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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: http://www.mygoblet.org/topic-tags/education, http://www.mygoblet.org/topic-tags/instruction, http://www.mygoblet.org/topic-tags/training

"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. http://www.mygoblet.org/topic-tags/education, http://www.mygoblet.org/topic-tags/instruction, http://www.mygoblet.org/topic-tags/training Educators Trainers Ontologists 2014-07-06 2017-03-28

Installation and configuration of NGiNX for Galaxy

Keywords: NGiNX, Galaxy

(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 NGiNX, Galaxy

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 2017-03-28

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: Sequencing

Keywords: http://www.mygoblet.org/topic-tags/de-novo-genome-assembly, http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/chipseq, http://www.mygoblet.org/topic-tags/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. Sequencing http://www.mygoblet.org/topic-tags/de-novo-genome-assembly, http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/chipseq, http://www.mygoblet.org/topic-tags/rnaseq postdocs Bench biologists PhD students Life Science Researchers 2014-01-17 2017-03-28

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Admin-Corner - Docker and Galaxy https://tess.elixir-europe.org/materials/admin-corner-introduction Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Admin-Corner - Galaxy Database schema https://tess.elixir-europe.org/materials/admin-corner-galaxy-database-schema Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Admin-Corner - Move from dev instance to production instance https://tess.elixir-europe.org/materials/admin-corner-move-from-dev-instance-to-production-instance Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

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. 2017-03-28

This training will teach you how to choose the appropriate statistical test for analyzing your data. Attention will be paid to the correct interpretation of the results of statistical tests. The training is intended for scientists who want to get an introduction in statistics without getting too...

Advanced statistics in R https://tess.elixir-europe.org/materials/advanced-statistics-in-r This training will teach you how to choose the appropriate statistical test for analyzing your data. Attention will be paid to the correct interpretation of the results of statistical tests. The training is intended for scientists who want to get an introduction in statistics without getting too much mathematical details. Emphasis will be placed on practical applications. To this end, theory will be complemented with hands-on exercises in R, a free software environment for statistical computing and graphics. Topics include distributions, basic plots, confidence intervals, hypothesis testing... post-docs PhD students Life Science Researchers 2016-04-22 2017-03-02

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

Focus on BAM format

Scientific topics: Alignment

Keywords: Alignment

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

This training is aimed at researchers who are applying or planning to use Affymetrix microarrays in their research. The aim of this training is to familiarise the participants with microarray data analysis methodologies and provide hands-on training on the use of Bioconductor for Affymetrix...

Analysis of Affymetrix microarray data using Bioconductor https://tess.elixir-europe.org/materials/analysis-of-affymetrix-microarray-data-using-bioconductor This training is aimed at researchers who are applying or planning to use Affymetrix microarrays in their research. The aim of this training is to familiarise the participants with microarray data analysis methodologies and provide hands-on training on the use of Bioconductor for Affymetrix microarray analysis. Participants can use their own data during the training as long as the design of the experiment is similar to those used in the training e.g. comparison of two or multiple groups of samples. Life Science Researchers PhD students post-docs beginner bioinformaticians 2016-04-22 2016-06-15

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-3c37fd6e-ed26-4b20-8546-d79a2a6dfaa6 Learn about and become familiar with phyloseq R package for the analysis of microbial census data Microbiomes, R 2016-04-01 2017-01-11

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

Keywords: R, Microbiomes

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 R, Microbiomes

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. PhD students post-docs Life Science Researchers 2016-04-22 2017-03-28

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, 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 Biomarkers post-docs Life Science Researchers PhD students 2016-04-22 2017-03-28

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

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 data analysis, Gene expression, PCR experiment Life Science Researchers PhD students post-docs 2016-04-22 2017-03-28

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. Life Science Researchers post-docs PhD students 2016-04-22 2017-03-28

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. 2017-03-28

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

This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress. This course was updated in December 2015. An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI...

Scientific topics: Gene expression, Gene expression and microarray, Functional genomics

Keywords: Gene Expression

ArrayExpress: Quick tour https://tess.elixir-europe.org/materials/arrayexpress-quick-tour This quick tour provides an overview of EMBL-EBI’s functional genomics database ArrayExpress. This course was updated in December 2015. An undergraduate-level understanding of biology is an advantage. You may wish to have a look at our Functional genomics: An introduction to EMBL-EBI resources before taking this course. Gene expression Gene expression and microarray Functional genomics Gene Expression Beginners 2016-06-14

Soils are highly complex ecosystems and are considered as one of the Earth’s main reservoirs of biological diversity. Bacteria account for a major part of this biodiversity, and it is now clear that such microorganisms have a key role in soil functioning processes. However, environmental factors...

Keywords: metagenomics

Assessing microbial biogeography by using a metagenomic approach https://tess.elixir-europe.org/materials/assessing-microbial-biogeography-by-using-a-metagenomic-approach-2010019e-528d-4947-9056-e67e089ad240 Soils are highly complex ecosystems and are considered as one of the Earth’s main reservoirs of biological diversity. Bacteria account for a major part of this biodiversity, and it is now clear that such microorganisms have a key role in soil functioning processes. However, environmental factors regulating the diversity of below-ground bacteria still need to be investigated, which limits our understanding of the distribution of such bacteria at various spatial scales. The overall objectives of this study were: (i) to determine the spatial patterning of bacterial community diversity in soils at a broad scale, and (ii) to rank the environmental filters most influencing this distribution. This study was performed at the scale of the France by using the French Soil Quality Monitoring Network. This network includes more than 2,200 soil samples along a systematic grid sampling. For each soil, bacterial diversity was characterized using a pyrosequencing approach targeting the 16S rRNA genes directly amplified from soil DNA, obtaining more than 18 million of high-quality sequences. This study provides the first estimates of microbial diversity at the scale of France, with for example, bacterial richness ranging from 555 to 2,007 OTUs (on average: 1,289 OTUs). It also provides the first extensive map of bacterial diversity, as well as of major bacterial taxa, revealing a bacterial heterogeneous and spatially structured distribution at the scale of France. The main factors driving bacterial community distribution are the soil physico-chemical properties (pH, texture...) and land use (forest, grassland, crop system...), evidencing that bacterial spatial distribution at a broad scale depends on local filters such as soil characteristics and land use when regarding the community (quality, composition) as a whole. Moreover, this study also offers a better evaluation of the impact of land uses on soil microbial diversity and taxa, with consequences in terms of sustainability for agricultural systems. metagenomics 2016-12-16 2017-01-11