EMBL-EBI Workshop: Genomics, transcriptomics and metagenomics tools and resources for biology research
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Date:
Tuesday 7 - Thursday 9 May 2019Venue:
Faculty of Sciences, University of Porto - Rua do Campo Alegre 1021/1055, 4169-007, Porto, PortugalApplication opens:
Friday 29 March 2019Application deadline:
Sunday 14 April 2019Participation:
Open application with selectionContact:
Sandra ArestaRegistration fee:
FreeRegistration closed
Course Overview
This workshop will provide training on computational analysis tools and databases that can be used to answers relevant questions in molecular ecology. Participants will learn how to browse, search and access biological data across the fields of genomics, transcriptomics and metagenomics. Data management and submission strategies using Biostudies will also be covered.
During this course you will learn about:
Audience
This course is intended for PhD students of Portuguese and international institutions (with a particular focus on students of the CIBIO-InBIO’s BIODIV, SUSFOR Doctoral Programs and University of Porto), but more experienced researchers that are initiating projects in the field of environmental metagenomics can also participate.
Prerequisite knowledge
No previous bioinformatics experience is required, but an undergraduate level understanding of biology would be an advantage.
Modules
- ensemblensembl-genomes
- arrayexpress-public-database-functional-genomics
- expression-atlas-gene-expression-across-species-and-biological-conditions
- european-nucleotide-sequence-archive-ena
Learning outcomes
After this course you should be able to:
- View genomic regions and manipulate the view to add features you are interested in
- Analyse genomic variants and associated phenotypes and your own variation data using the VEP
- Browse the ENA database in detail, learning about its structure and the type of data it contains
- Access, browse and visualise gene expression data from ArrayExpress and Expression Atlas
- Use Biostudies to search and quickly access data from a publication
- Search, browse and download metagenomics data using MGnify
Programme
Day 1: Ensembl genome browser
Day 2: ArrayExpress, Expression Atlas
Day 3: Biostudies, European Nucleotide Archive (ENA), ENA for metagenomics, MGnify
Day 1 – Tuesday 7 May 2019 |
||
|---|---|---|
| 08:30-09:00 | Arrival, registration | |
| 09:00-09:15 | Introduction to EMBL-EBI resources and tools | Ben Moore |
| 09:00-11:00 | Ensembl Genes and Transcripts | Ben Moore |
| 11:00-11:30 | Coffee Break | |
| 11:30-13:00 | Accessing and analysing variation data usingEnsembl | Ben Moore |
| 13:00-14:00 | Lunch | |
| 14:00-15:30 | Comparative genomics | Ben Moore |
| 15:30-16:00 | Break | |
| 16:00-17:30 | BioMart | Ben Moore |
| 17:30 | End of day 1 | |
Day 2 – Wednesday 8 May 2019 |
||
|---|---|---|
| 09:00-11:00 | Data quality: standards and ontologies | Silvie Fexova |
| 11:00-11:30 | CoffeeBreak | |
| 11:30-13:00 | ArrayExpress | Silvie Fexova |
| 13:00-14:00 | Lunch | |
| 14:00-15:30 | Expression Atlas | Silvie Fexova |
| 15:30-16:00 | Coffee Break | |
| 16:00-17:30 | Single-cell Expression Atlas | Silvie Fexova |
| 17:30 | End of day 2 | |
Day 3 – Thursday 9 May 2019 |
||
| 09:00-10:30 | Biostudies webinar | Ugis Sarkans and Silvie Fexova |
| 10:30-11:00 | Coffee Break | |
| 11:00-13:00 | European Nucleotide Archive | Sam Holt |
| 13:00-14:00 | Lunch | |
| 14:00-14:45 | European Nucleotide Archive for Metagenomics webinar | Josephine Burgin |
| 14:45-15:30 | Metagenomics - MGnify | Alex Mitchell |
| 15:30-16:00 | Coffee Break | |
| 16:00-17:30 | Metagenomics - MGnify | Alex Mitchell |
| 17:30-17:45 | Course wrap-up and feedback | Sam Holt and Alex Mitchell |
Additional information:
This course is included in the activities planned in the EnvMetagen project. This capacity building project is run at CIBIO-InBIO, a research center in the greater Porto area, and aims to increase expertise and knowledge in the field of environmental metagenomics in Portugal, through a large set of activities that include training in several areas related to this field. Previously, a similar event was organized with the aim of raising capacity in metabarcoding.
ICETA, University of Porto - EnvMetagen Project (EnvMetaGen, Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics, is an ERA Chair project funded by the European Commission (Grant #668981)
In association with
How to apply
To register for this event please click the "Apply Now" button.
Items marked * are mandatory. Incomplete registrations will not be processed.
Please note the course includes:
- Course materials
- Use of a computer in the IT Training Room throughout the course
Registration deadline: 14th April 23:30 GMT
Application deadline
14 April 2019
Number of places
30 places
Organisers
Piraveen Gopalasingam - EMBL-EBI, UK
Nuno Fonseca - University of Porto
Sandra Aresta - CIBIO-InBIO, University of Porto
Trainers
Benjamin Moore - EMBL-EBI, UK
Silvie Fexova - EMBL-EBI, UK
Sam Holt - EMBL-EBI, UK
Ugis Sarkans - EMBL-EBI, UK
Alex Mitchell - EMBL-EBI, UK