Hands-on training at EBI - A two-day dip into the EBI’s data resources: Understanding your data

Title: A two-day dip into the EBI’s data resources: Understanding your data
Date: 10-11 September 2007
Venue: Hinxton, Cambridge, UK
Organisers: IT-Training EBI
Registration Deadline: T.B.A.

About this Course

Topics include

• EB-eye search engine:
  The EB-eye search system is a high-performance, full-featured text search engine that provides rapid access to the EBI's data resources. Users can search globally across all EBI databases or narrow their selection to individually in selected resources by using the advance search option.
  
  
• EBI Literature resources
  CiteXplore is the EBI’s portal to the scientific literature, directing users to full text articles as well as relevant biological databases. It provides access to MEDLINE (NLM), Agricola (NAL), patent abstracts (EPO), Chinese Biological Abstracts (CBA) and CiteSeer (UPenn).
  
  
• Ensembl (genomes):
  A genomic sequence database providing a comprehensive and integrated source of annotation of mainly vertebrate genome sequences.
  
  
• ArrayExpress (microarray data):
  EMBL-EBI’s MIAME-compliant repository for gene expression data from microarray and transcriptomics experiments (MIAME - Minimum Information About a Microarray Experiment).
  
  
• UniProt (protein sequences):
  UniProt is a collaboratively maintained central repository of protein sequence and function. Users can access curated protein information through a central access point, the UniProt Knowledgebase (UniProtKB).
  
  
• PDBe (macromolecular structures):
  The EBI’s Protein Databank in Europe (PDBe) is Europe’s representative in the worldwide Protein Data Bank (http://www.wwpdb.org/). It contains structural data from crystallography, nuclear magnetic resonance spectroscopy and electron microscopy experiments, in addition to derived information linking structure to biochemical function, protein sequence and taxonomy.
  
  
• IntAct (protein–protein interactions):
  IntAct is a molecular interaction database and analysis system. The project is a member of the International Molecular Exchange (IMEx) consortium for exchanging molecular interaction data and supports the development of the Human Proteome Organisation (HUPO) community standard data model.
  
  
• PRIDE (proteomics):
  The Proteomics Identifications Database is a public data repository for proteomic identifications and associated mass spectra, linked to supporting publications.
  
  
• Reactome (pathways):
  Reactome is a curated knowledgebase of biological processes, containing reactions, pathways, proteins, DNA, small molecules and complexes. Reactome encompasses metabolism, signalling, cell cycle, apoptosis, gene expression, pathogen–host interactions and much more.

Course requirements

Trainers

David Croft Phil Jones Sandra Orchard Gabriella Rustici Vicky Schneider Giulietta Spudich

• David Croft is a bioinformatician and has been giving talks and training for the Reactome project since 2005. He is also involved in maintaining and updating the Reactome website. Prior to joining the EBI, he spent seven years in industry, designing bioinformatics and cheminformatics applications.
  
  
• Phil Jones is the technical lead software engineer for the PRIDE project. He has a background in both biological sciences and software engineering, and holds a Post-Graduate Certificate in Education. He has held positions in software engineering and in science education. He has given courses and talks on various software development projects in numerous locations worldwide.
  
  
• Sandra Orchard is a Senior Scientific Database Curator working across the Sequence Database, InterPro and Proteomics Services teams. She is responsible for the curation standards within the IntAct Molecular Interaction database as well as contributing to the annotation of the UniProtKB, InterPro and GOA databases and applies her experience to provide hand-on training in several resources including UniProtKB, IPI, InterPro and IntAct.
  
  
• Gabriella Rustici is a research scientist in the Microarray Informatics group at the EBI and her research focuses on meta-analysis of microarray datasets. She is also involved in training activities and applies her experience to provide hands-on training in several resources including ArrayExpress and Expression Profiler.
  
  
• Vicky Schneider is the EBI’s Scientific Training Officer and responsible for developing and coordinating the in-house and external training activities of the EBI. She has an academic background in behavioural ecology and adaptive evolution. Prior to joining the EBI, Vicky held an Assistant Professor position at the University of Bern, Switzerland.
  
  
• Giulietta Spudich is an outreach and training officer for Ensembl. She is also involved in providing technical support for the genome browser. She has a background in academic research (structural biology and biochemistry) and has taught lecture-style classes and day-long workshops for University of California, Berkeley (USA), University of Cambridge (UK) and gives world-wide workshops on Ensembl.

Program Contents