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De Novo

Training Materials from the 2015 De Novo course run by TGAC

Keywords: De novo, De novo genome assembly

De Novo https://tess.elixir-europe.org/materials/de-novo Training Materials from the 2015 De Novo course run by TGAC De novo, De novo genome assembly PhD PhD students post-docs postdoctoral researchers 2015-09-17 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
De Novo Assembly @ TGAC 2015

This course took place between 12-15 May 2015 Overview: The course will provide an introduction to de novo assembly, with a hands on introduction followed by in-depth analysis of the key steps in the process. It covers several aspects such as the initial setup of a de novo genome sequencing...

Keywords: De novo

De Novo Assembly @ TGAC 2015 https://tess.elixir-europe.org/materials/de-novo-assembly-tgac-2015 This course took place between 12-15 May 2015 Overview: The course will provide an introduction to de novo assembly, with a hands on introduction followed by in-depth analysis of the key steps in the process. It covers several aspects such as the initial setup of a de novo genome sequencing project, quality control and preprocessing of datasets, generation and evaluation of first pass assemblies, assembly improvement and finishing. Practical exercises will be performed on small-scale real datasets, including Illumina and Pacbio sequences, including best practices and tips based on TGAC’s faculty experience. The course will consist of a mixture of conceptual lectures, methodological lectures and hands on sessions, as well as group activities and discussions. The participants will gain first-hand experience and understanding on NGS assembly, working with the assistance of the faculty, troubleshooting small problems, and reviewing the results. De novo PhD post-docs 2015-07-14 2017-10-09
GOBLET Training portal

Presention

Keywords: Goblet

GOBLET Training portal https://tess.elixir-europe.org/materials/goblet-training-portal Presention Goblet 2015-07-01 2017-10-09
TGAC Metagenomics: From bench to data analysis

This course took place at TGAC on 8-12 September 2014 What is the workshop about? A substantial part of the course will be devoted to bioinformatics resources and tools relevant in metagenomics data analysis. Participants will start at the bench and end in front of the computers for a problem...

Scientific topics: Metagenomics

Keywords: Metagenomics

TGAC Metagenomics: From bench to data analysis https://tess.elixir-europe.org/materials/tgac-metagenomics-from-bench-to-data-analysis This course took place at TGAC on 8-12 September 2014 What is the workshop about? A substantial part of the course will be devoted to bioinformatics resources and tools relevant in metagenomics data analysis. Participants will start at the bench and end in front of the computers for a problem solving activity utilizing the bioinformatics training they will be receiving during the course. What will it cover? To provide an overview of the main aspects involved in metagenomics from the bench to data analysis and discussion around the interpretation and actual examples of the impact and applications of metagenomics derived research Target Audience: This course is aimed at advanced PhD students and post-doctoral researchers who are doing or planning to start research in the field of metagenomics. Metagenomics Metagenomics PhD postdocs 2015-06-25 2017-10-09
TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers

Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data...

Scientific topics: Sequence analysis, Plant biology, Database management, Bioinformatics

Keywords: Ngs, Ngs bioinformatics, Plants bioinformatics

TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers https://tess.elixir-europe.org/materials/tgac_seqahead-ngs-current-challenges-and-data-analysis-for-plant-researchers Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data analysis for plant species data Data quality checks Estimation of reproducibility Batch effects Statistical concepts Importance of standards Data formats Data integration What will I learn? To discuss and reflect on best practice of experimental design and control for using NGS technologies in their context of addressing biological questions Identify key challenges, opportunities and bottlenecks Offering a platform for discussion and exploration of the challenges in plant research with a particular emphasis for agri-bioinformatics Sequence analysis Plant biology Database management Bioinformatics Ngs, Ngs bioinformatics, Plants bioinformatics PhD students plant researchers post-docs 2015-06-22 2017-10-09
A mind map is a nice visual way of describing the content of a training course

A Mind Map can be built by arranging boxes with subject titles in a variety of ways. In this example, the objective was to create a visual aid to better understand the relationship between the subjects that had been covered. The diagram is centered in the core subject, and other subjects occupy...

Keywords: Mind map, Training technique, Visual aid

A mind map is a nice visual way of describing the content of a training course https://tess.elixir-europe.org/materials/a-mind-map-is-a-nice-visual-way-of-describing-the-content-of-a-training-course A Mind Map can be built by arranging boxes with subject titles in a variety of ways. In this example, the objective was to create a visual aid to better understand the relationship between the subjects that had been covered. The diagram is centered in the core subject, and other subjects occupy successive layers showing hierarchy. This diagram was generated at the end of the GTPB training course SMLMC15 - Structural Modelling for Large Macromolecular Complexes with Joanna Kasprzak and Mateusz Dobrychłop It was prepared using the X-Mind software (free version) Mind map, Training technique, Visual aid Structural Biologists Training Designers Training instructors 2015-05-09 2017-10-09
Bioinformatics approaches to Identify causative sequence variants in farm animals

ALLBIO and DEANN Training course: 12-16 May 2014, SLU, Uppsala, Sweden The training is mainly intended for researchers that want or already use techniques like genome-wide SNP genotyping, candidate gene sequencing, transcriptome sequencing and other bioinformatics tools in their work to...

Keywords: Allbio, Farm animals, Qtl, Rnaseq, Transcription factors

Bioinformatics approaches to Identify causative sequence variants in farm animals https://tess.elixir-europe.org/materials/bioinformatics-approaches-to-identify-causative-sequence-variants-in-farm-animals ALLBIO and DEANN Training course: 12-16 May 2014, SLU, Uppsala, Sweden The training is mainly intended for researchers that want or already use techniques like genome-wide SNP genotyping, candidate gene sequencing, transcriptome sequencing and other bioinformatics tools in their work to elucidate the specific contributions of genetic and other factors in shaping the phenotypic variability in farm animals. Allbio, Farm animals, Qtl, Rnaseq, Transcription factors Biologists bioinformaticians geneticists 2014-11-17 2017-10-09
STAO 2014 Understanding a genetic disease thanks to Bioinformatics

This workshop allows to discover several bioinformatics tools and databases (genome browser, alignment tool, BLAST, dbSNP, UniProtKB, PDB) in the context of the discovery of a rare variant leading to the production of a non functional insulin in a Norwegian family. Additional documents are ...

Keywords: Blast, Genome browsing, Introduction bioinformatics, Protein structure visualisation, Variant detection

STAO 2014 Understanding a genetic disease thanks to Bioinformatics https://tess.elixir-europe.org/materials/stao-2014-understanding-a-genetic-disease-thanks-to-bioinformatics This workshop allows to discover several bioinformatics tools and databases (genome browser, alignment tool, BLAST, dbSNP, UniProtKB, PDB) in the context of the discovery of a rare variant leading to the production of a non functional insulin in a Norwegian family. Additional documents are available: http://education.expasy.org/cours/Toronto Blast, Genome browsing, Introduction bioinformatics, Protein structure visualisation, Variant detection high school 2014-11-10 2017-10-09
Metagenome data analysis Workshop, May 21-23, 2014

SciLifelab and AllBio are arranging a workshop on the analysis and interpretation of metagenomics data. In this workshop we will combine talks by experts in the field with practical tutorials guiding the participants in the analysis of representative datasets. Speakers: Lex Nederbragt, Oslo...

Keywords: Allbio, Assembly, Binning, Bioinformatics, Data analysis, Metagenomics

Metagenome data analysis Workshop, May 21-23, 2014 https://tess.elixir-europe.org/materials/metagenome-data-analysis-workshop-may-21-23-2014 SciLifelab and AllBio are arranging a workshop on the analysis and interpretation of metagenomics data. In this workshop we will combine talks by experts in the field with practical tutorials guiding the participants in the analysis of representative datasets. Speakers: Lex Nederbragt, Oslo University, Norway, Saskia Smits, Erasmus University Rotterdam, Netherlands, Joakim Larsson, Göteborg University, Sweden Paul Wilmes, University of Luxembourg, Luxembourg, Anders Andersson, SciLifeLab, Sweden Noan Le Bescot, UPMC (Tara expedition), France Tutorial supervisors: Ino de Bruijn, SciLifeLab, Sweden Johannes Alneberg, SciLifeLab, Sweden Luisa Hugerth, SciLifeLab, Sweden Johan Bengtsson, Göteborg University, Sweden Mikael Huss, SciLifeLab, Sweden Venue: Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden Conference room Air/Fire, Gamma building Organisers: Mikael Huss (mikael.huss@scilifelab.se) Thomas Svensson (thomas.svensson@scilifelab.se) Allbio, Assembly, Binning, Bioinformatics, Data analysis, Metagenomics 2014-09-29 2017-10-09
Presentation About GOBLET Portal

This is a presentation I gave at the Jornadas de Bioinformática in Seville, Spain (24/09/14)

Keywords: Goblet, Training portal

Presentation About GOBLET Portal https://tess.elixir-europe.org/materials/presentation-about-goblet-portal This is a presentation I gave at the Jornadas de Bioinformática in Seville, Spain (24/09/14) Goblet, Training portal Bioinformatics General Interest Trainers Users 2014-09-26 2017-10-09
Plant and Pathogen Bioinformatics

This package contains presentations and other training material given at the AllBio Plant and Pathogen Bioinformatics training course, held at the European Bioinformatics Institute, Hinxton, United Kingdom, Tuesday, July 8, 2014 - Friday, July 11, 2014. The course was aimed at giving an...

Keywords: Allbio, Bioinformatics, Biological databases, Genome sequence analysis, Pathogenesis, Phytopathogens, Plants

Plant and Pathogen Bioinformatics https://tess.elixir-europe.org/materials/plant-and-pathogen-bioinformatics This package contains presentations and other training material given at the AllBio Plant and Pathogen Bioinformatics training course, held at the European Bioinformatics Institute, Hinxton, United Kingdom, Tuesday, July 8, 2014 - Friday, July 11, 2014. The course was aimed at giving an introduction to researchers wishing to work in the plant-pathogen interactions area, covering major database resources and basis data analysis techniques. The aims of the course were to teach participants how to browse and access a range of data types from leading public repositories; use bioinformatic tools to explore plant and pathogen-related biological data; discuss the benefits and limitations of various bioinformatic techniques; and assess the purpose of specific analyses in a wider context. We would like to thank all presenters for their contributions and their willingness to further distribute their material via Goblet. Allbio, Bioinformatics, Biological databases, Genome sequence analysis, Pathogenesis, Phytopathogens, Plants beginner bioinformaticians early stage phytopathogen researchers 2014-09-11 2017-10-09
SV-Autopilot: the new face of Structural Variant Detection

Although there are many tools designed for structural variation (SV) analysis there has been no bench mark study to guide scientists in choosing the best tool for their particular data set. In this test case, AllBio Test Case 2 – Identification of Large Structural Variants, a researcher is eager...

Keywords: Ngs bioinformatics, Structural variations

SV-Autopilot: the new face of Structural Variant Detection https://tess.elixir-europe.org/materials/sv-autopilot-the-new-face-of-structural-variant-detection Although there are many tools designed for structural variation (SV) analysis there has been no bench mark study to guide scientists in choosing the best tool for their particular data set. In this test case, AllBio Test Case 2 – Identification of Large Structural Variants, a researcher is eager to identify large structural variants in multiple accessions of Arabidopsis. What is needed is a tool which can identify the type and quality of the sequencing reads, assemble them with regards to a reference genome, and predict large structural variants (>30nt). Lastly, it is desirable that the tool should have a user-friendly interface with which bench scientists can easily examine structural variants in their accession(s) of interest that need to be validated. Here we have not only created the benchmark data, but have also created a Virtual Machine framework that can automate this process using multiple SV prediction algorithms in parallel and refine the output to reduce false positive calls. We call this SV-AUTOPILOT, a Structural Variation AUTOmated PIpeLine Optimization Tool. This tool was tested by participants during the workshop. Link to SV-Autopilot: https://github.com/ALLBio/allbiotc2 Ngs bioinformatics, Structural variations Biologists bioinformaticians software developers, bioinformaticians 2014-09-10 2017-10-09
GOBLET Talk at INCoB 2014

Supporting Trainers to Improve Bioinformatics Education Globally Speaker: Dr. Michelle Brazas A needs assessment isn’t necessary to realize that across the globe, there is a high demand for quality bioinformatics training in all domains of life science. Delivering on this demand however is not...

Keywords: Goblet

GOBLET Talk at INCoB 2014 https://tess.elixir-europe.org/materials/goblet-talk-at-incob-2014 Supporting Trainers to Improve Bioinformatics Education Globally Speaker: Dr. Michelle Brazas A needs assessment isn’t necessary to realize that across the globe, there is a high demand for quality bioinformatics training in all domains of life science. Delivering on this demand however is not trivial. In addition to computational infrastructure and software tools, quality bioinformatics training depends upon excellent trainers and training resources. With a focus on the trainer in the learning equation, the Global Organization for Bioinformatics Learning, Education and Training (GOBLET) aims to facilitate the advancement of bioinformatics education globally by training and supporting a network of bioinformatics trainers. Activities include coordinating training efforts, sharing data sets and teaching materials, discussing best practices and building up teaching standards and teaching recognition. Examples to improve your bioinformatics training programs were provided. Through support and development of trainer excellence, GOBLET is working to improve the global landscape in bioinformatics education. Goblet General Interest 2014-08-14 2017-10-09
Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Benjamin Good

Online Gaming in Bioinformatics: The ‘Fun’ Model to Online Bioinformatics Education Benjamin Good, Senior Staff Scientist, Department of Molecular and Experimental Medicine, The Scripps Research Institute. Dr. Good’s research focuses on games with a purpose in crowdsourcing biological knowledge....

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Gaming, Online learning

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Benjamin Good https://tess.elixir-europe.org/materials/workshop-on-education-in-bioinformatics-2014-ismb-2014-benjamin-good Online Gaming in Bioinformatics: The ‘Fun’ Model to Online Bioinformatics Education Benjamin Good, Senior Staff Scientist, Department of Molecular and Experimental Medicine, The Scripps Research Institute. Dr. Good’s research focuses on games with a purpose in crowdsourcing biological knowledge. To this end, his research has contributed to the development of a suite of interactive video games that allow for play, learning and contributions to science: genegames.org. Dr. Good spoke on online games for bioinformatics and how they can (or cannot) be used to teach bioinformatics at WEB 2014 at ISMB 2014. Bioinformatics Bioinformatics, Gaming, Online learning General Interest 2014-08-14 2017-10-09
Workshop on Education in Bioinformatics 2014 - ISMB 2014 - David Searls

Self-directed Learning: Does online learning in bioinformatics work? Proposed Speaker: (CONFIRMED) David Searls, Adjunct Associate Professor, Perleman School of Medicine, University of Pennsylvania. Dr. Searls is an independent consultant in bioinformatics and former Senior VP of Bioinformatics...

Keywords: Bioinformatics, Mooc, Online learning

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - David Searls https://tess.elixir-europe.org/materials/workshop-on-education-in-bioinformatics-2014-ismb-2014-david-searls Self-directed Learning: Does online learning in bioinformatics work? Proposed Speaker: (CONFIRMED) David Searls, Adjunct Associate Professor, Perleman School of Medicine, University of Pennsylvania. Dr. Searls is an independent consultant in bioinformatics and former Senior VP of Bioinformatics at GlaxoSmithKline Pharmaceuticals. He recently authored “Ten Simple Rules for Online Learning” and “An Online Bioinformatics Curriculum”. Dr. Searls spoke on the opportunities and challenges of online learning in bioinformatics from a learner's perspective at WEB 2014 at ISMB 2014. Bioinformatics, Mooc, Online learning General Interest 2014-08-14 2017-10-09
Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Michael Love

MOOCs in Bioinformatics: The Online Course Model to Online Bioinformatics Education Dr. Michael Love, edX Faculty and post-doctoral fellow in Dept. Biostatistics, Dana Farber Cancer Institute and Harvard School of Public Health. Dr. Love teaches the Data Analysis for Genomics course offered...

Keywords: Bioinformatics, Mooc

Workshop on Education in Bioinformatics 2014 - ISMB 2014 - Michael Love https://tess.elixir-europe.org/materials/workshop-on-education-in-bioinformatics-2014-ismb-2014-michael-love MOOCs in Bioinformatics: The Online Course Model to Online Bioinformatics Education Dr. Michael Love, edX Faculty and post-doctoral fellow in Dept. Biostatistics, Dana Farber Cancer Institute and Harvard School of Public Health. Dr. Love teaches the Data Analysis for Genomics course offered through edX. His research focuses on inferring biologically meaningful patterns from high-throughput sequencing read counts. He also develops open-source statistical software for the analysis of exome sequencing and RNA sequencing experiments for the Bioconductor Project. Dr. Love spoke on how open online courses operate and how they can (or cannot) be used to teach bioinformatics at WEB 2014 at ISMB 2014. Bioinformatics, Mooc 2014-08-14 2017-10-09
UPGMA Worked Example

A walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any objects A-G for which pairwise distances can be calculated. A small CGI...

Keywords: Molecular phylogeny, Phylogenetics, Upgma

UPGMA Worked Example https://tess.elixir-europe.org/materials/upgma-worked-example A walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any objects A-G for which pairwise distances can be calculated. A small CGI site for generating a UPGMA tree from a distance matrix can be found here. The source data for this worked example is a subset of Cytochrome C distances from Table 3 of one of the seminal phylogenetic papers: Fitch WM & Margoliash E (1967). Construction of phylogenetic trees. Science 155:279-84. PowerPoint timings are set up to be consistent with autolooping the presentation. Molecular phylogeny, Phylogenetics, Upgma Beginners 2014-08-04 2017-10-09
QuickGuides

A range of Quick Guides to commonly used bioinformatics tools and resources.

Keywords: Blast, Emboss, Mysql, Perl, Phylip, Unixlinux, Velvet

QuickGuides https://tess.elixir-europe.org/materials/quickguides A range of Quick Guides to commonly used bioinformatics tools and resources. Blast, Emboss, Mysql, Perl, Phylip, Unixlinux, Velvet Beginners 2014-07-31 2017-10-09
Basic bioinformatics and HOPE

Many bioinformatics tools have been developed over the last decennium, most of which were meant to be used in the lab of the life scientist. Unfortunately, only a few made it, because the tools are often too non-intuitive and too much a black box to the life scientist. Therefore Hanka Venselaar...

Keywords: Disease causing mutation, Predicting effect mutation protein function, Predicting effect mutation structure

Basic bioinformatics and HOPE https://tess.elixir-europe.org/materials/basic-bioinformatics-and-hope Many bioinformatics tools have been developed over the last decennium, most of which were meant to be used in the lab of the life scientist. Unfortunately, only a few made it, because the tools are often too non-intuitive and too much a black box to the life scientist. Therefore Hanka Venselaar developed HOPE to at least make the explanation of the phenotypic effect of mutations in (human) proteins intuitive for the non-bioinformatics expert. We developed this course to explain the basics of this program, and the underlying theory. Disease causing mutation, Predicting effect mutation protein function, Predicting effect mutation structure 2014-07-23 2017-10-09
GOBLET Poster at ISMB 2014

This is a PDF of the GOBLET poster presentation at ISMB 2014 in Boston.

Keywords: Goblet survey life scientists

GOBLET Poster at ISMB 2014 https://tess.elixir-europe.org/materials/goblet-poster-at-ismb-2014 This is a PDF of the GOBLET poster presentation at ISMB 2014 in Boston. Goblet survey life scientists 2014-07-07 2017-10-09
"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,...

Keywords: Education, Instruction, 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. Education, Instruction, Training Educators Ontologists Trainers 2014-07-06 2017-10-09
Perl 1 Training Course - For Programming Beginners

A set of slides from The Sainsbury Laboratory Perl course for absolute beginners

Keywords: Perl, Programming

Perl 1 Training Course - For Programming Beginners https://tess.elixir-europe.org/materials/perl-1-training-course-for-programming-beginners A set of slides from The Sainsbury Laboratory Perl course for absolute beginners Perl, Programming Beginners Bench biologists 2014-07-03 2017-10-09
RNA-seq Analysis 2014 Module 4 - Isoform discovery and alternative expression

Explore use of Cufflinks in reference annotation based transcript (RABT) assembly mode and ‘de novo’ assembly mode. Both modes require a reference genome sequence.  

Scientific topics: RNA

Keywords: Alternative expression, Transcript isoforms

RNA-seq Analysis 2014 Module 4 - Isoform discovery and alternative expression https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-4-isoform-discovery-and-alternative-expression Explore use of Cufflinks in reference annotation based transcript (RABT) assembly mode and ‘de novo’ assembly mode. Both modes require a reference genome sequence.   RNA Alternative expression, Transcript isoforms Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 3 - Expression and Differential Expression

Get FPKM style expression estimates using Cufflinks Perform differential expression analysis with Cuffdiff Perform summary analysis with CummeRbund Downstream interpretation of expression analysis (multiple testing, clustering, heatmaps, classification, pathway analysis, etc.)  

Keywords: Differential expression, Transript expression

RNA-seq Analysis 2014 Module 3 - Expression and Differential Expression https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-3-expression-and-differential-expression Get FPKM style expression estimates using Cufflinks Perform differential expression analysis with Cuffdiff Perform summary analysis with CummeRbund Downstream interpretation of expression analysis (multiple testing, clustering, heatmaps, classification, pathway analysis, etc.)   Differential expression, Transript expression Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 2 - Alignment and Visualization

Use of Bowtie/TopHat ‘Regular mode’ vs. ‘Fusion mode’ Introduction to the BAM format Basic manipulation of BAMs with samtools, etc. Visualization of RNA-seq alignments - IGV BAM read counting and determination of variant allele expression status    

Keywords: Data visualization, Rna seq alignment

RNA-seq Analysis 2014 Module 2 - Alignment and Visualization https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-2-alignment-and-visualization Use of Bowtie/TopHat ‘Regular mode’ vs. ‘Fusion mode’ Introduction to the BAM format Basic manipulation of BAMs with samtools, etc. Visualization of RNA-seq alignments - IGV BAM read counting and determination of variant allele expression status     Data visualization, Rna seq alignment Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 1 - Introduction to RNA-seq Analysis

Basic introduction to biology of RNA-seq Experimental design considerations Commonly asked questions Data visualization using IGV  

Keywords: Experimental design rna seq, Igv, Introduction rna seq analysis

RNA-seq Analysis 2014 Module 1 - Introduction to RNA-seq Analysis https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-1-introduction-to-rna-seq-analysis Basic introduction to biology of RNA-seq Experimental design considerations Commonly asked questions Data visualization using IGV   Experimental design rna seq, Igv, Introduction rna seq analysis Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
Bioinformatics Introductory Module

This Bioinformatics Introductory Module for self-study was designed for future students of the  Molecular Mechanisms of Disease (MMD) master’s program at Radboud University Medical Centre. To level out the starting differences in bioinformatics knowledge between this incoming heterogeneous group...

Keywords: Bioinformatics, Genome browsing, Genomics, Protein structure

Bioinformatics Introductory Module https://tess.elixir-europe.org/materials/bioinformatics-introductory-module This Bioinformatics Introductory Module for self-study was designed for future students of the  Molecular Mechanisms of Disease (MMD) master’s program at Radboud University Medical Centre. To level out the starting differences in bioinformatics knowledge between this incoming heterogeneous group of students as much as possible, we have designed an introductory course module that should allow them – via self study and hands-on exercises – to acquire sufficient basic bioinformatics knowledge. Keywords: Databases, Sequence homology, Phylogeny, Protein structure, Microarrays, Proteomics, Expression analysis, Protein-protein interaction, Cluster analysis, protein modelling, networks, bioinformatics. Anticipated time needed to complete the module: 40 hours.  Answers for all the exercises are available on request. Of course you do need internet connection to perform the hands-on exercises. There is no need, however, to install programs onto your computer and also low-speed data transfer should be sufficient. All literature that is cited and used throughout the module was taken from open access sources.   Bioinformatics, Genome browsing, Genomics, Protein structure Life Science Researchers Master students 2014-06-27 2017-10-09
Pathway and Network Analysis 2014 Module 5 - Network Visualization

Introduction to network visualization Visualizing omics data on a network or pathway Active modules in Cytoscape

Keywords: Cytoscape, Network visualization

Pathway and Network Analysis 2014 Module 5 - Network Visualization https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-5-network-visualization Introduction to network visualization Visualizing omics data on a network or pathway Active modules in Cytoscape Cytoscape, Network visualization Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 4 - Pathway and Network Analysis

Introduction to pathway and network analysis Basic network concepts Types of pathway and network information Pathway Databases: Reactome, KEGG, etc. Pathway analysis of large scale genomics data sets, including cancer genomics

Keywords: Biological networks, Kegg, Pathway analysis, Reactome

Pathway and Network Analysis 2014 Module 4 - Pathway and Network Analysis https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-4-pathway-and-network-analysis Introduction to pathway and network analysis Basic network concepts Types of pathway and network information Pathway Databases: Reactome, KEGG, etc. Pathway analysis of large scale genomics data sets, including cancer genomics Biological networks, Kegg, Pathway analysis, Reactome Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09