NGS overview
This course covers:
Sequencing technologies
Applications
Categories of analysis
Sample preparation
Potential services in NGS
Appendix
Scientific topics: Sequencing, High-throughput sequencing
Keywords: bioinformatics, Australia
NGS overview
http://vlsci.github.io/lscc_docs/tutorials/ngs_overview/NGS_Overview/
https://tess.elixir-europe.org/materials/ngs-overview
This course covers:
Sequencing technologies
Applications
Categories of analysis
Sample preparation
Potential services in NGS
Appendix
Simon Gladman
Vicky Schneider
Sequencing
High-throughput sequencing
bioinformatics, Australia
Biologists
Python Overview
Introduction to Python
Keywords: bioinformatics, Australia
Python Overview
http://vlsci.github.io/lscc_docs/tutorials/python_overview/python_overview/
https://tess.elixir-europe.org/materials/python-overview
Introduction to Python
Bernie Pope
Catherine de Burgh-Day
Vicky Schneider
bioinformatics, Australia
Biologists
Galaxy workflows
This workshop/tutorial will familiarise you with the Galaxy workflow engine. It will cover the following topics:
Logging in to the server
How to construct and use a workflow by various methods
How to share a workflow
Scientific topics: Workflows
Keywords: bioinformatics
Galaxy workflows
http://vlsci.github.io/lscc_docs/tutorials/galaxy-workflows/galaxy-workflows/
https://tess.elixir-europe.org/materials/galaxy-workflows
This workshop/tutorial will familiarise you with the Galaxy workflow engine. It will cover the following topics:
Logging in to the server
How to construct and use a workflow by various methods
How to share a workflow
Simon Gladman
Vicky Schneider
Workflows
bioinformatics
Biologists
What is GenomeSpace?
GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses...
Keywords: bioinformatics, GVL
What is GenomeSpace?
http://vlsci.github.io/lscc_docs/tutorials/genomespace/genomespace/
https://tess.elixir-europe.org/materials/what-is-genomespace
GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer.
Simon Gladman
Vicky Schneider
bioinformatics, GVL
Biologists
Introduction to Galaxy
Basic Introduction to Galaxy
Introduction to Galaxy
http://vlsci.github.io/lscc_docs/tutorials/galaxy_101/galaxy_101/
https://tess.elixir-europe.org/materials/introduction-to-galaxy
Basic Introduction to Galaxy
Simon Gladman
Vicky Schneider
bioinformatics
Biologists
Researcher Training Day for Life Scientists_ Rad-seq with Stacks in Galaxy
This materials are associated to the Galaxy Australasia Meeting 2017 kicks off on Friday 3rd February with the Researcher Training Day.
This event targets life scientists working with Next-Generation Sequencing data, in particular RNA-Seq, RAD-Seq, and microbial genomes.
Researcher Training Day for Life Scientists_ Rad-seq with Stacks in Galaxy
https://www.embl-abr.org.au/game2017/training-day/#rad-seq-back1
https://tess.elixir-europe.org/materials/researcher-training-day-for-life-scientists_-rad-seq-with-stacks-in-galaxy
This materials are associated to the Galaxy Australasia Meeting 2017 kicks off on Friday 3rd February with the Researcher Training Day.
This event targets life scientists working with Next-Generation Sequencing data, in particular RNA-Seq, RAD-Seq, and microbial genomes.
Vicky Schneider
Pip Griffin
Sonika Tyagi
bioinformatics
Biologists
EMBL-ABR workshop on Open Source and Software Development Best Practice
This workshop will provide an interactive forum to discuss, review and gain an overview of Open Source and Software Development and will be based on content from the ELIXIR Software Development Best Practices group and aims to explore how to harmonise EMBL-ABR efforts in this area
Scientific topics: Software engineering
Keywords: bioinformatics
EMBL-ABR workshop on Open Source and Software Development Best Practice
https://www.embl-abr.org.au/bioinformatics-sw-workshop/
https://tess.elixir-europe.org/materials/embl-abr-workshop-on-open-source-and-software-development-best-practice
This workshop will provide an interactive forum to discuss, review and gain an overview of Open Source and Software Development and will be based on content from the ELIXIR Software Development Best Practices group and aims to explore how to harmonise EMBL-ABR efforts in this area
Vicky Schneider
Rafael C Jimenez
Jason Williams
Software engineering
bioinformatics
software developers, bioinformaticians
EMBL-ABR/ELIXIR/CyVerse workshop: Registries in Bioinformatics
This workshop will provide an introduction to existing solutions and methods for registries across a variety of areas relevant to bioinformatics, such as tools, datasets, standards, events and training.
EMBL-ABR/ELIXIR/CyVerse workshop: Registries in Bioinformatics
https://www.embl-abr.org.au/registries-workshop/
https://tess.elixir-europe.org/materials/embl-abr-elixir-cyverse-workshop-registries-in-bioinformatics
This workshop will provide an introduction to existing solutions and methods for registries across a variety of areas relevant to bioinformatics, such as tools, datasets, standards, events and training.
Vicky Schneider
Rafael C Jimenez
Jason Williams
Sonika Tyagi
bioinformatics
bioinformaticians
EMBL-ABR Best Practice workshop series: the data life-cycle
From 24-28 October 2016, the EMBL-ABR Hub ran a week-long Best Practice workshop series focussing on the Data Life Cycle for biological and bioinformatics data. International and local faculty members joined highly engaged participants from around Australia: students, postdocs, lecturers, other...
Scientific topics: Data types and objects, Data management
Keywords: bioinformatics, data
EMBL-ABR Best Practice workshop series: the data life-cycle
https://www.embl-abr.org.au/workshop-bp-series/
https://tess.elixir-europe.org/materials/embl-abr-best-practice-workshop-series-the-data-life-cycle
From 24-28 October 2016, the EMBL-ABR Hub ran a week-long Best Practice workshop series focussing on the Data Life Cycle for biological and bioinformatics data. International and local faculty members joined highly engaged participants from around Australia: students, postdocs, lecturers, other scientists, research assistants and research data managers.
Vicky Schneider
Jyoti Khadake
Sandra Orchard
Dan Bolser
Suzanna Lewis
Data types and objects
Data management
bioinformatics, data
Biologists
bioinformaticians
Big Data, Genes, and Medicine
This course distills for you expert knowledge and skills mastered by professionals in Health Big Data Science and Bioinformatics. You will learn exciting facts about the human body biology and chemistry, genetics, and medicine that will be intertwined with the science of Big Data and skills to...
Keywords: life-sciences, computer-science, bioinformatics, algorithms
Big Data, Genes, and Medicine
https://www.coursera.org/learn/data-genes-medicine
https://tess.elixir-europe.org/materials/big-data-genes-and-medicine
This course distills for you expert knowledge and skills mastered by professionals in Health Big Data Science and Bioinformatics. You will learn exciting facts about the human body biology and chemistry, genetics, and medicine that will be intertwined with the science of Big Data and skills to harness the avalanche of data openly available at your fingertips and which we are just starting to make sense of. We’ll investigate the different steps required to master Big Data analytics on real datasets, including Next Generation Sequencing data, in a healthcare and biological context, from preparing data for analysis to completing the analysis, interpreting the results, visualizing them, and sharing the results.
Needless to say, when you master these high-demand skills, you will be well positioned to apply for or move to positions in biomedical data analytics and bioinformatics. No matter what your skill levels are in biomedical or technical areas, you will gain highly valuable new or sharpened skills that will make you stand-out as a professional and want to dive even deeper in biomedical Big Data. It is my hope that this course will spark your interest in the vast possibilities offered by publicly available Big Data to better understand, prevent, and treat diseases.
life-sciences, computer-science, bioinformatics, algorithms
2017-03-24
Bioinformatics: Life Sciences on Your Computer
What makes bioinformatics education exciting is that people of a variety of education levels can get started quickly, with just a computer and internet access.
Keywords: life-sciences, bioinformatics
Bioinformatics: Life Sciences on Your Computer
https://www.coursera.org/learn/bioinform
https://tess.elixir-europe.org/materials/bioinformatics-life-sciences-on-your-computer
What makes bioinformatics education exciting is that people of a variety of education levels can get started quickly, with just a computer and internet access.
life-sciences, bioinformatics
2016-06-29
Bioinformatic Methods II
Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful...
Keywords: life-sciences, bioinformatics
Bioinformatic Methods II
https://www.coursera.org/learn/bioinformatics-methods-2
https://tess.elixir-europe.org/materials/bioinformatic-methods-ii
Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful information pertaining to the system being studied. This course focuses on employing existing bioinformatic resources – mainly web-based programs and databases – to access the wealth of data to answer questions relevant to the average biologist, and is highly hands-on.
Topics covered include multiple sequence alignments, phylogenetics, gene expression data analysis, and protein interaction networks, in two separate parts.
The first part, Bioinformatic Methods I, dealt with databases, Blast, multiple sequence alignments, phylogenetics, selection analysis and metagenomics.
This, the second part, Bioinformatic Methods II, will cover motif searching, protein-protein interactions, structural bioinformatics, gene expression data analysis, and cis-element predictions.
This pair of courses is useful to any student considering graduate school in the biological sciences, as well as students considering molecular medicine.
These courses are based on one taught at the University of Toronto to upper-level undergraduates who have some understanding of basic molecular biology. If you're not familiar with this, something like https://learn.saylor.org/course/bio101 might be helpful. No programming is required for this course although some command line work (though within a web browser) occurs in the 5th module.
life-sciences, bioinformatics
2017-05-04
Bioinformatics Capstone: Big Data in Biology
In this course, you will learn how to use the BaseSpace cloud platform developed by Illumina (our industry partner) to apply several standard bioinformatics software approaches to real biological data.
In particular, in a series of Application Challenges will see how genome assembly can be used...
Keywords: life-sciences, computer-science, bioinformatics, algorithms
Bioinformatics Capstone: Big Data in Biology
https://www.coursera.org/learn/bioinformatics-project
https://tess.elixir-europe.org/materials/bioinformatics-capstone-big-data-in-biology
In this course, you will learn how to use the BaseSpace cloud platform developed by Illumina (our industry partner) to apply several standard bioinformatics software approaches to real biological data.
In particular, in a series of Application Challenges will see how genome assembly can be used to track the source of a food poisoning outbreak, how RNA-Sequencing can help us analyze gene expression data on the tissue level, and compare the pros and cons of whole genome vs. whole exome sequencing for finding potentially harmful mutations in a human sample.
Plus, hacker track students will have the option to build their own genome assembler and apply it to real data!
life-sciences, computer-science, bioinformatics, algorithms
2017-03-25
Bioinformatics: Introduction and Methods 生物信息学: 导论与方法
A big welcome to “Bioinformatics: Introduction and Methods” from Peking University! In this MOOC you will become familiar with the concepts and computational methods in the exciting interdisciplinary field of bioinformatics and their applications in biology, the knowledge and skills in...
Keywords: life-sciences, bioinformatics
Bioinformatics: Introduction and Methods 生物信息学: 导论与方法
https://www.coursera.org/learn/bioinformatics-pku
https://tess.elixir-europe.org/materials/bioinformatics-introduction-and-methods
A big welcome to “Bioinformatics: Introduction and Methods” from Peking University! In this MOOC you will become familiar with the concepts and computational methods in the exciting interdisciplinary field of bioinformatics and their applications in biology, the knowledge and skills in bioinformatics you acquired will help you in your future study and research.
Course materials are available under the CC BY-NC-SA License.
life-sciences, bioinformatics
2017-10-09
Bioinformatic Methods I
Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful...
Keywords: life-sciences, bioinformatics
Bioinformatic Methods I
https://www.coursera.org/learn/bioinformatics-methods-1
https://tess.elixir-europe.org/materials/bioinformatic-methods-i
Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful information pertaining to the system being studied. This course focuses on employing existing bioinformatic resources – mainly web-based programs and databases – to access the wealth of data to answer questions relevant to the average biologist, and is highly hands-on.
Topics covered include multiple sequence alignments, phylogenetics, gene expression data analysis, and protein interaction networks, in two separate parts.
The first part, Bioinformatic Methods I (this one), deals with databases, Blast, multiple sequence alignments, phylogenetics, selection analysis and metagenomics.
This, the second part, Bioinformatic Methods II, covers motif searching, protein-protein interactions, structural bioinformatics, gene expression data analysis, and cis-element predictions.
This pair of courses is useful to any student considering graduate school in the biological sciences, as well as students considering molecular medicine. Both provide an overview of the many different bioinformatic tools that are out there.
These courses are based on one taught at the University of Toronto to upper-level undergraduates who have some understanding of basic molecular biology. If you're not familiar with this, something like https://learn.saylor.org/course/bio101 might be helpful. No programming is required for this course.
life-sciences, bioinformatics
2017-10-09