Search results

Showing 15 materials.
Ensembl browser webinar series (2016)

Ensembl browser webinar series (2016) from http://www.ebi.ac.uk/training/online/course/ensembl-browser-webinar-series-2016.

Keywords: DNA RNA

Ensembl browser webinar series (2016) https://tess.elixir-europe.org/materials/ensembl-browser-webinar-series-2016 Ensembl browser webinar series (2016) from http://www.ebi.ac.uk/training/online/course/ensembl-browser-webinar-series-2016. DNA RNA 2016-06-14
Ensembl tools: webinar

Ensembl tools: webinar from http://www.ebi.ac.uk/training/online/course/ensembl-tools-webinar.

Keywords: DNA RNA

Ensembl tools: webinar https://tess.elixir-europe.org/materials/ensembl-tools-webinar Ensembl tools: webinar from http://www.ebi.ac.uk/training/online/course/ensembl-tools-webinar. DNA RNA 2016-06-14
Ensembl: Browsing chordate genomes

Ensembl: Browsing chordate genomes from http://www.ebi.ac.uk/training/online/course/ensembl-browsing-chordate-genomes.

Keywords: DNA RNA

Ensembl: Browsing chordate genomes https://tess.elixir-europe.org/materials/ensembl-browsing-chordate-genomes Ensembl: Browsing chordate genomes from http://www.ebi.ac.uk/training/online/course/ensembl-browsing-chordate-genomes. DNA RNA 2016-06-14
Ensembl: Filmed API workshop

Ensembl: Filmed API workshop from http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop.

Keywords: DNA RNA

Ensembl: Filmed API workshop https://tess.elixir-europe.org/materials/ensembl-filmed-api-workshop Ensembl: Filmed API workshop from http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop. DNA RNA 2016-06-14
Ensembl: Filmed browser workshop

Ensembl: Filmed browser workshop from http://www.ebi.ac.uk/training/online/course/ensembl-filmed-browser-workshop.

Keywords: DNA RNA

Ensembl: Filmed browser workshop https://tess.elixir-europe.org/materials/ensembl-filmed-browser-workshop Ensembl: Filmed browser workshop from http://www.ebi.ac.uk/training/online/course/ensembl-filmed-browser-workshop. DNA RNA 2016-06-14
Ensembl: Quick tour

Ensembl: Quick tour from http://www.ebi.ac.uk/training/online/course/ensembl-quick-tour-0.

Keywords: DNA RNA

Ensembl: Quick tour https://tess.elixir-europe.org/materials/ensembl-quick-tour Ensembl: Quick tour from http://www.ebi.ac.uk/training/online/course/ensembl-quick-tour-0. DNA RNA 2016-06-14
Browsing plant and pathogen genomes with Ensembl Genomes

Complete course materials from the Ensembl Genomes course.

Keywords: Earlham Institute

Browsing plant and pathogen genomes with Ensembl Genomes https://tess.elixir-europe.org/materials/browsing-plant-and-pathogen-genomes-with-ensembl-genomes Complete course materials from the Ensembl Genomes course. Earlham Institute
Ensembl Genomes (non-chordates): Quick tour

Ensembl Genomes (non-chordates): Quick tour from http://www.ebi.ac.uk/training/online/course/ensembl-genomes-non-chordates-quick-tour.

Keywords: DNA RNA

Ensembl Genomes (non-chordates): Quick tour https://tess.elixir-europe.org/materials/ensembl-genomes-non-chordates-quick-tour Ensembl Genomes (non-chordates): Quick tour from http://www.ebi.ac.uk/training/online/course/ensembl-genomes-non-chordates-quick-tour. DNA RNA 2016-06-14
Ensembl Variant Effect Predictor (VEP): webinar

Ensembl Variant Effect Predictor (VEP): webinar from http://www.ebi.ac.uk/training/online/course/ensembl-variant-effect-predictor-vep-webinar.

Keywords: DNA RNA

Ensembl Variant Effect Predictor (VEP): webinar https://tess.elixir-europe.org/materials/ensembl-variant-effect-predictor-vep-webinar Ensembl Variant Effect Predictor (VEP): webinar from http://www.ebi.ac.uk/training/online/course/ensembl-variant-effect-predictor-vep-webinar. DNA RNA 2016-06-14
Identifier mapping with Cytoscape

This vignette will show you how to map or translate identifiers from one database (e.g., Ensembl) to another (e.g, Entrez Gene). This is a common requirement for data analysis. In the context of Cytoscape, for example, identifier mapping is needed when you want to import data to overlay on a...

Keywords: ELIXIR RIR, BridgeDb

Identifier mapping with Cytoscape https://tess.elixir-europe.org/materials/identifier-mapping-with-cytoscape This vignette will show you how to map or translate identifiers from one database (e.g., Ensembl) to another (e.g, Entrez Gene). This is a common requirement for data analysis. In the context of Cytoscape, for example, identifier mapping is needed when you want to import data to overlay on a network but you don’t have matching keys. ELIXIR RIR, BridgeDb
Ensembl gene set enrichment analysis with EGSEA

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Enrichment

Ensembl gene set enrichment analysis with EGSEA https://tess.elixir-europe.org/materials/ensembl-gene-set-enrichment-analysis-with-egsea Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Enrichment
UCSC Genome Browser

The UCSC Genome Browser provides a way to examine data from many genomes and includes extensive annotation tracks for various data types such as known UCSC (and Ensembl) genes, predicted genes, SNPs, miRNAs, comparative multi-species analysis and much more. During this training you will learn how...

UCSC Genome Browser https://tess.elixir-europe.org/materials/ucsc-genome-browser The UCSC Genome Browser provides a way to examine data from many genomes and includes extensive annotation tracks for various data types such as known UCSC (and Ensembl) genes, predicted genes, SNPs, miRNAs, comparative multi-species analysis and much more. During this training you will learn how to navigate this vital tool for your research. Required skills No specific prior knowledge is required.  BITS provides 15 laptops for their training sessions. Depending on the number of participants (max 20), it is possible that you have to share the laptop with one other participant but you can also choose to bring your own laptop for this training session. Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09
RNA-Seq Analysis with Biocluster and R

Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model

RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
eBioKit

Extensive teaching experience gained by conducting bioinformatics training courses in Kenya, Uganda, Mauritius (UoM), SriLanka, Sweden, Chile and Zimbabwe showed that it was difficult to successfully teach and demonstrate several bioinformatics resources, due to and often limited by slow Internet...

Keywords: Advanced bioinformatics training, Introduction bioinformatics

eBioKit https://tess.elixir-europe.org/materials/ebiokit Extensive teaching experience gained by conducting bioinformatics training courses in Kenya, Uganda, Mauritius (UoM), SriLanka, Sweden, Chile and Zimbabwe showed that it was difficult to successfully teach and demonstrate several bioinformatics resources, due to and often limited by slow Internet access. For that reason a bioinformatics platform, eBioKit  was engineered to ease the administrative burden of regularly updating large databases and installing software. This platform contains more than 300 bioinformatics applications (EMBOSS, Galaxy, Blast, RSAT etc),  and most relevant databases (ENSEMBL, Uniprot, OMIM, PDB, etc) locally, solving the network speed related problems and problems associated with the installation of software. Version 2 of this system has been successfully tested in real world situations both for capacity building and research in Kenya at ILRI, the Biosciences eastern and central Africa (BecA), KEMRI Wellcome Trust Research Programme (KWTRP) and The International Centre of Insect Physiology and Ecology (ICIPE). The system has further been deployed in the SANBio bioinformatics network in Southern Africa (10 countries) and Sri Lanka (Version 1) and has recently been adopted by the H3ABioNet African Bioinformatics Network as a platform to provide bioinformatics training and bioinformatics computing services at nodes in the network (http://www.h3abionet.org).  Advanced bioinformatics training, Introduction bioinformatics Bachelor students Bench biologists Life Science Researchers PhD students 2013-10-03 2017-10-09
Python @ TGAC - Python for Life Scientists: Managing biological data with Python

Python is an object-oriented programming language that is ideal for biological data analysis. The course will start with very basic language concepts and instructions and will cover all the main language aspects, including variables, types, modules, functions, exceptions, control of flux, input,...

Keywords: Biopython, Python, Python biologists

Python @ TGAC - Python for Life Scientists: Managing biological data with Python https://tess.elixir-europe.org/materials/python-tgac-python-for-life-scientists-managing-biological-data-with-python Python is an object-oriented programming language that is ideal for biological data analysis. The course will start with very basic language concepts and instructions and will cover all the main language aspects, including variables, types, modules, functions, exceptions, control of flux, input, output, and classes. All the examples and practical sessions will focus on solving particular biological problems. In particular, examples and practical sessions will cover: Working with DNA and protein sequences Data retrieval from files and their manipulation Running applications, such as BLAST, locally and from a script Finding motifs in sequences Parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc. Biopython will be also introduced and applied to some of the mentioned examples. The course is meant to be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the students will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics record and to run applications from scripts. Unix/Linux basic skills will be provided at the beginning of the course. Biopython, Python, Python biologists PhD post-docs 2015-07-14 2017-10-09
Showing 5 workflows.
  • ELIXIR Structural Bioinformatics 2: Exploring protein domains and functional sites

    This training workflow introduces how to search (using query protein sequences or structures) for protein domains, conservation and protein family information, surface and topological interfaces, and possible ligand binding sites.

    It is designed to lead you through the process of finding...

  • Fork of ELIXIR Structural Bioinformatics 2: Exploring protein domains and functional sites

    This training workflow introduces how to search (using query protein sequences or structures) for protein domains, conservation and protein family information, surface and topological interfaces, and possible ligand binding sites.

    It is designed to lead you through the process of finding...

  • Training course in Transcriptomics

    Workflow for Transcirptomics course for CABANA learning

  • ELIXIR Structural Bioinformatics 1: Getting a structure for a protein of interest

    This training workflow is designed to lead you through the process of finding experimentally-determined structures for a protein you are interested in - or predicting structure information if one is not available.

    It will then help guide you through visualising that structure as a prerequisite...

  • ELIXIR Structural Bioinformatics 3: Predicting the effect of mutation on protein function

    This workflow builds on the previous training workflows in this series on building protein models and identifying functional domains or ligand binding sites - and introduces methods to predict how mutations can impact on protein function.

    It is designed to lead you through the process of...