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.

Showing 30 materials out of 95. View all results.

BioJS is a library of graphical components easy to reuse to represent biological information

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

BioJS https://tess.elixir-europe.org/materials/biojs BioJS is a library of graphical components easy to reuse to represent biological information http://www.mygoblet.org/topic-tags/javascript, http://www.mygoblet.org/topic-tags/bioinformatics web developers bioinformaticians 2013-07-11 2017-06-23

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

Keywords: http://www.mygoblet.org/topic-tags/biojs, http://www.mygoblet.org/topic-tags/standards, http://www.mygoblet.org/topic-tags/javascript, 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/biojs, http://www.mygoblet.org/topic-tags/standards, http://www.mygoblet.org/topic-tags/javascript, http://www.mygoblet.org/topic-tags/software software developers, bioinformaticians 2014-02-27 2017-06-23

This tutorial on Bioinformatics for Mass spectrometry analysis was part of a full series of tutorials that I have organised in 2009 while sitting in the Educational Committee of the European Proteomics Association (EuPA). Some information on bioinformatics tools would need to be verified, but the...

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

Bioinformatics for Mass spectrometry analysis https://tess.elixir-europe.org/materials/bioinformatics-for-mass-spectrometry-analysis This tutorial on Bioinformatics for Mass spectrometry analysis was part of a full series of tutorials that I have organised in 2009 while sitting in the Educational Committee of the European Proteomics Association (EuPA). Some information on bioinformatics tools would need to be verified, but the core of slides is still up to date. It introduces the basic ideas behind mass spectrometry and bioinformatics for protein identification from mass spectrometry data. http://www.mygoblet.org/topic-tags/protein-identification, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/mass-spectrometry bioinformaticians Post-Doctoral Fellows Technicians Bench biologists master PhD students 2013-10-30 2017-06-23

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 2017-06-23

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

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/next-generation-sequencing, http://www.mygoblet.org/topic-tags/qc-ngs-data, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/next-generation-sequencing-data-analysis, http://www.mygoblet.org/topic-tags/ngs-bioinformatics, http://www.mygoblet.org/topic-tags/cloud Beginners 2014-01-13 2017-06-23

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 2017-06-23

Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further...

Keywords: http://www.mygoblet.org/topic-tags/animal-pathogens, http://www.mygoblet.org/topic-tags/e-learning, http://www.mygoblet.org/topic-tags/phylogenetics

Phylogenetics of animal viral pathogens https://tess.elixir-europe.org/materials/phylogenetics-of-animal-viral-pathogens Background The vast diversity of the pathogens affecting livestock demands a very specific diagnostic procedure in identification and characterization of each pathogen. In this context, the enormous amount of sequence and genotype data is being generated on animal pathogens, which is further useful in understanding their pathogenicity and molecular epidemiology. The usage of this data in developing efficient molecular diagnostic tools needs basic understanding of the phylogenetic analysis. Phylogenetic classification, construction of trees, interpretation unveils the geographical distribution and migration of pathogens which helps in better management of animal diseases. The present course is designed with introduction to phylogenetics, tools, building and interpreting trees and finally its application to veterinary diagnostics. Though the course is driven in veterinary aspects, the same implicates to the human and plant pathogen study. 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 SIB Swiss Institute of Bioinformatics   http://www.mygoblet.org/topic-tags/animal-pathogens, http://www.mygoblet.org/topic-tags/e-learning, http://www.mygoblet.org/topic-tags/phylogenetics Biologists Laboratory technicians Researchers Veterinarians Bench biologists 2014-04-28 2017-06-23

I present the points of view, the challenges and advantages of developing training materials through the cloud.

Keywords: http://www.mygoblet.org/topic-tags/cloud-computing, http://www.mygoblet.org/topic-tags/training, http://www.mygoblet.org/topic-tags/advanced-bioinformatics-training

Training Bioinformatics in the Cloud https://tess.elixir-europe.org/materials/training-bioinformatics-in-the-cloud I present the points of view, the challenges and advantages of developing training materials through the cloud. http://www.mygoblet.org/topic-tags/cloud-computing, http://www.mygoblet.org/topic-tags/training, http://www.mygoblet.org/topic-tags/advanced-bioinformatics-training Bench biologists beginner bioinformaticians 2014-05-20 2017-06-23

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/protein-structure, http://www.mygoblet.org/topic-tags/bioinformatics, 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/protein-structure, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/genome-browsing, http://www.mygoblet.org/topic-tags/genomics Life Science Researchers Master students 2014-06-27 2017-06-23

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 PhD postdocs 2015-06-25 2017-06-23

This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis. Materials have been annotated following the standards and guidelines proposed at the “Best practices...

Scientific topics: Bioinformatics, Data architecture, analysis and design

Keywords: http://www.mygoblet.org/topic-tags/rna-seq-chip-seq-anayses, http://www.mygoblet.org/topic-tags/variant-calling, http://www.mygoblet.org/topic-tags/high-throughput-sequencing-analysis

High-throughput sequencing training materials repository https://tess.elixir-europe.org/materials/high-throughput-sequencing-training-materials-repository This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis. Materials have been annotated following the standards and guidelines proposed at the “Best practices in next-generation sequencing data analysis” workshop which took place at the University of Cambridge, UK, on 13-14 January 2015. Following this workshop, a Git repository has been set up for sharing annotated materials. This repository uses Git, hence it is decentralized and self-managed by the community and can be forked/built-upon by all users. Bioinformatics Data architecture, analysis and design http://www.mygoblet.org/topic-tags/rna-seq-chip-seq-anayses, http://www.mygoblet.org/topic-tags/variant-calling, http://www.mygoblet.org/topic-tags/high-throughput-sequencing-analysis Life Science Researchers Trainers post-docs beginner bioinformaticians PhD students 2015-12-17 2017-06-23

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

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/identification, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/mass-spectrometry identification bioinformatics mass spectrometry 2013-07-05 2017-06-23

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...

Scientific topics: Database management

Keywords: http://www.mygoblet.org/topic-tags/genome-sequence-analysis, http://www.mygoblet.org/topic-tags/biological-databases, http://www.mygoblet.org/topic-tags/plants, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/allbio, http://www.mygoblet.org/topic-tags/phytopathogens, http://www.mygoblet.org/topic-tags/pathogenesis

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. Database management http://www.mygoblet.org/topic-tags/genome-sequence-analysis, http://www.mygoblet.org/topic-tags/biological-databases, http://www.mygoblet.org/topic-tags/plants, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/allbio, http://www.mygoblet.org/topic-tags/phytopathogens, http://www.mygoblet.org/topic-tags/pathogenesis early stage phytopathogen researchers beginner bioinformaticians 2014-09-11 2017-06-23

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

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/perl, http://www.mygoblet.org/topic-tags/python Bench biologists 2013-07-28 2017-06-23

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: http://www.mygoblet.org/topic-tags/variant-detection, http://www.mygoblet.org/topic-tags/introduction-bioinformatics, http://www.mygoblet.org/topic-tags/blast, http://www.mygoblet.org/topic-tags/protein-structure-visualisation, http://www.mygoblet.org/topic-tags/genome-browsing

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 http://www.mygoblet.org/topic-tags/variant-detection, http://www.mygoblet.org/topic-tags/introduction-bioinformatics, http://www.mygoblet.org/topic-tags/blast, http://www.mygoblet.org/topic-tags/protein-structure-visualisation, http://www.mygoblet.org/topic-tags/genome-browsing high school 2014-11-10 2017-06-23

This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of...

Scientific topics: Bioinformatics, Data architecture, analysis and design, RNA, Sequencing

Keywords: http://www.mygoblet.org/topic-tags/differential-expression, http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/rna-seq

RNA-seq data analysis: from raw reads to differentially expressed genes https://tess.elixir-europe.org/materials/rna-seq-data-analysis-from-raw-reads-to-differentially-expressed-genes This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of 10-30 minute lectures intertwined with hands-on exercises, and it can be accomplished in a day. As the user-friendly Chipster software is used in the exercises, no prior knowledge of R/Bioconductor or Unix ir required, and the course is thus suitable for everybody. Our book RNA-seq data analysis: A practical approach (CRC Press) can be used as background reading. The following topics and analysis tools are covered: 1. Introduction to the Chipster analysis platform 2. Quality control of raw reads (FastQC, PRINSEQ) 3. Preprocessing (Trimmomatic, PRINSEQ) 4. Alignment to reference genome (TopHat2) 5. Alignment level quality control (RseQC) 6. Quantitation (HTSeq) 7. Experiment level quality control with PCA and MDS plots 8. Differential expression analysis (DESeq2, edgeR) -normalization -dispersion estimation -statistical testing -controlling for batch effects, multifactor designs -filtering -multiple testing correction 9. Visualization of reads and results -genome browser -Venn diagram -volcano plot -plotting normalized counts for a gene -expression profiles 10. Experimental design Bioinformatics Data architecture, analysis and design RNA Sequencing http://www.mygoblet.org/topic-tags/differential-expression, http://www.mygoblet.org/topic-tags/ngs, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/rna-seq Life Science Researchers Bench biologists 2015-12-04 2017-06-23

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 2017-06-23

This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list  data structure. The...

Keywords: http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/record-parsing, http://www.mygoblet.org/topic-tags/python-biologists, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/python

Parsing data records using Python programming https://tess.elixir-europe.org/materials/parsing-data-records-using-python-programming This is a module from the "Python for Biologists" course. One typical problem in bioinformatics is parsing data files. This module explains how to parse FASTA files and GenBank records. It also introduces the if/elif/else construct to make choice in programming and the list  data structure. The text of exercises is provided in a separate file.  http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/record-parsing, http://www.mygoblet.org/topic-tags/python-biologists, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/python Biologists bioinformaticians programmers beginner bioinformaticians 2013-07-05 2017-06-23

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 Post-Doctoral Fellows Graduate Students Researchers Biologists, Genomicists, Computer Scientists 2014-06-26 2017-06-23

Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...

Keywords: http://www.mygoblet.org/topic-tags/phylogenetics, http://www.mygoblet.org/topic-tags/molecular-evolution

Interpreting Phylogenies https://tess.elixir-europe.org/materials/interpreting-phylogenies Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday. Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic trees. Includes exercises on visulaising and manipulating trees using Dendroscope and NJplot to reinforce some of these ideas, while also providing a very basic overview of steps involved in a generic phylogenetic analysis. http://www.mygoblet.org/topic-tags/phylogenetics, http://www.mygoblet.org/topic-tags/molecular-evolution field biologist researchers experimeintal biologist researchers 2013-09-13 2017-06-23

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 Post-Doctoral Fellows Graduate Students Researchers Biologists, Genomicists, Computer Scientists 2014-06-26 2017-06-23

"Evolution Academy" videos (http://post.queensu.ca/~forsdyke/videolectures.htm). The latter are a course of 54 short (15 min) videos that follow the style of Salman Khan's "Khan Academy," and are addressed primarily to High School and beginning College students. There are also several longer (1...

Scientific topics: Evolutionary biology

Keywords: http://www.mygoblet.org/topic-tags/evolutionary-biology, http://www.mygoblet.org/topic-tags/biohistory, http://www.mygoblet.org/topic-tags/evolutionary-bioinformatics

Evolutionary Bioinformatics Videos https://tess.elixir-europe.org/materials/evolutionary-bioinformatics-videos "Evolution Academy" videos (http://post.queensu.ca/~forsdyke/videolectures.htm). The latter are a course of 54 short (15 min) videos that follow the style of Salman Khan's "Khan Academy," and are addressed primarily to High School and beginning College students. There are also several longer (1 h) conference presentations that bring together various themes. These are backed by several webpages (accessible by way of http://post.queensu.ca/~forsdyke/homepage.htm ), and a textbook, now in its third edition (2016; for Introduction see Materials File). Evolutionary biology http://www.mygoblet.org/topic-tags/evolutionary-biology, http://www.mygoblet.org/topic-tags/biohistory, http://www.mygoblet.org/topic-tags/evolutionary-bioinformatics Researchers University and College Level Students High School Students 2017-04-04 2017-06-23

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

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/bootstrap, http://www.mygoblet.org/topic-tags/consensus-trees, http://www.mygoblet.org/topic-tags/phylogenetic-splits, http://www.mygoblet.org/topic-tags/phylogenetics Bench biologists 2013-10-23 2017-06-23

This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological...

Keywords: http://www.mygoblet.org/topic-tags/pattern-matching, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/python-biologists, http://www.mygoblet.org/topic-tags/python

Pattern Matching https://tess.elixir-europe.org/materials/pattern-matching This is a module from the "Python for Biologists" course. It teaches how to do pattern matching in Python, i.e. how to find a substring (or a set of substrings) in a string. To this aim, it introduces the regular expression syntax, and the tools needed to search regular expressions in biological sequences and in regular text, such as PubMed abstracts. Exercises and suggested solutions are presented in a separate file. http://www.mygoblet.org/topic-tags/pattern-matching, http://www.mygoblet.org/topic-tags/programming, http://www.mygoblet.org/topic-tags/python-biologists, http://www.mygoblet.org/topic-tags/python Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-06-23

This quick and simple tutorial demonstrates some of the easy plotting tools in the R core software. the data are in the "data" directory and come from an old two-colour microarray experiment where spots on the array were printed with different buffers, in different concentrations and with...

Keywords: http://www.mygoblet.org/topic-tags/plotting-data, http://www.mygoblet.org/topic-tags/microarray-data-analysis, http://www.mygoblet.org/topic-tags/r, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/visualisation

Simple plotting in R https://tess.elixir-europe.org/materials/simple-plotting-in-r This quick and simple tutorial demonstrates some of the easy plotting tools in the R core software. the data are in the "data" directory and come from an old two-colour microarray experiment where spots on the array were printed with different buffers, in different concentrations and with different pins.  Also, both channels Cy5 and Cy3 were spotted identically, and so the fold ratio for all spots should be 1 - this helps us see bias in the data http://www.mygoblet.org/topic-tags/plotting-data, http://www.mygoblet.org/topic-tags/microarray-data-analysis, http://www.mygoblet.org/topic-tags/r, http://www.mygoblet.org/topic-tags/bioinformatics, http://www.mygoblet.org/topic-tags/visualisation Beginners Scientists Researchers PhD students 2014-01-14 2017-06-23

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 2017-06-23

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 Biologists bioinformaticians biocurators 2013-07-16 2017-06-23

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

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/protein-family-characterisation, http://www.mygoblet.org/topic-tags/protein-sequence-analysis, http://www.mygoblet.org/topic-tags/integrated-diagnostic-tools postdoc postgrad beginner bioinformaticians biocurators 2013-07-12 2017-06-23

Overview of transcription Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data Basics of processing data Pattern discovery

Keywords: http://www.mygoblet.org/topic-tags/transcriptional-regulation, http://www.mygoblet.org/topic-tags/pattern-discovery

Pathway and Network Analysis 2014 Module 3 - Gene Regulation Analysis https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-3-gene-regulation-analysis Overview of transcription Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data Basics of processing data Pattern discovery http://www.mygoblet.org/topic-tags/transcriptional-regulation, http://www.mygoblet.org/topic-tags/pattern-discovery Post-Doctoral Fellows Graduate Students Researchers Biologists, Genomicists, Computer Scientists 2014-06-26 2017-06-23

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

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

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/experimental-design-rna-seq, http://www.mygoblet.org/topic-tags/introduction-rna-seq-analysis, http://www.mygoblet.org/topic-tags/igv Post-Doctoral Fellows Graduate Students Researchers Biologists, Genomicists, Computer Scientists 2014-06-27 2017-06-23
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