GOBLET

GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training, is a legally registered foundation providing a global, sustainable support and networking structure for bioinformatics educators/trainers and students/trainees.

GOBLET https://tess.elixir-europe.org/content_providers/goblet GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training, is a legally registered foundation providing a global, sustainable support and networking structure for bioinformatics educators/trainers and students/trainees. /system/content_providers/images/000/000/004/original/logo_goblet_trans.png?1469458222
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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: http://www.mygoblet.org/topic-tags/structural-variations, http://www.mygoblet.org/topic-tags/ngs-bioinformatics

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 http://www.mygoblet.org/topic-tags/structural-variations, http://www.mygoblet.org/topic-tags/ngs-bioinformatics bioinformaticians Biologists software developers, bioinformaticians 2014-09-10 2017-10-09

Clinical Bioinformatics I is a 10 credit module of the new MSc in Clinical Bioinformatics, delivered by Nowgen/NGRL and the University of Manchester in the UK. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of work...

Keywords: http://www.mygoblet.org/topic-tags/introduction-bioinformatics, http://www.mygoblet.org/topic-tags/genomics, http://www.mygoblet.org/topic-tags/clinical-bioinformatics

Clinical Bioinformatics I - Tutor notes https://tess.elixir-europe.org/materials/clinical-bioinformatics-i-tutor-notes Clinical Bioinformatics I is a 10 credit module of the new MSc in Clinical Bioinformatics, delivered by Nowgen/NGRL and the University of Manchester in the UK. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of work placement based training interspersed with academic teaching.  The tutor notes describe the content taught on each day of the 5 day course, and the approach used to teach the materials. Each day is divided into two parts, a series of lectures in the morning to introduce the topics, then the afternoon sessions present a series of case studies for the students to work through in a 'problem based learning (PBL) approach to reinforce the lecture content.  http://www.mygoblet.org/topic-tags/introduction-bioinformatics, http://www.mygoblet.org/topic-tags/genomics, http://www.mygoblet.org/topic-tags/clinical-bioinformatics postgrad healthcare professionals Life Science Researchers 2013-11-28 2017-10-09

This presentation aims to provide a basic understanding of the range of contexts in which protein sequence alignments are used and are useful, focusing on the importance of sequence similarities and differences, and what they tell us. Overall, the objective is to offer different perspectives and...

Scientific topics: Sequence analysis

Keywords: http://www.mygoblet.org/topic-tags/sequence-analysis, http://www.mygoblet.org/topic-tags/protein-sequence-analysis, http://www.mygoblet.org/topic-tags/multiple-sequence-alignment

Understanding Multiple Sequence Alignments - Lecture Handouts & Utopia Hands-On https://tess.elixir-europe.org/materials/understanding-multiple-sequence-alignments-lecture-handouts-utopia-hands-on This presentation aims to provide a basic understanding of the range of contexts in which protein sequence alignments are used and are useful, focusing on the importance of sequence similarities and differences, and what they tell us. Overall, the objective is to offer different perspectives and insights into the meaning of alignments, and to convey an understanding of the use of metaphor and its role in interpreting alignments. The talk is accompanied by a hands-on practical analysis using the Utopia sequence analysis suite. Sequence analysis http://www.mygoblet.org/topic-tags/sequence-analysis, http://www.mygoblet.org/topic-tags/protein-sequence-analysis, http://www.mygoblet.org/topic-tags/multiple-sequence-alignment Life Science Researchers Biomedical researchers Postgraduate students 2013-12-17 2017-10-09

This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. At the end of...

Keywords: http://www.mygoblet.org/topic-tags/unix, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/problem-based-learning

UNIX Fundamentals https://tess.elixir-europe.org/materials/unix-fundamentals-35adf82d-ae32-449d-9627-43b5d18da8cc This self-learning tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. At the end of the course, participants are expected to be able to: Have some understanding on UNIX systems Navigate through the UNIX filesystem Execute and understand some UNIX process commands Correctly set file permissions Perform basic file management Participants are encouraged to follow the tutorial sections sequentially. The tutorial content is sometimes an oversimplification of the Truth - yes, we know! Due to the diversity of computer systems, we will just assume that participants do have access to a terminal. For help, please contact your IT support - or a good friend!Authors are affiliated to the SIB Swiss Institute of Bioinformatics: Vassilios IoannidisWith some content provided by Frédéric Schütz, Volker Flegel and Heinz StockingerContent integration by Grégoire Rossier and Vassilios Ioannidis http://www.mygoblet.org/topic-tags/unix, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/problem-based-learning Bench biologists Clinical Scientists biocurators beginner bioinformaticians Graduate Students 2014-01-13 2017-10-09

Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of...

Keywords: http://www.mygoblet.org/topic-tags/blast, http://www.mygoblet.org/topic-tags/e-learning, http://www.mygoblet.org/topic-tags/multiple-sequence-alignment

BLAST and multiple sequence alignment (MSA) programs https://tess.elixir-europe.org/materials/blast-and-multiple-sequence-alignment-msa-programs Background The rapid identification of pathogens infecting livestock is essential to appropriately respond to the threat. The number and the variety of pathogen sequenced genomes have been growing more dramatically these recent years, because of the new sequencing technologies. This wealth of new data is very useful to the research field through the development of bioinformatics tools and databases that deal with large amount of sequences. Among them, BLAST (Basic Local Alignment Search Tool) and MSA () programs are very efficient for protein or nucleotide sequence similarity search. The present course introduces the main biological databases, alignment tool BLAST and Multiple sequence alignments (MSA) programs, and interpretation of results. Goal The ultimate aim is the better management of animal diseases by preparing laboratory technicians, veterinarians and molecular epidemiologists from diagnostic and research laboratories of developing FAO and IAEA member states, to be self-sufficient in the data analysis by interpreting the phylogenetic trees and their relationships. Target audience Researchers, Laboratory technicians, veterinarians, epidemiologists from diagnostic and research laboratories of member states of IAEA and FAO. The concepts are explained in generalized way to help all academicians, researchers, students from all countries working in the field of molecular genetics and epidemiology. AuthorsViral-zone, Swiss-Prot group at the SIB Swiss Institute of Bioinformatics   http://www.mygoblet.org/topic-tags/blast, http://www.mygoblet.org/topic-tags/e-learning, http://www.mygoblet.org/topic-tags/multiple-sequence-alignment Bench biologists Laboratory technicians Biologists Researchers Veterinarians 2014-04-28 2017-10-09

An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could...

Keywords: http://www.mygoblet.org/topic-tags/introduction-bioinformatics

Introduction to Bioinformatics https://tess.elixir-europe.org/materials/introduction-to-bioinformatics An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could be wrong, and what we can do to spot it. http://www.mygoblet.org/topic-tags/introduction-bioinformatics Bench biologists 2013-10-23 2017-10-09

Training Materials from the 2015 De Novo course run by TGAC

Keywords: http://www.mygoblet.org/topic-tags/de-novo, http://www.mygoblet.org/topic-tags/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 http://www.mygoblet.org/topic-tags/de-novo, http://www.mygoblet.org/topic-tags/de-novo-genome-assembly post-docs PhD students PhD postdoctoral researchers 2015-09-17 2017-10-09

Ensembl is a joint project between European Bioinformatics Institute (EMBL-EBI) and the Wellcome Trust Sanger Institute to provide a source of thorough, integrated annotation data across a variety of genomes. This one-day workshop not only offers participants the opportunity to glean background...

Ensembl Browser Workshop: Plants and Microbes https://tess.elixir-europe.org/materials/ensembl-browser-workshop-plants-and-microbes Ensembl is a joint project between European Bioinformatics Institute (EMBL-EBI) and the Wellcome Trust Sanger Institute to provide a source of thorough, integrated annotation data across a variety of genomes. This one-day workshop not only offers participants the opportunity to glean background information about the project and resulting resources, but also to gain vital hands-on experience in the use of the Ensembl genome browser. This workshop is themed according to the target audience and is aimed at wetlab researchers, as well as being customisable to include an introduction for complete novices up to advanced usage for the more frequent users. 2016-04-14 2017-10-09

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: http://www.mygoblet.org/topic-tags/python, http://www.mygoblet.org/topic-tags/python-biologists, http://www.mygoblet.org/topic-tags/biopython

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. http://www.mygoblet.org/topic-tags/python, http://www.mygoblet.org/topic-tags/python-biologists, http://www.mygoblet.org/topic-tags/biopython post-docs PhD 2015-07-14 2017-10-09

This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins. It will use practical examples in the popular open-source tool Cytoscape and the...

Keywords: http://www.mygoblet.org/topic-tags/cytoscape

Network Analysis with Cytoscape and PSICQUIC https://tess.elixir-europe.org/materials/network-analysis-with-cytoscape-and-psicquic This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins. It will use practical examples in the popular open-source tool Cytoscape and the PSICQUIC client to access several protein interaction repositories at the same time to integrate protein data from different sources. Data from external sources will then be incorporated using different Cytoscape apps to perform clustering and GO enrichment analysis over our newly created networks. http://www.mygoblet.org/topic-tags/cytoscape Biologists, Genomicists, Computer Scientists 2016-04-14 2017-10-09

Presention

Keywords: http://www.mygoblet.org/topic-tags/goblet

GOBLET Training portal https://tess.elixir-europe.org/materials/goblet-training-portal Presention http://www.mygoblet.org/topic-tags/goblet Training GOBLET 2015-07-01 2017-10-09

The first part of this course introduces the UNIX command line on a Linux or Mac. The second part provides a basic introduction to string searches and scripting with AWK and BASH.

Keywords: http://www.mygoblet.org/topic-tags/unix, http://www.mygoblet.org/topic-tags/bash, http://www.mygoblet.org/topic-tags/awk

UNIX command line and scripting https://tess.elixir-europe.org/materials/unix-command-line-and-scripting The first part of this course introduces the UNIX command line on a Linux or Mac. The second part provides a basic introduction to string searches and scripting with AWK and BASH. http://www.mygoblet.org/topic-tags/unix, http://www.mygoblet.org/topic-tags/bash, http://www.mygoblet.org/topic-tags/awk awk unix bash 2016-04-21 2017-10-09

Using quantiles to set a gate based on a negative control Using median and standard deviation to set a gate based on a negative control Exploring rangeGate: an automated way to set a 1D gate for each sample individually Recording proportions of cells in subpopulations of interest by...

Keywords: http://www.mygoblet.org/topic-tags/1d-dynamic-gating, http://www.mygoblet.org/topic-tags/flow-cytometry-data

Flow Cytometry 2013 Module 5 - 1D Dynamic gating https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-5-1d-dynamic-gating Using quantiles to set a gate based on a negative control Using median and standard deviation to set a gate based on a negative control Exploring rangeGate: an automated way to set a 1D gate for each sample individually Recording proportions of cells in subpopulations of interest by creating a spreadsheet file Recording a visual record of the gating results by creating JPEG image files http://www.mygoblet.org/topic-tags/1d-dynamic-gating, http://www.mygoblet.org/topic-tags/flow-cytometry-data Flow cytometry data 1D Dynamic gating 2013-06-26 2017-10-09

Problem Based Learning (PBL) is an innovative approach to learning that we used to deliver the Clinical Bioinformatics I module of the new MSc in Clinical Bioinformatics. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of...

Keywords: http://www.mygoblet.org/topic-tags/teaching-aid, http://www.mygoblet.org/topic-tags/problem-based-learning, http://www.mygoblet.org/topic-tags/train-trainer

Problem Based Learning Guide https://tess.elixir-europe.org/materials/problem-based-learning-guide Problem Based Learning (PBL) is an innovative approach to learning that we used to deliver the Clinical Bioinformatics I module of the new MSc in Clinical Bioinformatics. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of work placement based training interspersed with academic teaching which is delivered by Nowgen/NGRL and the University of Manchester in the UK.  This booklet is a guide for lecturers to design and deliver material using the PBL approach. It has been a successful tool for the delivery of our course and it may provide useful for others involved in course design and delivery http://www.mygoblet.org/topic-tags/teaching-aid, http://www.mygoblet.org/topic-tags/problem-based-learning, http://www.mygoblet.org/topic-tags/train-trainer Trainers Lecturers 2014-01-12 2017-10-09

How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate Visualizing the proportions using a density...

Keywords: http://www.mygoblet.org/topic-tags/1d-static-gating, http://www.mygoblet.org/topic-tags/flow-cytometry-data

Flow Cytometry 2013 Module 4 - 1D Static gating https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-4-1d-static-gating How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate Visualizing the proportions using a density plot, histogram, bean/violin plot Automating a sequential gating strategy in R to obtain cell proportions for a desired phenotype http://www.mygoblet.org/topic-tags/1d-static-gating, http://www.mygoblet.org/topic-tags/flow-cytometry-data 1D Static gating Flow cytometry data 2013-06-26 2017-10-09

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

Keywords: http://www.mygoblet.org/topic-tags/network-visualization, http://www.mygoblet.org/topic-tags/cytoscape

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 http://www.mygoblet.org/topic-tags/network-visualization, http://www.mygoblet.org/topic-tags/cytoscape Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists 2014-06-26 2017-10-09

This is a lecture on linear motifs and phophorylation sites (P-sites). Some materials from other lectures are reused. The lecture is basically about computational approaches to encode, predict, analyse, and use functional motifs and P-sites. Here you can find: A definition of linear motifs and...

Keywords: http://www.mygoblet.org/topic-tags/bioinformatics

Linear Motifs and Phosphorylation Sites https://tess.elixir-europe.org/materials/linear-motifs-and-phosphorylation-sites This is a lecture on linear motifs and phophorylation sites (P-sites). Some materials from other lectures are reused. The lecture is basically about computational approaches to encode, predict, analyse, and use functional motifs and P-sites. Here you can find: A definition of linear motifs and P-sites Computational methods to identify them How you can represent and use them Resources and tools to deal with them http://www.mygoblet.org/topic-tags/bioinformatics biocurators bioinformaticians Biologists 2013-07-16 2017-10-09

This  course provides an introduction to Unix, Perl and Python. In addition to lecture material (in the form of slides), there are exercises, answers to the exercises and pointers to addition resources.

Keywords: http://www.mygoblet.org/topic-tags/unix, http://www.mygoblet.org/topic-tags/python, http://www.mygoblet.org/topic-tags/perl

An Introduction to Unix, Perl and Python https://tess.elixir-europe.org/materials/an-introduction-to-unix-perl-and-python This  course provides an introduction to Unix, Perl and Python. In addition to lecture material (in the form of slides), there are exercises, answers to the exercises and pointers to addition resources. http://www.mygoblet.org/topic-tags/unix, http://www.mygoblet.org/topic-tags/python, http://www.mygoblet.org/topic-tags/perl Bench biologists 2013-07-28 2017-10-09

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    

Scientific topics: RNA-Seq alignment

Keywords: http://www.mygoblet.org/topic-tags/data-visualization, http://www.mygoblet.org/topic-tags/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     RNA-Seq alignment http://www.mygoblet.org/topic-tags/data-visualization, http://www.mygoblet.org/topic-tags/rna-seq-alignment Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists 2014-06-27 2017-10-09

Functional association networks and gene function prediction Homology based prediction Guilt-by-association: GeneMANIA

Keywords: http://www.mygoblet.org/topic-tags/functional-association-networks, http://www.mygoblet.org/topic-tags/gene-function-prediction, http://www.mygoblet.org/topic-tags/genemania

Pathway and Network Analysis 2014 Module 6 - Gene Function Prediction https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-6-gene-function-prediction Functional association networks and gene function prediction Homology based prediction Guilt-by-association: GeneMANIA http://www.mygoblet.org/topic-tags/functional-association-networks, http://www.mygoblet.org/topic-tags/gene-function-prediction, http://www.mygoblet.org/topic-tags/genemania Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists 2014-06-26 2017-10-09

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: http://www.mygoblet.org/topic-tags/transript-expression, http://www.mygoblet.org/topic-tags/differential-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.)   http://www.mygoblet.org/topic-tags/transript-expression, http://www.mygoblet.org/topic-tags/differential-expression Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists 2014-06-27 2017-10-09

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: http://www.mygoblet.org/topic-tags/disease-causing-mutation, http://www.mygoblet.org/topic-tags/predicting-effect-mutation-structure, http://www.mygoblet.org/topic-tags/predicting-effect-mutation-protein-function

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. http://www.mygoblet.org/topic-tags/disease-causing-mutation, http://www.mygoblet.org/topic-tags/predicting-effect-mutation-structure, http://www.mygoblet.org/topic-tags/predicting-effect-mutation-protein-function predicting effect of mutation on protein function Disease causing mutation Predicting effect of mutation on structure 2014-07-23 2017-10-09

Link to the GitHub repo containing all the publicly available files from the 2015 Metagenomics course held at TGAC in November 2015

Scientific topics: Metagenomics

Keywords: http://www.mygoblet.org/topic-tags/metagenomics

Metagenomics 2015 https://tess.elixir-europe.org/materials/metagenomics-2015 Link to the GitHub repo containing all the publicly available files from the 2015 Metagenomics course held at TGAC in November 2015 Metagenomics http://www.mygoblet.org/topic-tags/metagenomics post-docs PhD 2015-11-23 2017-10-09

Introduction to BioJS a standard for visualisation of biological data in JavaScript

Keywords: http://www.mygoblet.org/topic-tags/javascript, http://www.mygoblet.org/topic-tags/standards, http://www.mygoblet.org/topic-tags/biojs, http://www.mygoblet.org/topic-tags/software

BioJS https://tess.elixir-europe.org/materials/biojs-1ff5ad84-3b06-4997-bba6-e18a4dcf32c0 Introduction to BioJS a standard for visualisation of biological data in JavaScript http://www.mygoblet.org/topic-tags/javascript, http://www.mygoblet.org/topic-tags/standards, http://www.mygoblet.org/topic-tags/biojs, http://www.mygoblet.org/topic-tags/software software developers, bioinformaticians 2014-02-27 2017-10-09

Introduction to Linux basic command line

Scientific topics: Computer science

Keywords: http://www.mygoblet.org/topic-tags/linux-basics

Introduction to Linux Command Line https://tess.elixir-europe.org/materials/introduction-to-linux-command-line Introduction to Linux basic command line Computer science http://www.mygoblet.org/topic-tags/linux-basics Computer science Linux basics 2015-10-28 2017-10-09

Introductory lecture to the Unix/Linux command-line Description of the computer shell and the command-line interface Differences between graphical and command-line interfaces The most commond Unix/Linux commands are provided    

Keywords: http://www.mygoblet.org/topic-tags/unixlinux, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/bioinformatics

Introduction to Unix https://tess.elixir-europe.org/materials/introduction-to-unix Introductory lecture to the Unix/Linux command-line Description of the computer shell and the command-line interface Differences between graphical and command-line interfaces The most commond Unix/Linux commands are provided     http://www.mygoblet.org/topic-tags/unixlinux, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/bioinformatics Anyone wants to start using the Unix/Linux OS 2013-07-04 2017-10-09

Preprocessing Removing margin events Data transformation: log vs. biexponential Data normalization Quality Assurance Overview of quality assurance concepts: total raw/viable cell count, margin event count, outlier detection based on density of common...

Keywords: http://www.mygoblet.org/topic-tags/preprocessing, http://www.mygoblet.org/topic-tags/quality-assurance, http://www.mygoblet.org/topic-tags/flow-cytometry-data

Flow Cytometry 2013 Module 3 - Preprocessing and Quality Assurance of FCM Data https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-3-preprocessing-and-quality-assurance-of-fcm-data Preprocessing Removing margin events Data transformation: log vs. biexponential Data normalization Quality Assurance Overview of quality assurance concepts: total raw/viable cell count, margin event count, outlier detection based on density of common parameters Building quality assurance objects using flowQ and generating summary HTML reports http://www.mygoblet.org/topic-tags/preprocessing, http://www.mygoblet.org/topic-tags/quality-assurance, http://www.mygoblet.org/topic-tags/flow-cytometry-data Quality Assurance Flow cytometry data Preprocessing 2013-06-26 2017-10-09

A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...

Keywords: http://www.mygoblet.org/topic-tags/consensus-trees, http://www.mygoblet.org/topic-tags/phylogenetics, http://www.mygoblet.org/topic-tags/bootstrap, http://www.mygoblet.org/topic-tags/phylogenetic-splits

Summarising sets of phylogenies https://tess.elixir-europe.org/materials/summarising-sets-of-phylogenies A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes examples of applications of these tools, along with introducing ideas of tree topology and some terminology associated with it. Designed for remote training. http://www.mygoblet.org/topic-tags/consensus-trees, http://www.mygoblet.org/topic-tags/phylogenetics, http://www.mygoblet.org/topic-tags/bootstrap, http://www.mygoblet.org/topic-tags/phylogenetic-splits Bench biologists 2013-10-23 2017-10-09

Lecture on how tools to be demonstrated have been used in research and clinical applications Description of data and underlying biological problem Summary of a typical work flow to be covered in the workshop: transformation, margin event removal, quality assurance, gating, recording and...

Keywords: http://www.mygoblet.org/topic-tags/review-r, http://www.mygoblet.org/topic-tags/introduction-flow-cytometry

Flow Cytometry 2013 Module 1 - Introduction to Flow Cytometry Analysis in R https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-1-introduction-to-flow-cytometry-analysis-in-r Lecture on how tools to be demonstrated have been used in research and clinical applications Description of data and underlying biological problem Summary of a typical work flow to be covered in the workshop: transformation, margin event removal, quality assurance, gating, recording and visualizing results Short R refresher of tools to be used Variable assignment, simple arithmetic Vectors, matrices, lists, names Functions, apply, sapply, lapply Simple plotting functions http://www.mygoblet.org/topic-tags/review-r, http://www.mygoblet.org/topic-tags/introduction-flow-cytometry Review of R Introduction to flow cytometry 2013-06-25 2017-10-09

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: http://www.mygoblet.org/topic-tags/alternative-expression, http://www.mygoblet.org/topic-tags/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 http://www.mygoblet.org/topic-tags/alternative-expression, http://www.mygoblet.org/topic-tags/transcript-isoforms Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists 2014-06-27 2017-10-09
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