
NGS overview
http://vlsci.github.io/lscc_docs/tutorials/ngs_overview/NGS_Overview/
http://tess.elixir-uk.org/materials/ngs-overview
This course covers:
Sequencing technologies
Applications
Categories of analysis
Sample preparation
Potential services in NGS
Appendix
Simon Gladman
Vicky Schneider
Sequencing
High-throughput sequencing
bioinformatics, Australia
Biologists
Python Overview
Introduction to Python
Keywords: bioinformatics, Australia
Python Overview
http://vlsci.github.io/lscc_docs/tutorials/python_overview/python_overview/
http://tess.elixir-uk.org/materials/python-overview
Introduction to Python
Bernie Pope
Catherine de Burgh-Day
Vicky Schneider
bioinformatics, Australia
Biologists
Galaxy workflows
This workshop/tutorial will familiarise you with the Galaxy workflow engine. It will cover the following topics:
Logging in to the server
How to construct and use a workflow by various methods
How to share a workflow
Scientific topics: Workflows
Keywords: bioinformatics
Galaxy workflows
http://vlsci.github.io/lscc_docs/tutorials/galaxy-workflows/galaxy-workflows/
http://tess.elixir-uk.org/materials/galaxy-workflows
This workshop/tutorial will familiarise you with the Galaxy workflow engine. It will cover the following topics:
Logging in to the server
How to construct and use a workflow by various methods
How to share a workflow
Simon Gladman
Vicky Schneider
Workflows
bioinformatics
Biologists