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Dear All
We have been busy here at Edinburgh Genomics organising some new courses to help you gain those bioinformatics skills you need for your research! We have some exciting new stuff including a new course from Dr Martin Jones and GATK variant analysis course by the training team at the Broad Institute. See our upcoming courses below.
We are also pleased to announce that we have some full-fee bursaries available from the National Environment Research Council (NERC) for students or researchers working on NERC-funded or NERC-remit science. If you believe that your work falls into this category please get in touch with us ([email protected]) and let us know what you work on and what course you are interested in. The deadline for allocating these bursaries is the 27th March, so please get in touch before this point!
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R for Genomics 30 - 31 March 2020
The aim of this course is to introduce participants to the statistical computing language 'R' using examples and skills relevant to genomic data science. This two day workshop is taught by experienced Edinburgh Genomics’ bioinformaticians and trainers. By the end of the workshop, you will be comfortable with the basics of the R and R studio environments, learning about the rules of the language and how R works with different data types. We then move on to using functions, including those specific to genomic science. We look at how to handle various genomic data files and where to find relevant tools via online resources. Finally we use mock RNA-seq data to learn how to visualise your data to generate publication ready plots using the package ggplot2.
Tutors: Nathan Medd, Training Manager, Edinburgh Genomics
Registration fee (including lunch and refreshments): £250 (University of Edinburgh Staff/Students); £400 (Non- University of Edinburgh Staff/Students)
Where: G04 Ashworth Buildings, The Kings Buildings, Edinburgh.
Register here
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Data Science for Everyone 6 - 10 April 2020
This course is an excellent introduction to data handling and analysis using Python, ragardless of what field you work in or what coding experience you have.
Python is a dynamic, readable language that is a popular platform for all types of data analysis work, from simple one-off scripts to large, complex software projects. One of the strengths of the Python language is the availability of mature, high-quality libraries for working with scientific data. Integration between the most popular libraries has lead to the concept of a "scientific Python stack": a collection of packages which are designed to work well together.
Tutors: Dr. Martin Jones (Founder, Python for Biologists)
Registration fee (including refreshments): £400 (University of Edinburgh Staff/Students); £550 (Non- University of Edinburgh Staff/Students)
Where: G04 Ashworth Buildings, The Kings Buildings, Edinburgh.
Register here
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Alignment, Analysis and Visualisation with Jalview
Jalview (www.jalview.org]) is one of the most widely used applications for visualising and analysing DNA, RNA and protein multiple sequence alignments. Available as a web based tool and desktop application, it is designed to enable anyone working with protein, RNA and DNA sequences to investigate their structure, function and evolution, and create high-quality figures for publication. In a full day introductory workshop and a half-day advanced workshop, Jalview’s lead developer and outreach officer will take participants through a series of hands-on exercises covering all of Jalview’s key capabilities and latest features.
Tutors: Dr. Martin Jones (Founder, Python for Biologists)
Registration fee (including refreshments): £45
Where: G07 Murchison House, The Kings Buildings, Edinburgh.
Register here
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GATK Best Practices Workshop 11 -15 May 2020
The workshop focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. Participants will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of their dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint discovery of germline short variants in cohorts, somatic short variant discovery using Mutect2, and somatic copy number variation discovery using GATK-CNV. We also exercise the use of pipelining tools to assemble and execute GATK workflows.
Tutors: GATK training team
Registration fee (including refreshments): £120 (including refreshments)
Where: JCMB, The Kings Buildings, Edinburgh.
Register here
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Bioinformatics for Genomics 25 - 29 May 2020
This is a week-long workshop that combines our popular ‘Linux for Genomics’, ‘R for Genomics’, and ‘Introduction to RNA-seq Data Analysis’, taught by Edinburgh Genomics’ Bioinformaticians. By the end of the five days, you will be: comfortable on the Linux command line; able to view, filter and manipulate large text files; able to write pipelines to perform certain bioinformatics tasks; familiar with and able to use the basics of R; confident using several data QC and processing tools; able to generate gene counts and differential expression statistics; and prepared to put it all together with visualization, interpretation, and gene set analysis.
Tutors: Tim Booth (Bioinformatician/Programmer, Urmi Trivedi (Bioinformatician), Frances Turner (Bioinformatician), Nathan Medd (Training and Outreach Manager)
Registration fee (including lunch and refreshments): £500 (University of Edinburgh Staff/Students); £750 (Non- University of Edinburgh Staff/Students)
Where: JCMB, The Kings Buildings, Edinburgh.
Register here
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Introduction to Python for Biologists 13th - 17th July 2020
Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way.
Tutors: Dr. Martin Jones (Founder, Python for Biologists)
Registration fee (including refreshments): £400 (University of Edinburgh Staff/Students); £550 (Non- University of Edinburgh Staff/Students)
Where: JCMB, The Kings Buildings, Edinburgh.
Register here
We have been busy here at Edinburgh Genomics organising some new courses to help you gain those bioinformatics skills you need for your research! We have some exciting new stuff including a new course from Dr Martin Jones and GATK variant analysis course by the training team at the Broad Institute. See our upcoming courses below.
We are also pleased to announce that we have some full-fee bursaries available from the National Environment Research Council (NERC) for students or researchers working on NERC-funded or NERC-remit science. If you believe that your work falls into this category please get in touch with us ([email protected]) and let us know what you work on and what course you are interested in. The deadline for allocating these bursaries is the 27th March, so please get in touch before this point!
.............................................................
R for Genomics 30 - 31 March 2020
The aim of this course is to introduce participants to the statistical computing language 'R' using examples and skills relevant to genomic data science. This two day workshop is taught by experienced Edinburgh Genomics’ bioinformaticians and trainers. By the end of the workshop, you will be comfortable with the basics of the R and R studio environments, learning about the rules of the language and how R works with different data types. We then move on to using functions, including those specific to genomic science. We look at how to handle various genomic data files and where to find relevant tools via online resources. Finally we use mock RNA-seq data to learn how to visualise your data to generate publication ready plots using the package ggplot2.
Tutors: Nathan Medd, Training Manager, Edinburgh Genomics
Registration fee (including lunch and refreshments): £250 (University of Edinburgh Staff/Students); £400 (Non- University of Edinburgh Staff/Students)
Where: G04 Ashworth Buildings, The Kings Buildings, Edinburgh.
Register here
.............................................................
Data Science for Everyone 6 - 10 April 2020
This course is an excellent introduction to data handling and analysis using Python, ragardless of what field you work in or what coding experience you have.
Python is a dynamic, readable language that is a popular platform for all types of data analysis work, from simple one-off scripts to large, complex software projects. One of the strengths of the Python language is the availability of mature, high-quality libraries for working with scientific data. Integration between the most popular libraries has lead to the concept of a "scientific Python stack": a collection of packages which are designed to work well together.
Tutors: Dr. Martin Jones (Founder, Python for Biologists)
Registration fee (including refreshments): £400 (University of Edinburgh Staff/Students); £550 (Non- University of Edinburgh Staff/Students)
Where: G04 Ashworth Buildings, The Kings Buildings, Edinburgh.
Register here
.............................................................
Alignment, Analysis and Visualisation with Jalview
Jalview (www.jalview.org]) is one of the most widely used applications for visualising and analysing DNA, RNA and protein multiple sequence alignments. Available as a web based tool and desktop application, it is designed to enable anyone working with protein, RNA and DNA sequences to investigate their structure, function and evolution, and create high-quality figures for publication. In a full day introductory workshop and a half-day advanced workshop, Jalview’s lead developer and outreach officer will take participants through a series of hands-on exercises covering all of Jalview’s key capabilities and latest features.
Tutors: Dr. Martin Jones (Founder, Python for Biologists)
Registration fee (including refreshments): £45
Where: G07 Murchison House, The Kings Buildings, Edinburgh.
Register here
.............................................................
GATK Best Practices Workshop 11 -15 May 2020
The workshop focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. Participants will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of their dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint discovery of germline short variants in cohorts, somatic short variant discovery using Mutect2, and somatic copy number variation discovery using GATK-CNV. We also exercise the use of pipelining tools to assemble and execute GATK workflows.
Tutors: GATK training team
Registration fee (including refreshments): £120 (including refreshments)
Where: JCMB, The Kings Buildings, Edinburgh.
Register here
.............................................................
Bioinformatics for Genomics 25 - 29 May 2020
This is a week-long workshop that combines our popular ‘Linux for Genomics’, ‘R for Genomics’, and ‘Introduction to RNA-seq Data Analysis’, taught by Edinburgh Genomics’ Bioinformaticians. By the end of the five days, you will be: comfortable on the Linux command line; able to view, filter and manipulate large text files; able to write pipelines to perform certain bioinformatics tasks; familiar with and able to use the basics of R; confident using several data QC and processing tools; able to generate gene counts and differential expression statistics; and prepared to put it all together with visualization, interpretation, and gene set analysis.
Tutors: Tim Booth (Bioinformatician/Programmer, Urmi Trivedi (Bioinformatician), Frances Turner (Bioinformatician), Nathan Medd (Training and Outreach Manager)
Registration fee (including lunch and refreshments): £500 (University of Edinburgh Staff/Students); £750 (Non- University of Edinburgh Staff/Students)
Where: JCMB, The Kings Buildings, Edinburgh.
Register here
.............................................................
Introduction to Python for Biologists 13th - 17th July 2020
Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way.
Tutors: Dr. Martin Jones (Founder, Python for Biologists)
Registration fee (including refreshments): £400 (University of Edinburgh Staff/Students); £550 (Non- University of Edinburgh Staff/Students)
Where: JCMB, The Kings Buildings, Edinburgh.
Register here
