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Installation and configuration of NGiNX for Galaxy

Keywords: Galaxy, NGiNX

(Proxy) Web Server Choices and Configuration https://tess.oerc.ox.ac.uk/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.oerc.ox.ac.uk/materials/200-billion-sequences-and-counting-analysis-discovery-and-exploration-of-datasets-with-ebi-metagenomics 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

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.oerc.ox.ac.uk/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

The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high...

Advanced FlowJo training https://tess.oerc.ox.ac.uk/materials/advanced-flowjo-training The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high dimensionality. Prerequisites Participants must have experience with FlowJo. Schedule See the TRAINING AT VIB website for a detailed schedule of this training. Training material Not available Links Not available Scientific topics FlowJo Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22

The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high...

Advanced FlowJo training https://tess.oerc.ox.ac.uk/materials/advanced-flowjo-training-2225a001-9e0a-489c-ab02-424e0f02302c The training will start with an introduction to FlowJo v10 but there will be enough details and features to make it worth even for advanced users. In the afternoon, advanced tools in FlowJo and new plugins (tSNE, SPADE) will be presented showing you how to work in high dimensionality. Prerequisites Participants must have experience with FlowJo. Schedule See the TRAINING AT VIB website for a detailed schedule of this training. Training material Not available Links Not available Scientific topics FlowJo Target audience Life Science Researchers, PhD students, post-docs, beginner bioinformaticians Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22

The aim of this course is to teach you how to create informative scientific plots using the ggplot package in R.

Advanced plotting with ggplot in R https://tess.oerc.ox.ac.uk/materials/advanced-plotting-with-ggplot-in-r The aim of this course is to teach you how to create informative scientific plots using the ggplot package in R.

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.oerc.ox.ac.uk/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.

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.oerc.ox.ac.uk/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.oerc.ox.ac.uk/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.oerc.ox.ac.uk/materials/alignment-of-rna-seq-data Focus on BAM format Alignment

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.oerc.ox.ac.uk/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 focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of...

Scientific topics: Metabolomics

Analysis of metabolome data https://tess.oerc.ox.ac.uk/materials/analysis-of-metabolome-data This training will focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of differential metabolites will be introduced. Afterwards, the trainee should be able to perform independently a comparative analysis of raw metabolome data and to pinpoint the well-known metabolites in the chromatogram. Metabolomics Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22

This training will focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of...

Scientific topics: Metabolomics

Analysis of metabolome data https://tess.oerc.ox.ac.uk/materials/analysis-of-metabolome-data-64788da2-7a74-4591-871c-b1c11369364f This training will focus on the processing of raw data obtained via either Gas Chromatography- (GC) or Liquid Chromatography- (LC) mass spectrometry (MS). In addition, based on the comparative analysis between two sample sets (e.g. control vs treatment), the subsequent identification of differential metabolites will be introduced. Afterwards, the trainee should be able to perform independently a comparative analysis of raw metabolome data and to pinpoint the well-known metabolites in the chromatogram. Metabolomics Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22

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.oerc.ox.ac.uk/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 PhD students post-docs 2016-04-22

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.oerc.ox.ac.uk/materials/analysis-of-public-microarray-data-sets-3c490908-d62e-436f-b2b1-19dbec5d136d 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 PhD students post-docs 2016-04-22

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: Biomarkers, Gene expression, Gene expression analysis

Analysis of public microarray data using Genevestigator https://tess.oerc.ox.ac.uk/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. Biomarkers Gene expression Gene expression analysis Life Science Researchers PhD students post-docs 2016-04-22

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: Biomarkers, Gene expression, Gene expression analysis

Analysis of public microarray data using Genevestigator https://tess.oerc.ox.ac.uk/materials/analysis-of-public-microarray-data-using-genevestigator-c3d72cb5-c535-4b13-9357-9083ffcc3c9d 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. Biomarkers Gene expression Gene expression analysis Life Science Researchers PhD students post-docs 2016-04-22

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: Gene expression, Gene expression analysis, PCR experiment

Analysis of qPCR data using qbase+ https://tess.oerc.ox.ac.uk/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. Gene expression Gene expression analysis PCR experiment Life Science Researchers PhD students post-docs 2016-04-22

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: Gene expression, Gene expression analysis, PCR experiment

Analysis of qPCR data using qbase+ https://tess.oerc.ox.ac.uk/materials/analysis-of-qpcr-data-using-qbase-86bdcb18-cd12-470a-ae8f-d135aa31b6c9 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. Gene expression Gene expression analysis PCR experiment Life Science Researchers PhD students post-docs 2016-04-22

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.oerc.ox.ac.uk/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 PhD students post-docs 2016-04-22

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.oerc.ox.ac.uk/materials/analyzing-flow-cytometry-data-using-flowjo-baffdee6-80ed-4aa8-82de-f221fdf0f2d8 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 PhD students post-docs 2016-04-22

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

Keywords: Matlab

Analyzing Patient Data https://tess.oerc.ox.ac.uk/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.oerc.ox.ac.uk/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.oerc.ox.ac.uk/materials/anova-and-linear-regression-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.

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.oerc.ox.ac.uk/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

A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our...

Scientific topics: Pathway or network, Phylogenetics

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation

Resource type: Video

Art and Science: A partnership catalyzing discovery in biomedicine https://tess.oerc.ox.ac.uk/materials/art-and-science-a-partnership-catalyzing-discovery-in-biomedicine A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our understanding and treatment of disease. The challenge is to ensure that technical and non-technical researchers can access, use and learn from this wealth of data and analytical resources. Bang will present examples of solutions developed at the Broad Institute that draw on art and design to enable scientific discovery.Bang Wong is the creative director of the Broad Institute of MIT & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at the Johns Hopkins University School of Medicine. His work focuses on the design and development of computation-visualization tools to meet the analytical challenges of research data. He leads the data visualization initiative at the Broad and is the founding author of Points of View published by Nature Methods, a series of articles that focus on the fundamental aspects of data presentation in science. Created at: 3rd BiVi Annual Meeting (2017). Bang Wong Pathway or network Phylogenetics Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation 2017-05-12

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Assembly - De Bruijn Graph Assembly https://tess.oerc.ox.ac.uk/materials/assembly-de-bruijn-graph-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - What are the factors that affect genome assembly? - How does Genome assembly work? Objectives of the tutorial: - Perform an optimised Velvet assembly with the Velvet Optimiser - Compare this assembly with those we did in the basic tutorial - Perform an assembly using the SPAdes assembler.

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Assembly - Introduction to Genome Assembly https://tess.oerc.ox.ac.uk/materials/assembly-introduction-to-genome-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - How do we perform a very basic genome assembly from short read data? Objectives of the tutorial: - assemble some paired end reads using Velvet - examine the output of the assembly.

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Assembly - Unicycler Assembly https://tess.oerc.ox.ac.uk/materials/assembly-unicycler-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - How to perform an hybrid bacterial assembly with Unicycler Objectives of the tutorial: - Perform Quality Control on your reads - Perform a Small genome Assembly with Unicycler - Evaluate the Quality of the Assembly with Quast - Annotate the assembly with Prokka

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.oerc.ox.ac.uk/materials/assessing-microbial-biogeography-by-using-a-metagenomic-approach 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