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A short presentation describing a new participatory method that easily engages course participants in gamestorming and helps to consolidate new knowledge, by collectively agreeing on ways to place concepts in mind maps. "Key-terms" is a classroom game that can be played in a variety of contexts,...

Keywords: Training, Instruction, Education

"Key-terms", a learning game for conceptual consolidation https://tess.elixir-europe.org/materials/key-terms-a-learning-game-for-conceptual-consolidation A short presentation describing a new participatory method that easily engages course participants in gamestorming and helps to consolidate new knowledge, by collectively agreeing on ways to place concepts in mind maps. "Key-terms" is a classroom game that can be played in a variety of contexts, from group discussions to several forms of Non-Formal learning (e.g. training) events. It helps a lot in engaging a small audience, following any wrap-up (recapitulation) session. Learners capture terms that they find conceptually important and contribute to a merged list. Then they are invited to pin these terms on a cork board in specified ways, such as placing related terms together (clustering), placing high order terms above lower order ones, etc. The instructor/facilitator can intervene at several levels in minimal, non-disturbing interventions, that help to contextualise what is happening. A depiction of how concepts are perceived in a class emerges quickly. This is, in practice, a visual concept map. The technique is being tested in the context of technical training provision, with the help of IT. Training, Instruction, Education Ontologists Educators Trainers 2014-07-06 2017-09-20

Installation and configuration of NGiNX for Galaxy

Keywords: Galaxy, NGiNX

(Proxy) Web Server Choices and Configuration https://tess.elixir-europe.org/materials/proxy-web-server-choices-and-configuration Installation and configuration of NGiNX for Galaxy Galaxy, NGiNX

EBI metagenomics (EMG, https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of...

Keywords: metagenomics

200 billion sequences and counting: analysis, discovery and exploration of datasets with EBI Metagenomics https://tess.elixir-europe.org/materials/200-billion-sequences-and-counting-analysis-discovery-and-exploration-of-datasets-with-ebi-metagenomics-ea1b32d5-b113-436c-a7da-8c7d29648d36 EBI metagenomics (EMG, https://www.ebi.ac.uk/metagenomics/) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA). EMG has recently undergone rapid expansion, with an over 10-fold increase in data volumes in the first 5 months of 2016. It now houses ~ 50k publicly available data sets, and represents one of the largest collections of analysed metagenomic data. As its data content has grown, EMG has increasingly become a platform for data discovery. To support this process, we have made a series of user-interface improvements, including the classification of projects by biome, presentation of results data for better visualisation and more convenient download, and provision of project level summary files. More recently, we have indexed project metadata for use with the EBI search engine, enabling exploration across different datasets. For example, users are able to search with a particular taxonomic lineage or protein function and discover the projects, samples and sequencing runs in which that lineage or function is found. This functionality allows users to explore associations between biomes, environmental conditions and organisms and functions (e.g., discovering protein coding sequences that correspond to certain enzyme families found in aquatic environments at a given temperature range). Here, we give an overview of the EMG data analysis pipeline and web site, and illustrate the use of the new search facility for data discovery. metagenomics 2016-12-16 2017-01-11

Two-dimensional electrophoresis is a well known method for protein separation which is extremely useful in the field of proteomics. The basic idea is to separate proteins contained in a sample using two independent properties such isoelectric point and mass. In the gel, each spot represents a...

Keywords: Electrophoresis

2D gel electrophoreses (DIGE) https://tess.elixir-europe.org/materials/2d-gel-electrophoreses-dige Two-dimensional electrophoresis is a well known method for protein separation which is extremely useful in the field of proteomics. The basic idea is to separate proteins contained in a sample using two independent properties such isoelectric point and mass. In the gel, each spot represents a protein accumulation and its size depends on the amount of protein present in the sample. Electrophoresis 2014-01-26 2017-09-20

This document is the trainee exercise booklet for a 3 day hands-on Next Generation Sequencing workshop developed by Bioplatforms Australia, CSIRO and EMBL-EBI.  This workshop is aimed at bench biologists, PhD students or early career postdoctoral researchers or those new to the analysis of NGS...

Scientific topics: Bioinformatics, Data quality management, Sequence assembly, Topic, Sequencing

Keywords: NGS, ChIPSeq, De novo genome assembly, RNASeq

3-day hands-on NGS workshop https://tess.elixir-europe.org/materials/3-day-hands-on-ngs-workshop This document is the trainee exercise booklet for a 3 day hands-on Next Generation Sequencing workshop developed by Bioplatforms Australia, CSIRO and EMBL-EBI.  This workshop is aimed at bench biologists, PhD students or early career postdoctoral researchers or those new to the analysis of NGS data and assumes no prior knowledge of bioinformatics. This course covers the following topics: data quality control, read alignment, ChIPSeq, RNASeq and de novo assembly. The workshop starts with the Intro to the shell material from Software Carpentry (http://software-carpentry.org/v4/shell/index.html).  Introductory lectures on each topic are presented before trainees move on that topic. The workshop has been delivered a number of times in different cities in Australia to date, in a roadshow style, and is designed to run on virtual machines on the Australian research cloud. Trainees then use NoMachine NX client to provide a remote desktop like connection to their own dedicated VM for the duration of of the workshop.  Various contributors made this workshop possible and they are credited in the introduction to each section. Bioinformatics Data quality management Sequence assembly Topic Sequencing NGS, ChIPSeq, De novo genome assembly, RNASeq postdocs Bench biologists Life Science Researchers PhD students 2014-01-17 2017-09-20

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

Keywords: R programming, Babraham Institute

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

The aim of this course is to help computational biologists with complex data analysis problems. After discussing the theoretical foundations, the course will provide practical advice on how to use the presented methodogies with R.

Advanced regression methods https://tess.elixir-europe.org/materials/advanced-regression-methods The aim of this course is to help computational biologists with complex data analysis problems. After discussing the theoretical foundations, the course will provide practical advice on how to use the presented methodogies with R. 2017-09-20

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 https://tess.elixir-europe.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

Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales.

Scientific topics: RNA-Seq

Keywords: BAM, Populus-tremula, RNA-Seq, QC, Alignment

Alignment https://tess.elixir-europe.org/materials/alignment Introduction to short-read alignments, including a general overview of existing methods (Burrow-Wheeler-Transform, Maximum Mappable Prefix, _etc._) and some cautionary tales. RNA-Seq BAM, Populus-tremula, RNA-Seq, QC, Alignment

Focus on BAM format

Keywords: Alignment

Alignment of RNA-Seq data https://tess.elixir-europe.org/materials/alignment-of-rna-seq-data Focus on BAM format Alignment

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

Scientific topics: DNA methylation

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

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

Scientific topics: Sequence alignment

Keywords: Babraham Institute

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

Learn about and become familiar with phyloseq R package for the analysis of microbial census data

Keywords: Microbiomes, R

Analysis of community composition data using phyloseq https://tess.elixir-europe.org/materials/analysis-of-community-composition-data-using-phyloseq Learn about and become familiar with phyloseq R package for the analysis of microbial census data Microbiomes, R

This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session.

Analysis of public microarray data sets https://tess.elixir-europe.org/materials/analysis-of-public-microarray-data-sets This training will give you an overview of what GEO has to offer. Several experiments will be analyzed using simple tools to obtain differential gene lists. An introduction to downstream tools dedicated to functional enrichment will close the session. Life Science Researchers post-docs PhD students 2016-04-22 2017-09-20

The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression...

Scientific topics: Gene expression, Gene expression analysis, Biomarkers

Analysis of public microarray data using Genevestigator https://tess.elixir-europe.org/materials/analysis-of-public-microarray-data-using-genevestigator The morning session will give you an overview of the possibilities of Genevestigator, a search engine of curated and normalized publicly available gene expression data. The interface allows you to visualize spatio-temporal (tissue - developmental stage) and perturbational gene expression information of many species in a user-friendly graphical way. The afternoon session will focus on the practical applications in a hands-on tutorial on Genevestigator followed by concrete examples of software that can be used to further interpret the results of your Genevestigator searches, like Ingenuity Pathway Analysis and DAVID. Finally, you will be able to work on the questions that you want to answer in your own research under the supervision of the trainer. Participants are therefore encouraged to submit a description of the objectives of the analysis they want to perform. Gene expression Gene expression analysis Biomarkers post-docs Life Science Researchers PhD students 2016-04-22 2017-09-20

This hands-on training provides an introduction to the analysis of qPCR data using Biogazelle's qbase+ software. Although this software allows to do various types of analyses (gene expression, copy number analysis, miRNA profiling), we will focus in the training on gene expression analysis....

Scientific topics: PCR experiment, Gene expression, Gene expression analysis

Keywords: Gene expression data analysis, Gene expression, PCR experiment

Analysis of qPCR data using qbase+ https://tess.elixir-europe.org/materials/analysis-of-qpcr-data-using-qbase This hands-on training provides an introduction to the analysis of qPCR data using Biogazelle's qbase+ software. Although this software allows to do various types of analyses (gene expression, copy number analysis, miRNA profiling), we will focus in the training on gene expression analysis. qbase+ software is freely distributed by BITS to VIB scientists. Therefore the training will be limited to VIB scientists. PCR experiment Gene expression Gene expression analysis Gene expression data analysis, Gene expression, PCR experiment Life Science Researchers PhD students post-docs 2016-04-22 2017-09-20

Analyses of sequences Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

Analysis of sequences - Genome Annotation https://tess.elixir-europe.org/materials/analysis-of-sequences-genome-annotation Analyses of sequences Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

Analyses of sequences Questions of the tutorial: - What two things are crucial for a correct mapping? - What is BAM? Objectives of the tutorial: - You will learn what mapping is - A genome browser is shown that helps you to understand your data

Analysis of sequences - Mapping https://tess.elixir-europe.org/materials/analysis-of-sequences-mapping Analyses of sequences Questions of the tutorial: - What two things are crucial for a correct mapping? - What is BAM? Objectives of the tutorial: - You will learn what mapping is - A genome browser is shown that helps you to understand your data

Analyses of sequences Questions of the tutorial: - How to control quality of NGS data? - What are the quality parameters to check for each dataset? - How to improve the quality of a sequence dataset? Objectives of the tutorial: - Manipulate FastQ files - Control quality from a FastQ file -...

Analysis of sequences - Quality Control https://tess.elixir-europe.org/materials/analysis-of-sequences-quality-control Analyses of sequences Questions of the tutorial: - How to control quality of NGS data? - What are the quality parameters to check for each dataset? - How to improve the quality of a sequence dataset? Objectives of the tutorial: - Manipulate FastQ files - Control quality from a FastQ file - Use FastQC tool - Understand FastQC output - Use tools for quality correction

Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data without a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data without a reference genome - SNP calling from RAD sequencing data - Calculate...

Analysis of sequences - RAD-Seq de-novo data analysis https://tess.elixir-europe.org/materials/analysis-of-sequences-rad-seq-de-novo-data-analysis Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data without a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data without a reference genome - SNP calling from RAD sequencing data - Calculate population genomics statistics from RAD sequencing data

Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data using a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data using a reference genome - SNP calling from RAD sequencing data - Calculate population...

Analysis of sequences - RAD-Seq Reference-based data analysis https://tess.elixir-europe.org/materials/analysis-of-sequences-rad-seq-reference-based-data-analysis Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data using a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data using a reference genome - SNP calling from RAD sequencing data - Calculate population genomics statistics from RAD sequencing data

Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data for a genetic map study? Objectives of the tutorial: - SNP calling from RAD sequencing data - Find and correct haplotypes - Create input files for genetic map building software

Analysis of sequences - RAD-Seq to construct genetic maps https://tess.elixir-europe.org/materials/analysis-of-sequences-rad-seq-to-construct-genetic-maps Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data for a genetic map study? Objectives of the tutorial: - SNP calling from RAD sequencing data - Find and correct haplotypes - Create input files for genetic map building software

You already know a good bit about hypothesis testing with one or two samples. Now we take things further by making inferences based on three or more samples. We'll use the very special F-distribution to do it (F stands for "fabulous").

Keywords: Inferential statistics

Analysis of variance https://tess.elixir-europe.org/materials/analysis-of-variance You already know a good bit about hypothesis testing with one or two samples. Now we take things further by making inferences based on three or more samples. We'll use the very special F-distribution to do it (F stands for "fabulous"). Inferential statistics 2016-08-14

IPA is software that allows researchers to analyze, integrate and understand data derived from experiments that generate a list of relevant genes, proteins or chemicals. The software relies on the Ingenuity Knowledge Base, a thoroughly curated database of high quality information on biological...

Analyzing biological networks with Ingenuity Pathway Analysis https://tess.elixir-europe.org/materials/analyzing-biological-networks-with-ingenuity-pathway-analysis IPA is software that allows researchers to analyze, integrate and understand data derived from experiments that generate a list of relevant genes, proteins or chemicals. The software relies on the Ingenuity Knowledge Base, a thoroughly curated database of high quality information on biological interactions and functional annotation. The database is limited to information on human, mouse and rat. Life Science Researchers PhD students post-docs 2016-04-22 2016-06-15

Flowjo version10 is a newly designed version of the famous Flowjo software. In contrast with previous versions (iOS only), version 10 is now a multi-platform software tool (Windows, iOS, Linux). It now has a very intuitive user interface designed to analyze your data in a very practical and fast...

Analyzing flow cytometry data using FlowJo https://tess.elixir-europe.org/materials/analyzing-flow-cytometry-data-using-flowjo Flowjo version10 is a newly designed version of the famous Flowjo software. In contrast with previous versions (iOS only), version 10 is now a multi-platform software tool (Windows, iOS, Linux). It now has a very intuitive user interface designed to analyze your data in a very practical and fast way. The training will be focused on getting familiar with all the tools available within the software. post-docs PhD students Life Science Researchers 2016-04-22 2017-09-20

Analyzing Patient Data from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/01-intro.md.

Keywords: Matlab

Analyzing Patient Data https://tess.elixir-europe.org/materials/analyzing-patient-data Analyzing Patient Data from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/01-intro.md. Matlab Novice

This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses.

Scientific topics: RNA-Seq

Keywords: GFF3, Populus-tremula, RNA-Seq, Annotation

Annotation https://tess.elixir-europe.org/materials/annotation This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses. RNA-Seq GFF3, Populus-tremula, RNA-Seq, Annotation

The aim of this course is to introduce you to data modelling using R. We focus on linear regression and ANOVA in order to improve your generic statistics knowledge. Please note that we cannot go into the specific data analysis problems of your particular project.

ANOVA and linear regression with R https://tess.elixir-europe.org/materials/linear-models-with-r The aim of this course is to introduce you to data modelling using R. We focus on linear regression and ANOVA in order to improve your generic statistics knowledge. Please note that we cannot go into the specific data analysis problems of your particular project. 2017-09-20

Bernard de Bono presents a talk on using ApiNATOMY for the visualisation of multiscale physiology circuitboards at 3rd BiVi Annual Meeting in April 2017. Created at: 3rd BiVi Annual Meeting (2017).

Keywords: Anatomy Physiology and Atlases

Resource type: Video

ApiNATOMY visualisation of multiscale physiology circuitboards https://tess.elixir-europe.org/materials/apinatomy-visualisation-of-multiscale-physiology-circuitboards Bernard de Bono presents a talk on using ApiNATOMY for the visualisation of multiscale physiology circuitboards at 3rd BiVi Annual Meeting in April 2017. Created at: 3rd BiVi Annual Meeting (2017). Dr. Bernard de Bono Anatomy Physiology and Atlases 2017-05-12

ArrayExpress: Discover functional genomics data quickly and easily from http://www.ebi.ac.uk/training/online/course/arrayexpress-discover-functional-genomics-data-qui.

Keywords: Gene Expression

ArrayExpress: Discover functional genomics data quickly and easily https://tess.elixir-europe.org/materials/arrayexpress-discover-functional-genomics-data-quickly-and-easily ArrayExpress: Discover functional genomics data quickly and easily from http://www.ebi.ac.uk/training/online/course/arrayexpress-discover-functional-genomics-data-qui. Gene Expression 2016-06-14