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.

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Next generation sequencing (NGS) has become a commodity. With the commercialization of various affordable desktop sequencers, NGS will be of reach by more traditional wet-lab biologists . As seen in recent years, genome-wide scale computational analysis is increasingly being used as a backbone to...

Scientific topics: Sequencing

Keywords: http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/next-generation-sequencing

Next Generation Sequencing (NGS) wikibook https://tess.elixir-europe.org/materials/next-generation-sequencing-ngs-wikibook Next generation sequencing (NGS) has become a commodity. With the commercialization of various affordable desktop sequencers, NGS will be of reach by more traditional wet-lab biologists . As seen in recent years, genome-wide scale computational analysis is increasingly being used as a backbone to foster novel discovery in biomedical research. However, as the quantities of sequence data increase exponentially, the analysis bottle-neck is yet to be solved. The current sources for NGS informatics are extremely fragmented. A novice could read review articles in various journals, follow discussion threads on forums such as Biostar[1] or SEQanswers [2], or sign up for courses organized by various institutes. Finding a centralized synthesis is much more difficult. Books are available, but the development of the field is so fast that book chapters risk being obsoleted by the time they are even printed. Moreover, cost for a handful of authors to continually update their text would presumably take up a lot of their schedule. Drawing from the obvious goodwill and community spirit displayed on discussion forums, and exploiting the collaborative tools made available by the Wikimedia foundation, we propose to initiate the editing of a collaborative WikiBook on NGS. Our plan is to collect a sufficient amount of text that people will be incentivized to contribute to it, essentially providing the same information as a forum but in a tidier form. Ultimately, our goal is to create a collective lab book that explains the key concepts and describes best practices in NGS. Parnell LD, Lindenbaum P, Shameer K et al. BioStar: an online question & answer resource for the bioinformatics community, PLoS Comput Biol 2011;7:e1002216. Li JW, Schmieder R, Ward RM et al. SEQanswers: an open access community for collaboratively decoding genomes, Bioinformatics 2012;28:1272-1273 Join this initiative now and contribute to further expand and improve the contents and case studies in the NGS wikibook! Read about this initiative and the nine rules for NGS data analysis here: The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability Sequencing http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/next-generation-sequencing computational scientists Biologists bioinformaticians 2013-07-15 2017-08-22

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: http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/mooc, http://www.mygoblet.org/topic-tags/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. http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/mooc, http://www.mygoblet.org/topic-tags/online-learning General Interest 2014-08-14 2017-08-22

This course was created as part of the SeqAhead project and contains both powerpoint presentations and course materials that teach students how to set up an Amazon EC2 virtual machine, connect to it, download some Illumina data from  the short read archive (SRA), assess the quality of the data...

Keywords: http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/next-generation-sequencing, http://www.mygoblet.org/topic-tags/next-generation-sequencing-data-analysis, http://www.mygoblet.org/topic-tags/cloud, http://www.mygoblet.org/topic-tags/ngs-bioinformatics, http://www.mygoblet.org/topic-tags/qc-ngs-data

Quality Control of Illumina Sequencing data in the cloud https://tess.elixir-europe.org/materials/quality-control-of-illumina-sequencing-data-in-the-cloud This course was created as part of the SeqAhead project and contains both powerpoint presentations and course materials that teach students how to set up an Amazon EC2 virtual machine, connect to it, download some Illumina data from  the short read archive (SRA), assess the quality of the data and learn to trim both bad quality bases and adapter sequences http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/next-generation-sequencing, http://www.mygoblet.org/topic-tags/next-generation-sequencing-data-analysis, http://www.mygoblet.org/topic-tags/cloud, http://www.mygoblet.org/topic-tags/ngs-bioinformatics, http://www.mygoblet.org/topic-tags/qc-ngs-data Beginners 2014-01-13 2017-08-22

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 2017-08-22

Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project K-means explained flowMeans: smart k-means for FCM data flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering Biomarker discovery: flowType and RchyOptimyx, advanced tools used...

Keywords: http://www.mygoblet.org/topic-tags/biomarker-discovery, http://www.mygoblet.org/topic-tags/flow-cytometry-data, http://www.mygoblet.org/topic-tags/flowcap

Flow Cytometry 2013 Module 6 - Clustering and Additional FCM Tools https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-6-clustering-and-additional-fcm-tools Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project K-means explained flowMeans: smart k-means for FCM data flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering Biomarker discovery: flowType and RchyOptimyx, advanced tools used to explore novel phenotypes and find ones which correlate with a clinical diagnosis More R: Bioconductor.org, an open source software project full of bioinformatics packages created for R, including sample work flows GenePattern.org: web-interface for running analysis modules such as sample deidentication, extracting specic keywords, quality control, normalization, clustering, classification FlowRepository.org: online FCM data repository to share public or private data sets with collaborators while providing detailed descriptions of the experiment set up and each FCS file http://www.mygoblet.org/topic-tags/biomarker-discovery, http://www.mygoblet.org/topic-tags/flow-cytometry-data, http://www.mygoblet.org/topic-tags/flowcap Flow cytometry data FlowCAP Biomarker discovery 2013-06-26 2017-08-22

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 2017-08-22

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 2017-08-22

This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose. 

Keywords: http://www.mygoblet.org/topic-tags/integrated-diagnostic-tools, http://www.mygoblet.org/topic-tags/protein-family-characterisation, http://www.mygoblet.org/topic-tags/protein-sequence-analysis

InterPro: An introduction https://tess.elixir-europe.org/materials/interpro-an-introduction This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose.  http://www.mygoblet.org/topic-tags/integrated-diagnostic-tools, http://www.mygoblet.org/topic-tags/protein-family-characterisation, http://www.mygoblet.org/topic-tags/protein-sequence-analysis postgrad beginner bioinformaticians biocurators postdoc 2013-07-12 2017-08-22

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 bioinformaticians Biologists biocurators 2013-07-16 2017-08-22

This document is the trainee exercise booklet for a 3 day hands-on Next Generation Sequencing workshop developed by Bioplatforms Australia, CSIRO and EMBL-EBI.  This workshop is aimed at bench biologists, PhD students or early career postdoctoral researchers or those new to the analysis of NGS...

Scientific topics: Bioinformatics, Data quality management, Sequence assembly, Topic, Sequencing

Keywords: NGS, ChIPSeq, De novo genome assembly, RNASeq

3-day hands-on NGS workshop https://tess.elixir-europe.org/materials/3-day-hands-on-ngs-workshop This document is the trainee exercise booklet for a 3 day hands-on Next Generation Sequencing workshop developed by Bioplatforms Australia, CSIRO and EMBL-EBI.  This workshop is aimed at bench biologists, PhD students or early career postdoctoral researchers or those new to the analysis of NGS data and assumes no prior knowledge of bioinformatics. This course covers the following topics: data quality control, read alignment, ChIPSeq, RNASeq and de novo assembly. The workshop starts with the Intro to the shell material from Software Carpentry (http://software-carpentry.org/v4/shell/index.html).  Introductory lectures on each topic are presented before trainees move on that topic. The workshop has been delivered a number of times in different cities in Australia to date, in a roadshow style, and is designed to run on virtual machines on the Australian research cloud. Trainees then use NoMachine NX client to provide a remote desktop like connection to their own dedicated VM for the duration of of the workshop.  Various contributors made this workshop possible and they are credited in the introduction to each section. Bioinformatics Data quality management Sequence assembly Topic Sequencing NGS, ChIPSeq, De novo genome assembly, RNASeq Bench biologists postdocs PhD students Life Science Researchers 2014-01-17 2017-08-22

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/transcript-isoforms, http://www.mygoblet.org/topic-tags/alternative-expression

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/transcript-isoforms, http://www.mygoblet.org/topic-tags/alternative-expression Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows Graduate Students 2014-06-27 2017-08-22

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: http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/online-learning, http://www.mygoblet.org/topic-tags/gaming

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 http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/online-learning, http://www.mygoblet.org/topic-tags/gaming General Interest 2014-08-14 2017-08-22

Gene list analysis overview: Workflow of concepts and tools from gene list to pathway analysis Where do gene lists come from? Working with gene function information

Keywords: http://www.mygoblet.org/topic-tags/gene-ontology, http://www.mygoblet.org/topic-tags/gene-lists

Pathway and Network Analysis 2014 Module 1 - Introduction to Gene Lists https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-1-introduction-to-gene-lists Gene list analysis overview: Workflow of concepts and tools from gene list to pathway analysis Where do gene lists come from? Working with gene function information http://www.mygoblet.org/topic-tags/gene-ontology, http://www.mygoblet.org/topic-tags/gene-lists Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows Graduate Students 2014-06-26 2017-08-22

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 2017-08-22

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: Database management, Bioinformatics, Sequence analysis, Plants

Keywords: http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/ngs-bioinformatics, http://www.mygoblet.org/topic-tags/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 Database management Bioinformatics Sequence analysis Plants http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/ngs-bioinformatics, http://www.mygoblet.org/topic-tags/plants-bioinformatics plant researchers PhD students post-docs 2015-06-22 2017-08-22

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

Scientific topics: Molecular interactions, pathways and networks

Keywords: http://www.mygoblet.org/topic-tags/kegg, http://www.mygoblet.org/topic-tags/pathway-analysis, http://www.mygoblet.org/topic-tags/biological-networks, http://www.mygoblet.org/topic-tags/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 Molecular interactions, pathways and networks http://www.mygoblet.org/topic-tags/kegg, http://www.mygoblet.org/topic-tags/pathway-analysis, http://www.mygoblet.org/topic-tags/biological-networks, http://www.mygoblet.org/topic-tags/reactome Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows Graduate Students 2014-06-26 2017-08-22

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: http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/protein-structure, http://www.mygoblet.org/topic-tags/genome-browsing, http://www.mygoblet.org/topic-tags/genomics

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.   http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/protein-structure, http://www.mygoblet.org/topic-tags/genome-browsing, http://www.mygoblet.org/topic-tags/genomics Life Science Researchers Master students 2014-06-27 2017-08-22

Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of...

Keywords: http://www.mygoblet.org/topic-tags/blast, http://www.mygoblet.org/topic-tags/similarity-searching, http://www.mygoblet.org/topic-tags/hmmer, http://www.mygoblet.org/topic-tags/multiple-sequence-alignment, http://www.mygoblet.org/topic-tags/interpro

Similarity searching, multiple sequence alignment and protein families - undergraduate lab https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of the exercises make use of public databases they need to be checked and in some cases updated every time the lab is run. The lab is meant to be easily assessed using an online quiz (I use moodle). I provides a hands on introduction to NCBI BLAST, Interproscan, Clustal, MUSCLE and T-COFFEE, and HMMER.  http://www.mygoblet.org/topic-tags/blast, http://www.mygoblet.org/topic-tags/similarity-searching, http://www.mygoblet.org/topic-tags/hmmer, http://www.mygoblet.org/topic-tags/multiple-sequence-alignment, http://www.mygoblet.org/topic-tags/interpro biology and bioinformatics sophomore undergraduates 2013-11-12 2017-08-22

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/rna-seq-alignment, http://www.mygoblet.org/topic-tags/data-visualization

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/rna-seq-alignment, http://www.mygoblet.org/topic-tags/data-visualization Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows Graduate Students 2014-06-27 2017-08-22

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

Keywords: http://www.mygoblet.org/topic-tags/igv, http://www.mygoblet.org/topic-tags/introduction-rna-seq-analysis, http://www.mygoblet.org/topic-tags/experimental-design-rna-seq

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   http://www.mygoblet.org/topic-tags/igv, http://www.mygoblet.org/topic-tags/introduction-rna-seq-analysis, http://www.mygoblet.org/topic-tags/experimental-design-rna-seq Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows Graduate Students 2014-06-27 2017-08-22

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

Keywords: http://www.mygoblet.org/topic-tags/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. http://www.mygoblet.org/topic-tags/goblet-survey-life-scientists GOBLET survey of life scientists 2014-07-07 2017-08-22

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

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/bioinformatics, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/unixlinux Anyone wants to start using the Unix/Linux OS 2013-07-04 2017-08-22

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...

Scientific topics: Transcription factors and regulatory sites

Keywords: http://www.mygoblet.org/topic-tags/farm-animals, http://www.mygoblet.org/topic-tags/transcription-factors, http://www.mygoblet.org/topic-tags/qtl, http://www.mygoblet.org/topic-tags/allbio, http://www.mygoblet.org/topic-tags/rnaseq

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. Transcription factors and regulatory sites http://www.mygoblet.org/topic-tags/farm-animals, http://www.mygoblet.org/topic-tags/transcription-factors, http://www.mygoblet.org/topic-tags/qtl, http://www.mygoblet.org/topic-tags/allbio, http://www.mygoblet.org/topic-tags/rnaseq bioinformaticians Biologists geneticists 2014-11-17 2017-08-22

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: http://www.mygoblet.org/topic-tags/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 http://www.mygoblet.org/topic-tags/metagenomics postdocs PhD 2015-06-25 2017-08-22

The purpose of this course is to teach students the fundamental concepts underlying the analysis of proteins using mass spectrometry.

Keywords: http://www.mygoblet.org/topic-tags/mass-spectrometry, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/identification

Bioinformatics for MS analysis https://tess.elixir-europe.org/materials/bioinformatics-for-ms-analysis The purpose of this course is to teach students the fundamental concepts underlying the analysis of proteins using mass spectrometry. http://www.mygoblet.org/topic-tags/mass-spectrometry, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/identification identification bioinformatics mass spectrometry 2013-07-05 2017-08-22

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: http://www.mygoblet.org/topic-tags/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. http://www.mygoblet.org/topic-tags/de-novo PhD post-docs 2015-07-14 2017-08-22

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 PhD post-docs 2015-11-23 2017-08-22

Five PowerPoint presentations and an Excel worksheet for a Train the Trainer course developed by Chris Taylor (with contributions from Emily Angiolini, Jamie Edwards and Paul Yorke) while at the Earlham Institute working for the National Institutes of Science's Bioinformatics and Biomathematics...

Keywords: http://www.mygoblet.org/topic-tags/trainer-skills, http://www.mygoblet.org/topic-tags/pedagogy, http://www.mygoblet.org/topic-tags/course-development

Train the Trainer course materials https://tess.elixir-europe.org/materials/train-the-trainer-course-materials Five PowerPoint presentations and an Excel worksheet for a Train the Trainer course developed by Chris Taylor (with contributions from Emily Angiolini, Jamie Edwards and Paul Yorke) while at the Earlham Institute working for the National Institutes of Science's Bioinformatics and Biomathematics Training hub. The five slide decks cover pedagogical theory, trainer skills and course development. The Excel workbook implements a version of Honey and Mumford's Learning Styles Questionnaire. http://www.mygoblet.org/topic-tags/trainer-skills, http://www.mygoblet.org/topic-tags/pedagogy, http://www.mygoblet.org/topic-tags/course-development Prospective and existing trainers 2017-06-30 2017-08-22

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

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

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/standards, http://www.mygoblet.org/topic-tags/software, http://www.mygoblet.org/topic-tags/javascript, http://www.mygoblet.org/topic-tags/biojs software developers, bioinformaticians 2014-02-27 2017-08-22

Short history of the emergence of bioinformatics as a discipline in Europe, following the near simultaneous advent of high-throughput sequencing techniques and the World Wide Web, which made dissemination of the rapidly accumulating sequence data both simple and feasible on a large scale.

Keywords: http://www.mygoblet.org/topic-tags/bioinformatics-history, http://www.mygoblet.org/topic-tags/biomolecular-sequences, http://www.mygoblet.org/topic-tags/european-perspective, http://www.mygoblet.org/topic-tags/biomolecular-databases

Concepts, historical milestones & the central place of bioinformatics in modern biology: a European perspective https://tess.elixir-europe.org/materials/concepts-historical-milestones-the-central-place-of-bioinformatics-in-modern-biology-a-european-perspective Short history of the emergence of bioinformatics as a discipline in Europe, following the near simultaneous advent of high-throughput sequencing techniques and the World Wide Web, which made dissemination of the rapidly accumulating sequence data both simple and feasible on a large scale. http://www.mygoblet.org/topic-tags/bioinformatics-history, http://www.mygoblet.org/topic-tags/biomolecular-sequences, http://www.mygoblet.org/topic-tags/european-perspective, http://www.mygoblet.org/topic-tags/biomolecular-databases European perspective biomolecular sequences biomolecular databases bioinformatics history 2013-06-25 2017-08-22
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