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eBioKit

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

Keywords: Advanced bioinformatics training, Introduction bioinformatics

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

Keywords: Molecular evolution, Phylogenetics

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. Molecular evolution, Phylogenetics experimeintal biologist researchers field biologist researchers 2013-09-13 2017-10-09
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.

Keywords: Perl, Python, Unix

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. Perl, Python, Unix Bench biologists 2013-07-28 2017-10-09
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...

Keywords: 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 Bioinformatics Biologists biocurators bioinformaticians 2013-07-16 2017-10-09
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...

Keywords: Bioinformatics, Next generation sequencing, Ngs

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 Bioinformatics, Next generation sequencing, Ngs Biologists bioinformaticians computational scientists 2013-07-15 2017-10-09
Bioinformatics: Gene-protein-structure-function

This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The...

Keywords: Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast

Bioinformatics: Gene-protein-structure-function https://tess.elixir-europe.org/materials/bioinformatics-gene-protein-structure-function This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The presentation concludes with an analysis of 'expert' systems and integrated approaches (GeneQuiz, MAGPIE, InterPro, etc.), and dispels the commonly held notion that one database and/or one analysis tool is best. Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09
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. 

Keywords: Integrated diagnostic tools, Protein family characterisation, 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.  Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09
PRINTS: A protein family database with a difference

A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to...

Keywords: Functional diagnosis, Protein family characterisation, Protein sequence analysis

PRINTS: A protein family database with a difference https://tess.elixir-europe.org/materials/prints-a-protein-family-database-with-a-difference A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to demonstrate the importance of understanding how to interpret the results of different sequence analysis methods and, crucially, the differences between them, and the added value that fingerprints bring. Functional diagnosis, Protein family characterisation, Protein sequence analysis beginner bioinformaticians biocurators postdoc postgrad 2013-07-12 2017-10-09
BioJS

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

Keywords: Bioinformatics, Javascript

BioJS https://tess.elixir-europe.org/materials/biojs BioJS is a library of graphical components easy to reuse to represent biological information Bioinformatics, Javascript bioinformaticians web developers 2013-07-11 2017-10-09
Bioinformatics for MS analysis

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

Keywords: Bioinformatics, Identification, 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. Bioinformatics, Identification, Mass spectrometry 2013-07-05 2017-10-09
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...

Keywords: Bioinformatics, Programming, Python, Python biologists, Record parsing

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.  Bioinformatics, Programming, Python, Python biologists, Record parsing Biologists beginner bioinformaticians bioinformaticians programmers 2013-07-05 2017-10-09
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    

Keywords: Bioinformatics, Programming, 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     Bioinformatics, Programming, Unixlinux Anyone wants to start using the Unix/Linux OS 2013-07-04 2017-10-09
RNA-seq analysis

I give an overview of the analysis of gene expression in plants using RNA-seq data. This course provides a foundation on the tuxedo software suite: TopHat, Cufflinks, CummeRbund.

RNA-seq analysis https://tess.elixir-europe.org/materials/rna-seq-analysis I give an overview of the analysis of gene expression in plants using RNA-seq data. This course provides a foundation on the tuxedo software suite: TopHat, Cufflinks, CummeRbund. 2013-06-28 2017-10-09
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...

Keywords: 1d static gating, 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 1d static gating, Flow cytometry data 2013-06-26 2017-10-09
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...

Keywords: Biomarker discovery, Flow cytometry data, 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 Biomarker discovery, Flow cytometry data, Flowcap 2013-06-26 2017-10-09
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...

Keywords: 1d dynamic gating, 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 1d dynamic gating, Flow cytometry data 2013-06-26 2017-10-09
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...

Keywords: Flow cytometry data, Preprocessing, Quality assurance

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 Flow cytometry data, Preprocessing, Quality assurance 2013-06-26 2017-10-09
Flow Cytometry 2013 Module 2 - Exploring FCM data in R

Loading a single or groups of FCS files into R flowFrame and flowSet objects and their attributes Exploring sample annotation and keywords stored within the FCS file format, searching for specic samples (such as controls) using grep, highlighting the importance of correct sample annotation...

Keywords: Fcs files, Plotting data, R

Flow Cytometry 2013 Module 2 - Exploring FCM data in R https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-2-exploring-fcm-data-in-r Loading a single or groups of FCS files into R flowFrame and flowSet objects and their attributes Exploring sample annotation and keywords stored within the FCS file format, searching for specic samples (such as controls) using grep, highlighting the importance of correct sample annotation at point of acquisition Simple dot plots and density plots Fcs files, Plotting data, R 2013-06-26 2017-10-09
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...

Keywords: Introduction flow cytometry, Review r

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 Introduction flow cytometry, Review r 2013-06-25 2017-10-09
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.

Keywords: Bioinformatics history, Biomolecular databases, Biomolecular sequences, European perspective

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. Bioinformatics history, Biomolecular databases, Biomolecular sequences, European perspective 2013-06-25 2017-10-09
PRIDE and ProteomeXchange: webinar

PRIDE and ProteomeXchange: webinar from http://www.ebi.ac.uk/training/online/course/pride-and-proteomexchange-webinar, added automatically.

Keywords: Proteins

PRIDE and ProteomeXchange: webinar https://tess.elixir-europe.org/materials/pride-and-proteomexchange-webinar PRIDE and ProteomeXchange: webinar from http://www.ebi.ac.uk/training/online/course/pride-and-proteomexchange-webinar, added automatically. Proteins 2016-03-05
Phylogenetics: An introduction

Phylogenetics: An introduction from http://www.ebi.ac.uk/training/online/course/introduction-phylogenetics, added automatically.

Scientific topics: Phylogenetics

Keywords: DNA RNA

Phylogenetics: An introduction https://tess.elixir-europe.org/materials/phylogenetics-an-introduction Phylogenetics: An introduction from http://www.ebi.ac.uk/training/online/course/introduction-phylogenetics, added automatically. Phylogenetics DNA RNA 2016-03-05
PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure

PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure from http://www.ebi.ac.uk/training/online/course/pdbepisa-identifying-and-interpreting-likely-biolo, added automatically.

Keywords: Proteins, Structures

PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure https://tess.elixir-europe.org/materials/pdbepisa-identifying-and-interpreting-the-likely-biological-assemblies-of-a-protein-structure PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure from http://www.ebi.ac.uk/training/online/course/pdbepisa-identifying-and-interpreting-likely-biolo, added automatically. Proteins, Structures 2016-03-05
PDBeFold: Searching for structural homologues of a protein

PDBeFold: Searching for structural homologues of a protein from http://www.ebi.ac.uk/training/online/course/pdbefold-searching-structural-homologues-protein, added automatically.

Keywords: Proteins, Structures

PDBeFold: Searching for structural homologues of a protein https://tess.elixir-europe.org/materials/pdbefold-searching-for-structural-homologues-of-a-protein PDBeFold: Searching for structural homologues of a protein from http://www.ebi.ac.uk/training/online/course/pdbefold-searching-structural-homologues-protein, added automatically. Proteins, Structures 2016-03-05
PDBeChem: Searching for small molecules and small molecule fragments

PDBeChem: Searching for small molecules and small molecule fragments from http://www.ebi.ac.uk/training/online/course/pdbechem-searching-small-molecules-and-small-molec.

Scientific topics: Small molecules

Keywords: Proteins, Chemical biology, Structures

PDBeChem: Searching for small molecules and small molecule fragments https://tess.elixir-europe.org/materials/pdbechem-searching-for-small-molecules-and-small-molecule-fragments PDBeChem: Searching for small molecules and small molecule fragments from http://www.ebi.ac.uk/training/online/course/pdbechem-searching-small-molecules-and-small-molec. Small molecules Proteins, Chemical biology, Structures 2016-04-22
PDBe: Searching the Protein Data Bank

PDBe: Searching the Protein Data Bank from http://www.ebi.ac.uk/training/online/course/pdbe-searching-protein-data-bank.

Keywords: Proteins, Chemical biology, Structures

PDBe: Searching the Protein Data Bank https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank PDBe: Searching the Protein Data Bank from http://www.ebi.ac.uk/training/online/course/pdbe-searching-protein-data-bank. Proteins, Chemical biology, Structures 2016-05-26
PDBe: Quick tour

PDBe: Quick tour from http://www.ebi.ac.uk/training/online/course/pdbe-quick-tour.

Keywords: Proteins, Structures

PDBe: Quick tour https://tess.elixir-europe.org/materials/pdbe-quick-tour PDBe: Quick tour from http://www.ebi.ac.uk/training/online/course/pdbe-quick-tour. Proteins, Structures 2016-05-26
PDBe: Exploring a Protein Data Bank (PDB) entry

PDBe: Exploring a Protein Data Bank (PDB) entry from http://www.ebi.ac.uk/training/online/course/pdbe-exploring-protein-data-bank-pdb-entry.

Keywords: Proteins, Chemical biology, Structures

PDBe: Exploring a Protein Data Bank (PDB) entry https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry PDBe: Exploring a Protein Data Bank (PDB) entry from http://www.ebi.ac.uk/training/online/course/pdbe-exploring-protein-data-bank-pdb-entry. Proteins, Chemical biology, Structures 2016-06-14
myChEMBL: webinar

myChEMBL: webinar from http://www.ebi.ac.uk/training/online/course/mychembl-webinar.

Keywords: Chemical biology

myChEMBL: webinar https://tess.elixir-europe.org/materials/mychembl-webinar myChEMBL: webinar from http://www.ebi.ac.uk/training/online/course/mychembl-webinar. Chemical biology 2016-06-14
PDBe: An introduction to search and entry pages: webinar

PDBe: An introduction to search and entry pages: webinar from http://www.ebi.ac.uk/training/online/course/pdbe-introduction-search-and-entry-pages-webinar.

Keywords: Proteins, Chemical biology, Structures

PDBe: An introduction to search and entry pages: webinar https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar PDBe: An introduction to search and entry pages: webinar from http://www.ebi.ac.uk/training/online/course/pdbe-introduction-search-and-entry-pages-webinar. Proteins, Chemical biology, Structures 2016-04-14