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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

Keywords: Pattern discovery, Transcriptional regulation

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 Pattern discovery, Transcriptional regulation Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 2 - Finding Over-represented Pathways

Over-representation analysis (ORA) Statistics for detecting over-representation e.g. hypergeometric test, GSEA Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR Filtering Gene Ontology e.g. using evidence codes

Keywords: Gsea, Over representation analysis

Pathway and Network Analysis 2014 Module 2 - Finding Over-represented Pathways https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-2-finding-over-represented-pathways Over-representation analysis (ORA) Statistics for detecting over-representation e.g. hypergeometric test, GSEA Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR Filtering Gene Ontology e.g. using evidence codes Gsea, Over representation analysis Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
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

Keywords: Gene lists, Gene ontology

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 Gene lists, Gene ontology Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Training Bioinformatics in the Cloud

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

Keywords: Advanced bioinformatics training, Cloud computing, 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. Advanced bioinformatics training, Cloud computing, Training Bench biologists beginner bioinformaticians 2014-05-20 2017-10-09
BLAST and multiple sequence alignment (MSA) programs

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

Keywords: Blast, E learning, Multiple sequence alignment

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

Keywords: Animal pathogens, E learning, Phylogenetics

Resource type: ViralZone

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   Animal pathogens, E learning, Phylogenetics Bench biologists Biologists Laboratory technicians Researchers Veterinarians 2014-04-28 2017-10-09
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...

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. NGS, ChIPSeq, De novo genome assembly, RNASeq Bench biologists Life Science Researchers PhD students postdocs 2014-01-17 2017-10-09
Working with Affymetrix CEL files in R

This tutorial shows how to download some public Affymetrix microarray data, load the data into R, calculate expression values and do some very simple plotting

Keywords: Affymetrix, Microarrays, R

Working with Affymetrix CEL files in R https://tess.elixir-europe.org/materials/working-with-affymetrix-cel-files-in-r This tutorial shows how to download some public Affymetrix microarray data, load the data into R, calculate expression values and do some very simple plotting Affymetrix, Microarrays, R Beginners PhD students Researchers 2014-01-14 2017-10-09
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...

Keywords: Bioinformatics, Microarray data analysis, Plotting data, R, 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 Bioinformatics, Microarray data analysis, Plotting data, R, Visualisation Beginners PhD students Researchers Scientists 2014-01-14 2017-10-09
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...

Keywords: Bioinformatics, Cloud, Next generation sequencing, Next generation sequencing data analysis, Ngs bioinformatics, 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 Bioinformatics, Cloud, Next generation sequencing, Next generation sequencing data analysis, Ngs bioinformatics, Qc ngs data Beginners 2014-01-13 2017-10-09
UNIX Fundamentals

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

UNIX Fundamentals https://tess.elixir-europe.org/materials/unix-fundamentals This tutorial aims to present the UNIX environment and to provide the most basic commands to users with no or very little UNIX knowledge. The examples are taken from various Biological fields but have been chosen carefully to be easily accessible to a wide audience. 2014-01-13
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...

Keywords: Problem based learning, Teaching aid, 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 Problem based learning, Teaching aid, Train trainer Lecturers Trainers 2014-01-12 2017-10-09
Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies

Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.

Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment

Introduction to Multiple Sequence Alignments (MSAs) and Phylogenies https://tess.elixir-europe.org/materials/introduction-to-multiple-sequence-alignments-msas-and-phylogenies Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood. Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment Bench biologists Post-Doctoral Fellows Postgraduate students principle investigators 2013-12-19 2017-10-09
Understanding Multiple Sequence Alignments - Lecture Handouts & Utopia Hands-On

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

Keywords: Multiple sequence alignment, Protein sequence analysis, Sequence analysis

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

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

Keywords: Clinical bioinformatics, Genomics, Introduction bioinformatics

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

Keywords: Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching

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.  Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching biology and bioinformatics sophomore undergraduates 2013-11-12 2017-10-09
Multiple sequence alignment and phylogeny - undergraduate lab

This is lab 4 in a series of labs given as part of an undergraduate "Bioinformatics for biologists" course delivered to 2nd and 3rd year biology and bioinformatics undergraduate students, as part of a course focusing on using bioinformatics tools. Some instructions in it are specific to our lab...

Keywords: Clustalw, Multiple sequence alignment, Phylip, Phylogeny

Multiple sequence alignment and phylogeny - undergraduate lab https://tess.elixir-europe.org/materials/multiple-sequence-alignment-and-phylogeny-undergraduate-lab This is lab 4 in a series of labs given as part of an undergraduate "Bioinformatics for biologists" course delivered to 2nd and 3rd year biology and bioinformatics undergraduate students, as part of a course focusing on using bioinformatics tools. Some instructions in it are specific to our lab environment - including some not so current programs (clustalw, treetool, seaview, phylip) as that's what we have installed at the moment and they're stable, but the content can easily be adapted to other environments and programs. The lab is meant to be easily assessed and I get the students to answer the question in a moodle quiz which makes marking easier. The lab follows some lectures on multiple sequence alignment and molecular phylogeny. Clustalw, Multiple sequence alignment, Phylip, Phylogeny biology and bioinformatics sophomore undergraduates 2013-11-12 2017-10-09
Sequence comparison - undergraduate lab

This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of...

Keywords: Dotmatrix plots, Scoring matrices, Sequence alignment

Sequence comparison - undergraduate lab https://tess.elixir-europe.org/materials/sequence-comparison-undergraduate-lab This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of the lab should be easy to adapt to other environments. This lab makes use of EMBOSS programs, prss in the FASTA package, as well as the NCBI BLAST website. I usually deliver this lab after a series of lectures discussing dotmatrix plots and sequence alignment. Students enter their answers to the questions into a quiz set up within moodle which allows for easier marking. Dotmatrix plots, Scoring matrices, Sequence alignment Undergraduate students 2013-11-12 2017-10-09
Using R with Python

This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented...

Keywords: Programming, Python, Python biologists

Using R with Python https://tess.elixir-europe.org/materials/using-r-with-python This is a module from the "Python for Biologists" course. It describes the Python module interfacing the R package for statistics. The module shows how to calculate mean, standard deviation, z-score and p-value of a set of numbers, and how to generate plots. Input files for the scripts presented are also provided. Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians bioinformaticians 2013-11-04 2017-10-09
Searching data using Python

This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and...

Keywords: Programming, Python, Python biologists

Searching data using Python https://tess.elixir-europe.org/materials/searching-data-using-python This is a module from the "Python for Biologists" course. It describes how to use Python dictionary and set data structures to search your data. In particular, how to use a dictionary to represent the genetic code table and use it to translate a nucleotide sequence into a protein sequence, and how to use sets to find unique records in two datasets and remove redundancy.  Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
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...

Keywords: Pattern matching, Programming, Python, Python biologists

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. Pattern matching, Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Writing functions in Python programming

This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file. 

Scientific topics: Bioinformatics

Keywords: Programming, Python, Python biologists

Writing functions in Python programming https://tess.elixir-europe.org/materials/writing-functions-in-python-programming This is a module from the "Python for Biologists" course. It deals with functions and how to write and use them. It also introduces namespaces and the tuple data structure. The module contains several exercises and suggested solutions. The text of exercises is also provided in a separate file.  Bioinformatics Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
Python Programs

This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions. 

Keywords: Programming, Python, Python biologists

Python Programs https://tess.elixir-europe.org/materials/python-programs This is a module from the "Python for Biologists" course. It deals with Python programs, how to write and run them, and how to provide input and generate output. The module also contains exercises and suggested solutions.  Programming, Python, Python biologists Biologists Biologists, Genomicists, Computer Scientists beginner bioinformaticians 2013-11-04 2017-10-09
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...

Keywords: Bioinformatics, Mass spectrometry, Protein identification

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. Bioinformatics, Mass spectrometry, Protein identification Bench biologists PhD students Post-Doctoral Fellows Technicians bioinformaticians master 2013-10-30 2017-10-09
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...

Keywords: Bootstrap, Consensus trees, Phylogenetic splits, 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. Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics Bench biologists 2013-10-23 2017-10-09
Introduction to Multiple Sequence Alignment

An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of...

Keywords: Multiple sequence analysis, Protein structure, Sequence analysis

Introduction to Multiple Sequence Alignment https://tess.elixir-europe.org/materials/introduction-to-multiple-sequence-alignment An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of alignmetns (structural and evolutionary), and ways of building manual and automatic alignments, and an introduction to JalView Multiple sequence analysis, Protein structure, Sequence analysis Bench biologists 2013-10-23 2017-10-09
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...

Keywords: 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. Introduction bioinformatics Bench biologists 2013-10-23 2017-10-09
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