A walk through genes and proteins with EMBL-EBI databases and tools - Universidad de los Andes

Date:

  Monday 25 May 2015

Registration closed

Overview

The UniAndes will cover as well BioJS, a community initiative to develop JavaScript components in order to retrieve, parse, handle, and visualize biological data under common and well known standards and good practices.

Objectives

Disseminating data bases and tools provided by EMBL-EBI from a theoretic-practical perspective. Particularly data bases and tools related to genes (ENA, Ensembl) and proteins (UniProt) will be covered.

ime Topic Trainer
Day 1 - Monday 25th May 2015 - Universidad de los Andes
09:00 - 12:00 Introduction EMBL-EBI  
  Introduction to UniProt (including hands-on)  
13:00 - 17:00 Short Introduction to ENA  
  Introduction to Ensembl (Including hands-on)  
Day 2 - Tuesday 26th May 2015 - Universidad de los Andes
09:00 - 12:00 Introduction to BioJS (Including hands-on)  
13:00 - 17:00 Introduction to Ensembl (conclusion  

 

Learning outcomes

The following are the competencies to develop:

Introduction to EMBL-EBI

  • Learning about the core data resources available from EMBL-EBI
  • Learning the general schema for programmatic access via REST services

 

Introduction to European Nucleotide Archive ENA

  • Learning what ENA is and where the data comes from
  • Learning how to access and navigate the ENA Browser and the taxonomy portal
  • Being able to search ENA with text (such as a gene name) and a simple sequence

Click here for ENA course materials.

 

Introduction to Ensembl

  • Introduction to Ensembl including a look at the Region in Detail view for visualising genomic regions.
  • Ensembl gene and transcript annotation, and how to get data on them in the browser.
  • Using BioMart for data mining Ensembl.
  • Finding variant data in Ensembl and analysing your own variants with the Variant Effect Predictor (VEP).

Click here for Ensembl course materials.

 

Introduction to UniProt

  • Learning what UniProt is and what you can do with it
  • Exploring the wide range of information provided by UniProt and understand where it comes from
  • Being able to access, navigate, and search on the UniProt website
  • Being able to access, navigate, and search for proteomes
  • Being able to access, navigate, and search for information related to variation and diseases
  • Learning how to download data and know what formats are provided
  • Learning how to access data from a programmatic perspective, using REST services, and RDF

Additional information

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